No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
Genetic Diversity and Conservation of Common Wild Rice (Oryza Rufipogon) in China
Abstract
Common wild rice (Oryza rufipogon Griff.), known as the ancestor of Asian cultivated rice (Oryza sativa L.), is the most important germplasm for rice improvement. The first male sterility gene was found in the wild rice, and introduced to the cultivated rice, which launched the fast development of the high-yielding hybrid rice. Other agronomically beneficial traits in the wild rice, such as rice tungro virus resistance, bacterial leaf blight (Xa21 gene) resistance and acid sulfate soil tolerance, have played important roles in rice breeding. China has the northernmost distribution area of wild rice possessing great genetic diversity. However, most of the populations of this species have disappeared in China over the last three decades, mainly caused by habitat loss, fragmentation and other human disturbances. Unfortunately, the decline of existing populations still continues. In the present study, we reviewed studies on genetic diversity and conservation of this wild rice in China, concentrating on population structure, pollen competition, pollen/gene flow from cultivated rice to wild rice, and ecological restoration in relation to in situ conservation. The relatively high genetic diversity of populations of O. rufipogon in China suggests that there is great value for conservation. Considerable gene flow from cultivated rice to wild rice may alter the genetic structure of natural populations of O. rufipogon and eventually lead to its genetic erosion. Pollen competition between wild and cultivated rice has caused a low rate of crop-to-wild gene flow, but it does not completely prevent gene flow from the crop. Effective isolation measures should be undertaken in the regions where in situ conservation of O. rufipogon is carried out. Reintroduction is an important alternative for the in situ conservation of wild rice species. As wild rice is an important genetic resource, both in situ and ex situ conservation strategies are needed.
... However, the known in situ sites exclusively dedicated to wild rice conserve mainly the species O. rufipogon. In China, there are ten conservation sites distributed along the southern provinces (Song et al. 2005). In Thailand, two in situ areas are located inside the compounds of separate rice research centers (Kaewcheenchai et al. 2018). ...
... Reproductive barriers between species from the same series or genome group are not completely sealed. Introgression with cultivated rice has been detected in O. rufipogon in China (Song et al. 2005;Ji et al. 2016), Laos (Kuroda et al. 2007), Malaysia (Ngu et al. 2010), Thailand (Wedger et al. 2019, and globally . This was also observed in O. nivara in Laos (Kuroda et al. 2007) andO. ...
... In contrast, other wild species have been investigated for their conservation and utilization (Song et al. 2005;Henry et al. 2010). ...
Integrating greeneries into the indoor dwelling environment boosts work performance and relieves stress to add to the overall psychological well-being especially in deserted urban settings. In addition to mental soothing, thermal regulation, air purification, aesthetics, public health, and comfort, the addition of plants to indoor settings may also contribute to the conservation of dwindling floral biodiversity. Despite authorities’ pledge for sustainable urban management, the status of indoor gardening has hitherto remained unexplored in the emerging megapolis of Bangladesh—Chattogram—the second largest urban center of the country. In addressing that gap, this study aims to explore the composition, diversity, and management of indoor plants in urban dwellings at Halishahar of Chattogram based on interviews on 48 households selected through multistage random sampling. Data from all selected households were collected by using a semi-structured questionnaire through physically visiting the households. Almost half of the households (48%) living at Halishahar had indoor plants in their dwellings. The study recorded a handsome 120 indoor plant species belonging to 108 genera from 60 families. While the diversity was in no way comparable to the tropical ecosystem of the country, in consideration of the strict set of requirements for plants to be suitable for an indoor setting, the diversity seemed excellent as evident from four diversity indices. Soil mixed with compost, sand, and surki at different ratios is used as potting media. Pests were identified as the major challenge in managing the indoor plants. Application of domestic manure with the potting media was common as a means to maintain the nutrient flow. Bruised tea leaf is the most frequently added nutrient supplement. Apart from the aesthetic values, urban dwellers from Halishahar reported the immense potential of indoor gardening in supplementing daily nutrition and in mitigating the impacts of climate change. The lessons from this study can be used in informed policymaking for the promotion of biodiversity conservation and other benefits from indoor greening among urban dwellers in Bangladesh.
... However, the known in situ sites exclusively dedicated to wild rice conserve mainly the species O. rufipogon. In China, there are ten conservation sites distributed along the southern provinces (Song et al. 2005). In Thailand, two in situ areas are located inside the compounds of separate rice research centers (Kaewcheenchai et al. 2018). ...
... Reproductive barriers between species from the same series or genome group are not completely sealed. Introgression with cultivated rice has been detected in O. rufipogon in China (Song et al. 2005;Ji et al. 2016), Laos (Kuroda et al. 2007), Malaysia (Ngu et al. 2010), Thailand (Wedger et al. 2019, and globally . This was also observed in O. nivara in Laos (Kuroda et al. 2007) andO. ...
... In contrast, other wild species have been investigated for their conservation and utilization (Song et al. 2005;Henry et al. 2010). ...
Permaculture has been known to intentionally integrate diversity into the design of farms and mimic natural landscapes. This approach is in contrast to the mainstream monocropping system in conventional agriculture. The objectives of the study were to identify what plant species are commonly cultivated in permaculture farms and determine its uses as narrated by farmers and practitioners. The researchers conducted a crop inventory in 12 permaculture sites in the Philippines from August to November in 2018. To survey a 1 ha sampling area, a modified belt transect method with alternating 20 m2 plots was employed for full enumeration of plant species in each plot. To determine uses, key informant interviews and focus group discussions were conducted among farm staff. A total of 215 plant species were identified with an average species richness of 46 per farm. A comparison of crop inventories revealed that Colocasia esculenta and Capsicum frutescens were the most commonly cultivated crops found in ten sites (83%). It is followed by Annona muricata (nine sites) and Bambusoideae (eight). Results revealed that the majority of crops found were cultivated for household consumption.
... However, the known in situ sites exclusively dedicated to wild rice conserve mainly the species O. rufipogon. In China, there are ten conservation sites distributed along the southern provinces (Song et al. 2005). In Thailand, two in situ areas are located inside the compounds of separate rice research centers (Kaewcheenchai et al. 2018). ...
... Reproductive barriers between species from the same series or genome group are not completely sealed. Introgression with cultivated rice has been detected in O. rufipogon in China (Song et al. 2005;Ji et al. 2016), Laos (Kuroda et al. 2007), Malaysia (Ngu et al. 2010), Thailand (Wedger et al. 2019, and globally . This was also observed in O. nivara in Laos (Kuroda et al. 2007) andO. ...
... In contrast, other wild species have been investigated for their conservation and utilization (Song et al. 2005;Henry et al. 2010). ...
Breeders need access to unique genetic variability to meet the growing demand for food while maintaining sustainable agricultural production with the impacts of climate change for generating high-quality nutritional food. Changes in climate and anthropogenic activities and a multitude of environmental influences pose severe threats to food supply and preservation of natural diversity. For example, unpredictable droughts, elevated temperature, and new diseases and pests threaten crop production. Thus, breeding with crop wild relatives (CWR) gives significant resilience to modern agricultural systems and the ability to help sustainably boosting agricultural productivity. As a result, numerous genotype screenings are necessary for broad adaptability, producing a segregating material through fast breeding or rapid generation to shorten the breeding cycle and improving genetic gain. In addition, CWR genomics generates data that support CWR’s usage to boost agricultural genetic diversity. QTL mapping, identifying of candidate genes by next-generation sequencing, gene-based marker development, or significant candidate gene pyramiding of stress-responsive loci in popular cultivar are required to maintain the sustainability of crop production. Thus, genomic data is useful for identifying and isolating novel and dominant alleles of genes from crop gene pools that are agronomically important, which can be used to generate improved crop cultivars. Hence, the natural allelic difference in candidate genes that influences major agronomic characteristics and crop development initiatives is being investigated via allele mining. Among the CWRs of economically important crops, the wild species of rice is essential to improve modern rice cultivars. The awareness of novel genetic and genomic approaches of rice genetic resources for efficient utilization is crucial. Further, their conservation status and availability have not been quantified globally. As a result, a joint effort is required to improve the conservation and accessibility of crop wild relatives for rice breeding.
Keywords: Genomics of CWR, Crop improvement, Rice genetic resources
... Common wild rice (Oryza rufipogon Griff., 2n = 24, AA), an important CWR of cultivated rice, is a valuable genetic resource and is widely distributed around the tropical and subtropical zones of Asia. In China, it is distributed from 19 to 28°N in eight provinces: Guangdong, Hainan, Taiwan, Guangxi, Fujian, Yunnan, Hunan, and Jiangxi (Song et al. 2005;Huang et al. 2012;Li et al. 2006b;Sang and Ge 2007). Guangdong Province, one of the origins of Asian cultivated rice, is located in southern China and has favorable light and heat conditions. ...
... Moreover, researchers had shown that South China was a center of genetic diversity for wild rice. Wild rice plants in Guangdong Province were identified as having a high level of genetic diversity for disease resistance and male sterility (Li et al. 2006a;Song et al. 2005). However, populations of wild rice were rapidly shrinking due to urban and industrial occupation of their natural habitats (Gao et al. 2001(Gao et al. , 2002Shishido et al. 2006;Liu et al. 2016). ...
... These findings demonstrated that geographic location truly caused the genetic differences between populations and that in-situ conservation of wild rice is particularly important. Similar results were reported in previous studies (Zhou et al. 2003;Song et al. 2005;Shishido et al. 2006;Prathepha 2012). LD decay was estimated to be 0.52 kb, the point at which r 2 dropped to its half maximum, which was much lower than that found in cultivated rice (Xu et al. 2012(Xu et al. , 2016. ...
Common wild rice (Oryza rufipogon Griff.) is a valuable germplasm resource for rice genetic improvement. However, it is endangered due to habitat loss. Assessment of its genetic diversity is essential for germplasm characterization, utilization, and conservation. In the present study, we developed a 79,422-single-nucleotide polymorphism genome-wide array by specific-locus amplified fragment sequencing (SLAF-seq) and used it to genotype 110 common wild rice accessions from different agroclimatic zones in Guangdong Province, China. The number of SNPs on each chromosome was consistent with the physical length of the chromosome, and the average marker density was approximately 4.83 kb/SNP. The genome-wide linkage disequilibrium decayed to its half maximum within 0.52 kb for O. rufipogon. The common wild rice accessions were clustered into four subgroups, with some overlap in principal component analysis and a neighbor-joining tree that was also confirmed by model-based admixture. Analysis of molecular variance revealed significant genetic differentiation among individuals, accounting for 90.64% of the total molecular variance; however, the differences between the subgroups (Enping, Lufeng, Suixi and Fogang) were not significant. The significant genetic variations in resources collected in different years were observed in Enping and Suixi subgroups, but there was no significant genetic variation in Fogang subgroup. The pairwise fixation index (FST) suggested that the populations from Enping and Lufeng were most differentiated while those from Enping and Fogang were least differentiated. Our results illustrated clear genetic relationships among 110 common wild rice accessions, showing a potential molecular marker-based strategy for preserving the genetic diversity and accelerating the systematic utilization of these important wild rice resources.
... Common wild rice (Oryza rufipogon Griff.), the progenitor of Asian cultivated rice (Oryza sativa L.), is widely distributed in the tropics and subtropics of Asia, Papua New Guinea, and Australia [1,2]. Common wild rice has abundant genetic diversity and various resistance genes for the improvement of cultivated rice [3,4]. To fulfill the demands of food supply, there is a need to enhance the crop productivity significantly by exploitation and utilization of genetic resources, particularly those in the gene pool of wild species [4]. ...
... Common wild rice has abundant genetic diversity and various resistance genes for the improvement of cultivated rice [3,4]. To fulfill the demands of food supply, there is a need to enhance the crop productivity significantly by exploitation and utilization of genetic resources, particularly those in the gene pool of wild species [4]. However, the natural habitats of wild rice germplasm are becoming sparser due to the activity of modern agriculture, and many wild rice populations have become extinct [5]. ...
... China has a rich collection of diverse wild rice populations, and most of them are present in Hainan, Guangdong, Guangxi, Yunnan, Fujian, Taiwan, Hunan, and Jiangxi provinces [4,21,22]. Dongxiang, which is located at 28˚14 0 N latitude and 116˚30 0 E longitude, Jiangxi province, China, is considered to be the northernmost region in China and in the world where wild rice is present [9,23]. Dongxiang wild rice is a vast reservoir of beneficial genes that can use to breed cultivated rice, such as broad-spectrum NBS-LRR type resistance genes [9,23]. ...
Common wild rice (Oryza rufipogon Griff.) is an important germplasm for rice breeding, which contains many resistance genes. Re-sequencing provides an unprecedented opportunity to explore the abundant useful genes at whole genome level. Here, we identified the nucleotide-binding site leucine-rich repeat (NBS-LRR) encoding genes by re-sequencing of two wild rice lines (i.e. Huaye 1 and Huaye 2) that were developed from common wild rice. We obtained 128 to 147 million reads with approximately 32.5-fold coverage depth, and uniquely covered more than 89.6% (> = 1 fold) of reference genomes. Two wild rice lines showed high SNP (single-nucleotide polymorphisms) variation rate in 12 chromosomes against the reference genomes of Nipponbare (japonica cultivar) and 93–11 (indica cultivar). InDels (insertion/deletion polymorphisms) count-length distribution exhibited normal distribution in the two lines, and most of the InDels were ranged from -5 to 5 bp. With reference to the Nipponbare genome sequence, we detected a total of 1,209,308 SNPs, 161,117 InDels and 4,192 SVs (structural variations) in Huaye 1, and 1,387,959 SNPs, 180,226 InDels and 5,305 SVs in Huaye 2. A total of 44.9% and 46.9% genes exhibited sequence variations in two wild rice lines compared to the Nipponbare and 93–11 reference genomes, respectively. Analysis of NBS-LRR mutant candidate genes showed that they were mainly distributed on chromosome 11, and NBS domain was more conserved than LRR domain in both wild rice lines. NBS genes depicted higher levels of genetic diversity in Huaye 1 than that found in Huaye 2. Furthermore, protein-protein interaction analysis showed that NBS genes mostly interacted with the cytochrome C protein (Os05g0420600, Os01g0885000 and BGIOSGA038922), while some NBS genes interacted with heat shock protein, DNA-binding activity, Phosphoinositide 3-kinase and a coiled coil region. We explored abundant NBS-LRR encoding genes in two common wild rice lines through genome wide re-sequencing, which proved to be a useful tool to exploit elite NBS-LRR genes in wild rice. The data here provide a foundation for future work aimed at dissecting the genetic basis of disease resistance in rice, and the two wild rice lines will be useful germplasm for the molecular improvement of cultivated rice.
... Therefore, CWR can be utilized as an important germplasm to improve the cultivated rice in terms of disease/pest resistance, adaptability, grain yield, and grain quality. 'Chaling' CWR, distributed in a wetland named "Huli" (26°50′ N), Yaoshui town, Chaling county, Hunan province, China (Liu et al., 2001;Song et al., 2005), is one of the CWR populations widely distributed in the world. More importantly, it is one of the only two wild rice populations grown northernmost in the word (Liu et al., 2001). ...
... Much progress has been made on the studies of 'Chaling' CWR's geographical distribution and habitat, botanical characters and classification, anti-diseases/pests, abiotic stress tolerance, etc. Song et al., 2005 ;Sun, 1988;Xu et al., 2009). However, the photosynthetic characteristics of 'Chaling' CWR under cold stress remain unknown. ...
... The seeds of 'Chaling' CWR (Oryza rufipogon Griff.) were obtained from its tillers grown in an experimental paddy field in Hunan Normal University (Changsha, Hunan province, China). The tillers of 'Chaling' CWR for seed production were collected from its natural habitat, a swamp place named 'Huli' (26°50' N), Chaling county, Hunan province, China (Sun, 1988;Liu et al., 2001;Song et al., 2005). The seeds of standard rice cultivars (Oryza sativa L.) including indica 'Guangluai 4', indica super high grain yield hybrid 'Y-Liangyou 1', and japonica 'Nipponbare' were provided by Life Science College, Hunan Normal University. ...
‘Chaling’ common wild rice (CWR, Oryza rufipogon Griff.), found in Chaling county, Hunan province, China, is one of the only two wild rice populations grown northernmost in the world. Although the cold tolerance of ‘Chaling’ CWR is extremely strong, its photosynthetic characteristics under cold stress remain unknown. In this study, the photosynthetic parameters of leaves at tiller stage in ‘Chaling’ CWR were first determined under the conditions of cold stress (15 °C) and normal temperature (28 °C), and then compared with those in the standard rice cultivars including indica ‘Guangluai 4’, indica ‘Y-Liangyou 1’ (a Chinese hybrid rice with super high grain yield), and japonica ‘Nipponbare’ under the same temperature conditions. The results showed that the net photosynthetic rate, the total chlorophyll and total carotenoid contents, the maximum quantum yield of PSII, the apparent quantum yield, and the carboxylation efficiency in ‘Chaling’ CWR were all significantly higher than those in the standard rice cultivars under cold stress (P < 0.05). The ratios of these parameters in ‘Chaling’ CWR under cold stress to those under normal temperature condition were 47.9 ~ 84.9%, much higher than those in the standard rice cultivars, which were 3.1 ~ 73.8%. These results indicate that the photosynthetic characteristics of ‘Chaling’ CWR under cold stress are excellent. Our findings would have an enormous benefit if the trait of the cold stress tolerance of ‘Chaling’ CWR is transferred to the cultivated rice via the traditional breeding or molecular breeding.
... In China, wild rice is distributed from 19 to 28°N in eight provinces, i.e., Hainan, Guangdong, Guangxi, Yunnan, Fujian, Taiwan, Hunan, and Jiangxi. Many populations of genetically diverse wild rice are present in these provinces1234567. It is essential that wild germplasm be characterized so that plant breeders can identify and conserve accessions with agronomically favorable traits. ...
... South China is considered to be the center of genetic diversity of wild rice. Wild rice plants with a high level of genetic diversity for adaptive traits (such as drought and disease resistance) were reported to exist in Guangdong and Hainan provinces [1,891011. The natural habitats of wild rice species have been shrinking due to urbanization [1,12]. ...
... Wild rice plants with a high level of genetic diversity for adaptive traits (such as drought and disease resistance) were reported to exist in Guangdong and Hainan provinces [1,891011. The natural habitats of wild rice species have been shrinking due to urbanization [1,12]. Consequently, it is critical to evaluate the genetic diversity of available populations and develop a system to conserve the wild germplasm [13]. ...
Common wild rice (Oryza rufipogon Griff.), the progenitor of Asian cultivated rice (O. sativa L.), is endangered due to habitat loss. The objectives of this research were to evaluate the genetic diversity of wild rice species in isolated populations and to develop a core collection of representative genotypes for ex situ conservation. We collected 885 wild rice accessions from eight geographically distinct regions and transplanted these accessions in a protected conservation garden over a period of almost two decades. We evaluated these accessions for 13 morphological or phenological traits and genotyped them for 36 DNA markers evenly distributed on the 12 chromosomes. The coefficient of variation of quantitative traits was 0.56 and ranged from 0.37 to 1.06. SSR markers detected 206 different alleles with an average of 6 alleles per locus. The mean polymorphism information content (PIC) was 0.64 in all populations, indicating that the marker loci have a high level of polymorphism and genetic diversity in all populations. Phylogenetic analyses based on morphological and molecular data revealed remarkable differences in the genetic diversity of common wild rice populations. The results showed that the Zengcheng, Gaozhou, and Suixi populations possess higher levels of genetic diversity, whereas the Huilai and Boluo populations have lower levels of genetic diversity than do the other populations. Based on their genetic distance, 130 accessions were selected as a core collection that retained over 90% of the alleles at the 36 marker loci. This genetically diverse core collection will be a useful resource for genomic studies of rice and for initiatives aimed at developing rice with improved agronomic traits.
... Rice breeders have repeatedly transferred important traits for crop improvement from wild rice to various cultivars. Song et al. (2005) reviewed the utilisation of several wild rice traits for cultivated rice breeding programs including cold tolerance, male sterility, high yield, elongation ability and acid sulphate tolerance. ...
... Unfortunately, the present status of wild rice (O. rufipogon) in some countries is threatened because of urbanisation and the expansion of agricultural fields that has resulted in the decline or extirpation of wild rice populations (Song et al., 2005;Raj et al., 2010). At the same time, in other regions, the status of O. rufipogon populations is not known. ...
... Moreover, wild rice frequently coexists near cultivated rice fields, resulting in gene flow from the crop into wild rice populations (Chen et al., 2004;Pusadee et al., 2013). This process can lead to genetic erosion of the wild ancestor (Akimoto et al., 1999;Song et al., 2005). In addition to gene flow, agricultural practices also alter the genetic diversity and population structure of wild rice, leading to the loss of genetic diversity that may significantly affect the evolutionary potential of a species to respond to changing environments (Ellstrand & Elam, 1993;Vance, 2002). ...
Indochina Peninsula is the primary centre of diversity of rice and lies partly in the centre of origin of cultivated rice (Oryza sativa) where the wild ancestor (Oryza rufipogon) is still abundant. The wild gene pool is potentially endangered by urbanisation and the expansion of agriculture, and by introgression hybridisation with locally cultivated rice varieties. To determine genetic diversity and structure of the wild rice of the region we genotyped nearly 1000 individuals using 20 microsatellite loci. We found ecological differentiation in 48 populations, distinguishable by their life-history traits and the country of origin. Geographical divergence was suggested by isolation of the perennial Myanmar populations from those of Cambodia, Laos and Thailand. The annual types would be most likely to have lost genetic variation because of genetic drift and inbreeding. The growing of cultivated and wild rice together, however, gives ample opportunities for hybridisation, which already shows signs of genetic mixing, and will ultimately lead to replacement of the original wild rice gene pool. For conservation we suggest that wild rice should be conserved ex situ in order to prevent introgression from cultivated rice, along with in situ conservation in individual countries for the recurrent evolutionary process through local adaptation, but with sufficient isolation from cultivated rice fields to preserve genetic integrity of the wild populations.
... The wild ancestor of O. sativa is O. rufipogon Griff. (also known as Dongxiang wild rice), which has both perennial and annual types [19] widely distributed in the tropics and subtropics of Asia [22]. O. rufipogon accessions showed tolerance to some biotic and abiotic stresses [23]. ...
... O. rufipogon accessions showed tolerance to some biotic and abiotic stresses [23]. Since this wild rice is a diploid species with the same AA genome as the cultivated O. sativa, it has been used for gene transfer to cultivated rice indica cultivars in the breeding of disease-and insect-resistant rice [22], and drought-and salinity-tolerant rice [24][25][26][27]. In addition to using wild germplasm, many efforts have been made to develop high-yielding rice cultivars with improved tolerance to salt stress by crossing salt-tolerant with salt-sensitive O. sativa cultivars, either indica or japonica, with conventional and modern techniques [21,28,29]. ...
Domesticated rice Oryza sativa L. is a major staple food worldwide, and the cereal most sensitive to salinity. It originated from the wild ancestor Oryza rufipogon Griff., which was reported to possess superior salinity tolerance. Here, we examined the morpho-physiological responses to salinity stress (80 mM NaCl for 7 days) in seedlings of an O. rufipogon accession and two Italian O. sativa genotypes, Baldo (mildly tolerant) and Vialone Nano (sensitive). Under salt treatment, O. rufipogon showed the highest percentage of plants with no to moderate stress symptoms, displaying an unchanged shoot/root biomass ratio, the highest Na+ accumulation in roots, the lowest root and leaf Na+/K+ ratio, and highest leaf relative water content, leading to a better preservation of the plant architecture, ion homeostasis, and water status. Moreover, O. rufipogon preserved the overall leaf carbon to nitrogen balance and photosynthetic apparatus integrity. Conversely, Vialone Nano showed the lowest percentage of plants surviving after treatment, and displayed a higher reduction in the growth of shoots rather than roots, with leaves compromised in water and ionic balance, negatively affecting the photosynthetic performance (lowest performance index by JIP-test) and apparatus integrity. Baldo showed intermediate salt tolerance. Being O. rufipogon interfertile with O. sativa, it resulted a good candidate for pre-breeding towards salt-tolerant lines.
... Wild rice species possess many beneficial agronomic traits, such as resistance to diseases, insects, pests, drought, salt, alkali, and high temperature. These traits include resistance to bacterial blight in O. rufipogon and O. nivara, resistance to blast in O. rhizomatis, and high biomass in O. rufipogon [9,10]. O. rufipogon has been used as a source of genes to improve the elongation ability [11], high tolerance for salinity [12], and low-temperature tolerance [13]. ...
... O. rufipogon has been used as a source of genes to improve the elongation ability [11], high tolerance for salinity [12], and low-temperature tolerance [13]. Moreover, all five Sri Lankan wild rice species have been utilized for developing brown leaf hopper-resistant rice varieties through breeding [10]. These are considered one of the major pests in Sri Lankan rice fields. ...
Five species of wild Oryza (O. nivara, O. rufipogon, O. eichengeri, O. rhizomatis and O. granulata), including the endemic species O. rhizomatis, have been recorded in Sri Lanka. These species are facing continuous decline in their populations due to natural and anthropogenic processes, with habitat loss being the main threat. This study aimed to provide information on the distribution, the current status of ex situ and in situ conservation, and to identify high-priority species and sites of wild rice in Sri Lanka, in order to improve the effectiveness of conservation efforts. Occurrence records of Sri Lankan wild rice species were collected from literature, gene banks, and field surveys. The distribution of these species was mapped, and areas with high species richness were identified. A gap analysis was conducted to determine the high-priority areas and species for ex situ and in situ conservation. It was found that about 23% of the wild rice populations in Sri Lanka were within protected areas, and by expanding these protected areas by 1 km, an additional 22% of the populations located on the border of these areas could be effectively conserved. Our analysis also revealed that 62% of Sri Lankan wild rice populations were not represented in gene banks. The species-rich areas were found to be in only two districts (Polonnaruwa and Monaragala), and less than 50% of these areas were within protected areas. Based on these findings, O. rhizomatis, O. eichengeri, and O. rufipogon were identified as high-priority species for in situ conservation. Ex situ collections were also deemed necessary for O. granulata and O. rhizomatis to ensure diversity representation in gene banks.
... O. rufipogon Griff. (2n = 24, AA), an important CWR of cultivated rice, has accumulated many important agronomic characteristics over its long evolution, such as wide adaptability, resistance to insects, diseases and abiotic stresses, cytoplasmic male sterility, and better quality, which are desirable for the improvement of rice crops (Song et al., 2005;Henry, 2022). As one of the origins of cultivated rice in Asia, China has abundant wild rice resources, which are distributed in Guangdong, Guangxi, Hainan, Yunnan, Hunan, Jiangxi, Fujian and Taiwan (Liu et al., 2016). ...
... In this area, wild rice is widely distributed and exhibits abundant morphological and genetic diversity. Moreover, researchers have shown that South China is a centre of genetic diversity for wild rice (Li et al., 2006;Song et al., 2005). Therefore, O. rufipogon of Guangdong and Hainan Provinces play an important role in rice breeding improvement and basic research in China. ...
Oryza rufipogon Griff. is a valuable germplasm resource for rice genetic improvement. However, natural habitat loss has led to the erosion of the genetic diversity of wild rice populations. Genetic diversity analysis of O. rufipogon accessions and development of the core collection are crucial for conserving natural genetic diversity and providing novel traits for rice breeding. In the present study, we developed 1,592 SNPs by multiplex PCR and next-generation sequencing (NGS) technology and used them to genotype 998 O. rufipogon accessions from 14 agroclimatic zones in Guangdong and Hainan Provinces, China. These SNPs were mapped onto 12 chromosomes, and the average MAF value was 0.128 with a minimum of 0.01 and a maximum of 0.499. The O. rufipogon accessions were classified into ten groups. The mean Nei’s diversity index and Shannon–Wiener index (I) were 0.187 and 0.308, respectively, in all populations, indicating that O. rufipogon accessions had rich genetic diversity. There were also differences in the genetic diversity of O. rufipogon resources in the 14 regions. Hainan populations possessed higher levels of genetic diversity, whereas the Guangzhou population had lower levels of genetic diversity than did the other populations. Phylogenetic analysis revealed that the genetic relationship among the distribution sites of O. rufipogon was closely related to geographical location. Based on genetic distance, a core collection of 299 accessions captured more than 99% of the genetic variation in the germplasm. This study provides insights into O. rufipogon conservation, and the constructed core collection provides valuable resources for future research and genomics-assisted breeding of rice.
... Perennial O. rufipogon subtypes are found in deep swamps, while the annual subtypes are found in shallower, temporary swamps which are parched in the dry season (Morishima et al., 1984). O. rufipogon has been used for many decades for the breeding of disease-and insect-resistant rice (Song et al., 2005;Stein et al., 2018;Wing et al., 2018). O. nivara is an annual grass within the O. sativa complex that is distributed in India, Nepal, Cambodia, Laos, and Thailand. ...
... In rice, over the course of domestication, introgression of wild rice germplasm from cross compatible species such as O. rufipogon and O. nivara has occurred, and these species still stand out as active sources of germplasm for enhancement of salinity tolerance (Brar and Singh, 2011). Salinity-tolerant varieties have already been developed and released using these two wild rice species (Chen et al., 2004;Song et al., 2005). The other eight wild rice species with AA genomes can be easily hybridized by conventional breeding (Khush, 1997). ...
Salinity stress affects global food producing areas by limiting both crop growth and yield. Attempts to develop salinity-tolerant rice varieties have had limited success due to the complexity of the salinity tolerance trait, high variation in the stress response and a lack of available donors for candidate genes for cultivated rice. As a result, finding suitable donors of genes and traits for salinity tolerance has become a major bottleneck in breeding for salinity tolerant crops. Twenty-two wild Oryza relatives have been recognized as important genetic resources for quantitatively inherited traits such as resistance and/or tolerance to abiotic and biotic stresses. In this review, we discuss the challenges and opportunities of such an approach by critically analyzing evolutionary, ecological, genetic, and physiological aspects of Oryza species. We argue that the strategy of rice breeding for better Na⁺ exclusion employed for the last few decades has reached a plateau and cannot deliver any further improvement in salinity tolerance in this species. This calls for a paradigm shift in rice breeding and more efforts toward targeting mechanisms of the tissue tolerance and a better utilization of the potential of wild rice where such traits are already present. We summarize the differences in salinity stress adaptation amongst cultivated and wild Oryza relatives and identify several key traits that should be targeted in future breeding programs. This includes: (1) efficient sequestration of Na⁺ in mesophyll cell vacuoles, with a strong emphasis on control of tonoplast leak channels; (2) more efficient control of xylem ion loading; (3) efficient cytosolic K⁺ retention in both root and leaf mesophyll cells; and (4) incorporating Na⁺ sequestration in trichrome. We conclude that while amongst all wild relatives, O. rufipogon is arguably a best source of germplasm at the moment, genes and traits from the wild relatives, O. coarctata, O. latifolia, and O. alta, should be targeted in future genetic programs to develop salt tolerant cultivated rice.
... Both the ORSC and O. sativa are widely distributed across South, Southeast and Eastern Asia, but the wild stands exist mostly as small, isolated populations, adjoining or intermingling with cultivated fields (Vaughan et al. 2003). As such, wild stands are threatened by habitat destruction, admixture with O. sativa, and genetic erosion (Song et al. 2005). Seeds from thousands of crop wild relatives have been collected and preserved in gene banks around the world (Plucknett et al. 1983;Tanksley and McCouch 1997;Meilleur and Hodgkin 2004). ...
... Low diversity would be expected at the forefront of a range expansion or in isolated colonizing groups, as is the case for temperate japonica. Some wild diversity, particularly the ancestral populations from which the earliest japonica cultivars were domesticated, has surely also been lost as human civilization encroaches on its habitat (Song et al. 2005). In this study, W6 samples from southern China were more likely to share ancestry with W1 wild accessions than were samples from farther north, contributing to the loss of identity of the ancestral japonica gene pool (Wang et al. 2008). ...
Background
Understanding population structure of the wild progenitor of Asian cultivated rice (O. sativa), the Oryza rufipogon species complex (ORSC), is of interest to plant breeders and contributes to our understanding of rice domestication. A collection of 286 diverse ORSC accessions was evaluated for nuclear variation using genotyping-by-sequencing (113,739 SNPs) and for chloroplast variation using Sanger sequencing (25 polymorphic sites).
Results
Six wild subpopulations were identified, with 25 % of accessions classified as admixed. Three of the wild groups were genetically and geographically closely related to the O. sativa subpopulations, indica, aus and japonica, and carried O. sativa introgressions; the other three wild groups were genetically divergent, had unique chloroplast haplotypes, and were located at the geographical extremes of the species range. The genetic subpopulations were significantly correlated (r² = 0.562) with traditional species designations, O. rufipogon (perennial) and O. nivara (annual), differentiated based on morphology and life history. A wild diversity panel of 95 purified (inbred) accessions was developed for future genetic studies.
Conclusions
Our results suggest that the cultivated aus subpopulation is most closely related to an annual wild relative, japonica to a perennial wild relative, and indica to an admixed population of diverse annual and perennial wild ancestors. Gene flow between ORSC and O. sativa is common in regions where rice is cultivated, threatening the identity and diversity of wild ORSC populations. The three geographically isolated ORSC populations harbor variation rarely seen in cultivated rice and provide a unique window into the genetic composition of ancient rice subpopulations.
Electronic supplementary material
The online version of this article (doi:10.1186/s12284-016-0119-0) contains supplementary material, which is available to authorized users.
... sativa)的祖先种 (Khush, 1997), 是水稻育种最重要 的野生基因库之一, 是国家粮食安全的战略性资源 (Song et al, 2005)。温度是限制普通野生稻地理分布 的关键气候因子 (Huang et al, 2012), 普通野生稻最 北分布到中国长江以南的亚热带地区。这些北缘种 群已经适应当地较低温环境, 即具有本地适应性 (Zhao et al, 2013;Zhou et al, 2013) 2 结果 表 1 种群来源和栽培地点及其相互作用、区块对普通野生稻的表型性状的效应的广义线性模型分析结果(* < 0.05, ** < 0.01, *** < 0.001)。 Table 1 F-values generated from general linear model (GLM) analysis in testing the effects of population, growing site, their interaction and block on the traits of Oryza rufipogon (* < 0.05, ** < 0.01, *** < 0.001 ...
Aims: Understanding of phenotypic plasticity and local adaptation in marginal populations is fundamental for predicting how plants will respond to climate change. Common wild rice Oryza rufipogon is an endangered but agriculturally important rice species, which has its northernmost range in China. Climate warming is the main environmental stress that the northern populations of O. rufipogon have to face in the global climate change scenario. However, relatively little attention has been paid to the phenotypic plasticity and local adaptation of O. rufipogon. Here we test the northern and central populations of O. rufipogon for variations in plant fitness traits under the exposure of different temperatures.
Methods: Focusing on the northern population of O. rufipogon, with the center populations (middle and southern populations) as the controls, we established experimental populations at three common gardens along a latitudinal-gradient. According to the method of space-for-time substitution, three common gardens were set up in the northernmost boundary, relatively northern and southern areas of the range of O. rufipogon in China (i.e., high, middle and low latitude) to model the phenotypic performance of common wild rice populations under a future climate change scenario.
Results: The examined populations of O. rufipogon displayed strong phenotypic plasticity, and the levels of phenotypic plasticity varied between populations. The northern population had higher plant height, seed number, and overwintering survival rate at native common garden, suggesting the population’s adaption to relatively low temperature environment. This population could normally set seeds and complete life cycle regardless of whether it was planted northward or southward, demonstrating that it could survive under the future temperature changes. The middle and southern populations did not survive the winter in Shanghai common garden, implying that the low-latitude populations might be more vulnerable to extreme cold climate events.
Conclusion: These results indicate that O. rufipogon has adaptive differentiation between populations and strong phenotypic plasticity, by which both the northern and central populations can respond to climate warming.
... Dongxiang wild rice (DXWR, Oryza rufipogon Griff.) is the most northerly (28 • 14 N) wild rice germplasm resource found worldwide [29][30][31][32]. DXWR has numerous benefits such as high yield and biotic and abiotic stress resistance [33,34]. ...
Cold and salt stresses are major environmental factors that constrain rice production. Understanding their mechanisms is important to enhance cold and salt stress tolerance in rice. MicroRNAs (miRNAs) are a class of non-coding RNAs with only 21–24 nucleotides that are gene regulators in plants and animals. Previously, miR2871b expression was suppressed by cold stress in Dongxiang wild rice (DXWR, Oryza rufipogon Griff.). However, its biological functions in abiotic stress responses remain elusive. In the present study, miR2871b of DWXR was overexpressed to investigate its function under stress conditions. When miR2871b of DWXR was introduced into rice plants, the transgenic lines were more sensitive to cold and salt stresses, and their tolerance to cold and salt stress decreased. The increased expression of miR2871b in rice plants also increased the levels of reactive oxygen species (ROS) and malondialdehyde (MDA); however, it markedly decreased the activities of peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) and the contents of proline (Pro) and soluble sugar (SS). These data suggested that miR2871b of DXWR has negative regulatory effects on cold and salt stress tolerance. Meanwhile, 412 differentially expressed genes (DEGs) were found in rice transgenic plants using transcriptome sequencing, among which 266 genes were up-regulated and 146 genes were down-regulated. Furthermore, the upstream cis-acting elements and downstream targets of miR2871b were predicted and analyzed, and several critical acting elements (ABRE and TC-rich repeats) and potential target genes (LOC_Os03g41200, LOC_Os07g47620, and LOC_Os04g30260) were obtained. Collectively, these results generated herein further elucidate the vital roles of miR2871b in regulating cold and salt responses of DXWR.
... ex Watt and O. perennis Moench that have been used to introgress bacterial blight resistance, blast resistance, brown plant hopper resistance and cytoplasmic male sterility resistance, respectively (Brar and Khush 2018). Regrettably, the genetic pool of species of wild rice is rapidly shrinking due to habitat loss leading to dramatic declines, or even eradication (Akimoto et al. 1999), in populations size as exemplified by populations of O. rufipogon in China (Lu and Sharma 2003;Song et al. 2005). Hence, tapping into this rich source of genetic variation is a race against time as the demand for resilient rice is increasing while the supply from the natural germplasm is declining. ...
As climate change intensifies, the development of resilient rice that can tolerate abiotic stresses is urgently needed. In nature, many wild plants have evolved a variety of mechanisms to protect themselves from environmental stresses. Wild relatives of rice may have abundant and virtually untapped genetic diversity and are an essential source of germplasm for the improvement of abiotic stress tolerance in cultivated rice. Unfortunately, the barriers of traditional breeding approaches, such as backcrossing and transgenesis, make it challenging and complex to transfer the underlying resilience traits between plants. However, de novo domestication via genome editing is a quick approach to produce rice with high yields from orphans or wild relatives. African wild rice, Oryza longistaminata, which is part of the AA-genome Oryza species has two types of propagation strategies viz. vegetative propagation via rhizome and seed propagation. It also shows tolerance to multiple types of abiotic stress, and therefore O. longistaminata is considered a key candidate of wild rice for heat, drought, and salinity tolerance, and it is also resistant to lodging. Importantly, O. longistaminata is perennial and propagates also via rhizomes both of which are traits that are highly valuable for the sustainable production of rice. Therefore, O. longistaminata may be a good candidate for de novo domestication through genome editing to obtain rice that is more climate resilient than modern elite cultivars of O. sativa.
... insects, fungi, and bacteria), abiotic stress tolerance (e.g. wounding, salinity, cold, and flooding), and nutritional-and yield-related traits (Song et al., 2005). However, the utility of wild relatives for rice improvement depends on the availability of these genetic resources: in situ and ex situ conservation strategies are therefore crucial to preserve the wild relatives from extinction and to counteract the anthropogenic activity on their natural habitats (Medeiros et al., 2021). ...
The wild relatives of rice hold unexplored genetic diversity that can be employed to feed an estimated population of 10 billion by 2050. The Oryza Map Alignment Project (OMAP) initiated in 2003 has provided comprehensive genomic resources for comparative, evolutionary and functional characterization of the wild relatives of rice, facilitating the cloning of over 600 rice genes, including those for grain width (GW5) and submergence tolerance (SUB1A). Following the footsteps of the original project, the goal of “IOMAP: The Americas” is to investigate the present and historic genetic diversity of wild Oryza species endemic to the Americas through the sequencing of herbaria and in-situ specimens. The generation of a large diversity panel describing past and current genetic status and potential erosion of genetic variation in the populations will provide useful knowledge for the conservation of the biodiversity in these species. The wild relatives of rice in the Americas present a wide range of resistance traits useful for crop improvement and neodomestication approaches. In the race against time for a sustainable food future, the neodomestication of the first cereal species recently accomplished in O. alta opens the door to the potential neodomestication of the other wild Oryza species in Americas.
... The study of genetic diversity has the advantage of contributing to the advancement of conservation biology, population and community ecology. Population genetics provides estimators of genetic parameters that provide information on effective population size, gene flow, or differentiated gene pools (Diniz-Filho and De Campos-Telles, 2002) for the development of short-and long-term management strategy (Song et al., 2005;Watts et al., 2005). ...
This study aims to characterize the genetic diversity of two populations of Garcinia kola using five RAPD markers in order to contribute to the development of sustainable management and conservation strategy for this species. Genomic Deoxyribonucleic acid (DNA) extracted from leaf fragments of 94 trees from two agroecological (south and west) zones according to Cethyl Trimethyl Ammonium Bromide (CTAB) protocol was analyzed. The mean number of alleles was ranged from 14.2 to 21.2 and the effective number of alleles ranged from 8.62 to 9.44. The average Shannon diversity index was ranged from 2.08 to 2.59 and the average genetic diversity was estimated to be 0.80. A total of 58 polymorphic bands were identified with a polymorphism rate of 100%. According to analysis of molecular variance the most important component of the genetic variation was obtained within population (94%). The analysis of the genetic diversity of all the trees revealed the existence of two groups composed of the trees from the two populations. In addition, genetic differentiation between the two populations was relatively moderate (Fst = 0.061). Sustainable management of G. kola trees should be achieved through in situ conservation. But for ex situ conservation it would be more practical to take as many individuals as possible within populations.
... It is well known that wild rice has accumulated rich genetic diversity and possesses higher saline-alkali tolerance, drought tolerance, and disease resistance than cultivated rice [31]. Studying the characteristics of wild rice is beneficial to the improvement of cultivated rice. ...
Asian cultivated rice (Oryza sativa L.), domesticated from Asian wild rice, is a staple food crop for populations around the world. Asian cultivated rice has undergone physiological changes in the process of its evolution from Asian wild rice, and the closely related rhizosphere microorganisms may have changed in the process of plant domestication. However, the rhizosphere microorganisms of different Asian wild rice species and their related indica and japonica cultivated rice have not yet been illustrated clearly. This study aimed to illustrate the microbial community structures in the rhizosphere of Asian wild rice (common wild rice, nivara wild rice, medicinal wild rice, and spotted wild rice) and Asian cultivated rice (indica and japonica accessions) through the high-throughput sequencing of 16S rDNA, ITS amplifiers and metagenomic data. The results showed that there were significant differences between wild and cultivated rice in their rhizosphere microbial community structures. In view of the indica and japonica rice, the bacterial and fungal community structures of indica rice with the nivara wild rice and medicinal wild rice were more similar than the japonica rice species. The indica and japonica rice had the lowest proportion of Actinobacteria than the wild rice species, and indica rice has the highest relative abundance of Nitrospira. As for the microbial functions, methane metabolism and pyruvate metabolism were found to be the common pathway enriched in the rhizosphere of common and nivara wild rice in comparison with the indica and japonica rice; in addition, though it was found that the relative abundances of the pathogenic fungi in the rhizosphere soil of indica and japonica rice were significantly lower than that of the wild rice, the relative abundances of Magnaporthales and Ustilaginales were significantly higher in indica and japonica rice than that of the wild rice. This study is expected to provide a theoretical basis for the development and utilization of rhizosphere microbial resources for wild and cultivated rice.
... Wild rice species act as a source of germplasm for the improvement of cultivated rice. Indeed, several studies have aimed to characterize natural variation within the genus Oryza in the search of traits that might confer resistance to abiotic and biotic threats in cultivated rice (Sanchez et al., 2013;Song et al., 2005;Wang, Burgess, et al., 2020). Additionally, several studies have examined photosynthetic performance in wild rice species and in some cases have found higher rates for leaf CO 2 uptake in wild rice relative to cultivated (Giuliani et al., 2013;Zhao et al., 2008). ...
Wild rice species are a source of genetic material for improving cultivated rice (Oryza sativa) and a means to understand its evolutionary history. Renewed interest in non‐steady‐state photosynthesis in crops has taken place due its potential in improving sustainable productivity. Variation was characterized for photosynthetic induction and relaxation at two leaf canopy levels in three rice species. The wild rice accessions had 16%–40% higher rates of leaf CO2 uptake (A) during photosynthetic induction relative to the O. sativa accession. However, O. sativa had an overall higher photosynthetic capacity when compared to accessions of its wild progenitors. Additionally, O. sativa had a faster stomatal closing response, resulting in higher intrinsic water‐use efficiency during high‐to‐low light transitions. Leaf position in the canopy had a significant effect on non‐steady‐state photosynthesis, but not steady‐state photosynthesis. The results show potential to utilize wild material to refine plant models and improve non‐steady‐state photosynthesis in cultivated rice for increased productivity. We characterized non‐steady state photosynthesis in an elite rice cultivar and single accessions of its two closest wild relatives and ancestors. The two wild accessions can adjust more rapidly and assimilate more CO2 during transitions from shade to full sunlight. This suggests considerable breeding potential in using this and broader biodiversity in improving rice productivity.
... Oryza sativa has lost many desirable traits including disease and drought resistance in its course of domestication from O. rufipogon. This process of domestication is still evident from the occurrence of many natural hybrids between O. rufipogon and O. sativa reported from several locations (Suh et al. 1997;Song et al. 2002Song et al. , 2005. During the process of domestication of wild rice, the associated microorganisms such as endophytes, AMF, rhizobacteria, etc. also have undergone natural selection in the light of evolving host and changing environmental factors . ...
... Oryza sativa has lost many desirable traits including disease and drought resistance in its course of domestication from O. rufipogon. This process of domestication is still evident from the occurrence of many natural hybrids between O. rufipogon and O. sativa reported from several locations (Suh et al. 1997;Song et al. 2002Song et al. , 2005. During the process of domestication of wild rice, the associated microorganisms such as endophytes, AMF, rhizobacteria, etc. also have undergone natural selection in the light of evolving host and changing environmental factors . ...
This paper presents a comparative study of endophytic bacteria from cultivated (Oryza sativa) and wild rice (Oryza rufipogon) plants and their functional traits related to plant growth promotion. A total of 70 bacterial isolates were characterized by both biochemical and molecular identification methods. Taxonomic classification showed dominance of three major phyla, viz, Firmicutes (57.1%), Actinobacteria (20.0%) and Proteobacteria (22.8%). Screening for in vitro plant growth-promoting activities revealed a hitherto unreported endophytic bacterium from wild rice germplasm, Microbacterium laevaniformans RS0111 with highest indole acetic acid (28.39 ± 1.39 µg/ml) and gibberellic acid (67.23 ± 1.83 µg/ml) producing efficiency. Few other endophytic isolates from cultivated rice germplasm such as Bacillus tequilensis RHS01 showed highest phosphate solubilizing activity (81.70 ± 1.98 µg/ml), while Microbacterium testaceum MKLS01 and Microbacterium enclense MI03 L05 showed highest potassium (53.42 ± 0.75 µg/ml) and zinc solubilizing activity (157.50%). Fictibacillus aquaticus LP20 05 produced highest siderophore (64.8%). In vivo evaluation of plant growth-promoting efficiencies of the isolates showed that Microbacterium laevaniformans RS0111, Microbacterium testaceum MKLS01 and Bacillus tequilensis RHS 01 could increase rice grain yield by 3.4-fold when compared to the control group. This study indicates the potentiality of rice endophytes isolates as an effective bioinoculants.
... Rice is the main food crop in many countries around the world. There are two kinds of cultivated rice, Asian and African cultivated rice [34,35]. However, due to artificially overtargeted selection, rice has lost its fundamental resistance genes in the process of acclimation. ...
Antimicrobial genes are distributed in all forms of life and provide a primary defensive shield due to their unique broad-spectrum resistance activities. To better isolate these genes, we used the Bacillus subtilis expression system as the host cells to build Oryza rufipogon Griff cDNA libraries and screen potential candidate genes from the library at higher flux using built-in indicator bacteria. We observed that the antimicrobial peptides OrR214 and OrR935 have strong antimicrobial activity against a variety of Gram-positive and Gram-negative bacteria, as well as several fungal pathogens. Owing to their high thermal and enzymatic stabilities, these two peptides can also be used as field biocontrol agents. Furthermore, we also found that the peptide OrR214 (MIC 7.7-10.7 μM) can strongly inhibit bacterial growth compared to polymyxin B (MIC 5-25 μM) and OrR935 (MIC 33-44 μM). The cell flow analysis, reactive oxygen burst, and electron microscopy (scanning and transmission electron microscopy) observations showed that the cell membranes were targeted by peptides OrR214 and OrR935, which revealed the mode of action of bacteriostasis. Moreover, the hemolytic activity, toxicity, and salt sensitivity experiments demonstrated that these two peptides might have the potential to be used for clinical applications. Overall, OrR214 and OrR935 antimicrobial peptides have a high-throughput bacteriostatic activity that acts as a new form of antimicrobial agent and can be used as a raw material in the field of drug development.
... It also possesses some unique quantitative trait loci (QTLs) which contribute to its special features such as disease/pest resistance, and abiotic stress tolerance (Ma et al. 2015;Vaughan et al. 2003;Xiao et al. 1998). Chaling CWR is distributed in a wetland named "Huli," local to Yaoshui town, Chaling county, Hunan province (26°50′ N, 113°40′ E), China (Liu et al. 2001;Song et al. 2005). Studies have been established on its living habits, botanical characteristics (Sun 1988), cold tolerance (Xu et al. 2009;Xu et al. 2020), high photosynthetic efficiency (Xiang and Mengliang 2016), and disease resistance (Li et al. 2001). ...
Chaling common wild rice (Chaling CWR, Oryza rufipogon Griff.) is a kind of germplasm resource which possesses abundant genetic diversity and plays a pivotal role in improving cultivated rice. In this research, we used next-generation sequencing technology to reveal the genome sequence of Chaling CWR and investigate its elite genes. The results showed that the average coverage was 93.99%. 1,743,368 single-nucleotide polymorphism (SNP) and 387,381 insertion and deletion (InDel) variants have been detected in Chaling CWR compared with the Nipponbare genome. The variant density was found to be highest in chromosome 10 and lowest in chromosome 5, with an average density of 467.08 SNPs/100 kb and 109.59 InDels/100 kb across the whole genome. 109,684 non-synonymous SNPs were identified in 14,315 genes, and 26,051 InDels were detected in the coding regions. We further classified these genes based on the protein domains that were involved in host defense mechanisms and in the analysis of 37 NBS-LRRs, 71 LRRs, 136 NB-ARCs, 119 PKs, 19 WRKY transcription factors, and 25 resistant protein genes. Among the putative R-genes, Pish, Pita, Pi25, Pi9, Pi21, Pid2, Pikm, and Xa21 were further identified, as exhibiting high rates of polymorphism. Results from this study provide a foundation for future basic research and marker-assisted breeding of rice resistance.
... Introgression of favorable wild alleles into rice varieties has been successful for insect and disease resistance (Hajjar and Hodgkin 2007;Mammadov et al. 2018), but not for grain yield. Moreover, wild resources have become less and less available because the diminishing of their natural habitats (Akimoto et al. 1999;Song et al. 2005;Xie et al. 2010). Broadening genetic variations by means of artificial mutagenesis has been widely used. ...
Key message: A minor QTL for grain weight in rice, qTGW1.2b, was fine-mapped. Its casual gene OsVQ4 was confirmed through CRISPR/Cas9-targeted mutagenesis, exhibiting an effect that was larger than the original QTL effect.
Abstract: The CRISPR/Cas system exhibits a great potential for rice improvement, but the application was severely hindered due to insufficient target genes, especial the lack of validated genes underlying quantitative trait loci having small effects. In this study, a minor QTL for grain weight, qTGW1.2b, was fine-mapped into a 44.0 kb region using seven sets of near isogenic lines (NILs) developed from the indica rice cross (Zhenshan 97) 3 /Milyang 46, followed by validation of the causal gene using CRISPR/Cas9-targeted mutagenesis. In the NIL populations, 1000-grain weight of the Zhenshan 97 homozy-gous lines decreased by 0.9-2.0% compared with the Milyang 46 homozygous lines. A gene encoding VQ-motif protein, OsVQ4, was identified as the candidate gene based on parental sequence differences. The effect of OsVQ4 was confirmed by creating CRISPR/Cas9 knockout lines, whose 1000-grain weight decreased by 2.8-9.8% compared with the wild-type transgenic line and the recipient. These results indicate that applying genome editing system could create novel alleles with large phenotypic variation at minor QTLs, which is an effective way to validate causal genes of minor QTLs. Our study establishes a strategy for cloning minor QTLs, which could also be used to identify a large number of potential target genes for the application of CRISPR/Cas system.
... The effect of wind on pollen diffusion decreases with increasing distance from the pollen donor area. This is because the pollen density in the air decreases gradually with the increase in the distance from the pollen donor site 35 . Maize is a wind-pollinated plant. ...
The transmission of pollen is the main cause of maize gene flow. Under the compulsory labeling system for genetically modified (GM) products in China, isolation measures are crucial. At present, there is no effective isolation device for preventing and controlling the short-range flow of GM maize pollen. The purposes of the present experiments were to overcome the deficiencies of existing technology and to demonstrate a new isolation device for decreasing the gene flow distance of GM maize. The isolation device we invented was shown to be more robust than traditional isolation methods, and it can be disassembled and repeatedly reused. The most important point was that the frequency of gene flow could be greatly reduced using this device. When the distance from the isolation device was more than 1 m, the gene flow rate could be decreased to less than 1%, and when the distance from the isolation device was more than 10 m, the gene flow rate could be reduced to less than 0.1%. When the isolation device was adopted to isolate GM maize in conjunction with bagging the tassels of GM maize at the pollination stage, the gene flow could be controlled to less than 0.1% when the distance from the isolation device was more than 1 m. This device was, however, only applicable for small plots and can shorten the isolation distance of GM maize planting and improve the purity of seeds, all while meeting the needs of close isolation breeding. The use of this device represents a feasible method for risk prevention and control of GM crops.
... O. sativa includes two subspecies, japonica and indica (including an aus subgroup), is grown mainly in Asia and also throughout the world. Human selection has greatly shaped current rice cultivars to fit commercial needs and ecological environ-ments, but the genetic diversity of rice has decreased during the course of domestication and breeding (Sun et al., 2001;Song et al., 2005). The perennial common wild rice (O. ...
Oryza rufipogon Griff. is a wild progenitor of the Asian cultivated rice Oryza sativa. To better understand the genomic diversity of the wild rice, high-quality reference genomes of O. rufipogon populations are needed, which also facilitate utilization of the wild genetic resources in rice breeding. In this study, we generated a chromosome-level genome assembly of O. rufipogon using a combination of short-read sequencing, single-molecule sequencing, BioNano and Hi-C platforms. The genome sequence (399.8 Mb) was assembled into 46 scaffolds on the 12 chromosomes, with contig N50 and scaffold N50 of 13.2 Mb and 20.3 Mb, respectively. The genome contains 36,520 protein-coding genes, and 49.37% of the genome consists of repetitive elements. The genome has strong synteny with those of the O. sativa subspecies indica and japonica, but containing some large structural variations. Evolutionary analysis unveiled the polyphyletic origins of O. sativa, in which the japonica and indica genome formations involved different divergent O. rufipogon (including O. nivara) lineages, accompanied by introgression of genomic regions between japonica and indica. This high-quality reference genome provides insight on the genome evolution of the wild rice and the origins of the O. sativa subspecies, and valuable information for basic research and rice breeding.
... Hybridization-introgression representing gene flow between cultivated and wild rice has been widely observed in nature (Vaughan et al. 2008). The phenomenon of gene flow exists between the cultivated and weedy rice species (Chen et al. 2004), and though pollen competition between wild and cultivated rice has caused a low rate of crop-towild gene flow, but it does not completely prevent gene flow from the crop (Song et al. 2005). Thus, it may alter the genetic structure of natural populations and eventually lead to its genetic erosion. ...
... As an example, for the development of high yielding hybrid rice varieties, a male sterility (MS) gene found in O. rufipogon was first introduced to the cultivated rice. Other agronomically favourable characters, such as genes resistant to tungro virus and bacterial leaf blight in rice (Xa23 gene) and tolerant to acid sulfate soil found in common wild rice, are of great importance for rice genetic improvement (Song et al., 2005). O. rufipogon is broadly distributed in the regions of tropics and subtropics in Asia (Vaughan, 1994). ...
Wild species of rice (Oryza) have superior agronomic characteristics to be incorporated in rice breeding programs worldwide. Population studies of wild relatives of rice in Sri Lanka have not been well documented despite a few attempts. In the present study, phenotypic diversity of Oryza rufipogon populations exist in Sri Lanka were characterized based on nine quantitative morphological traits. Populations (P1, P2, P3, P4 and P5) were established in a common-garden and were characterized. The results revealed moderate phenotypic diversity among O. rufipogon populations studied. However, flag leaf length and awn length were the most variable traits while plant height, flag leaf angle, flag leaf panicle neck length and spikelet angle were the least variable traits. O. rufipogon can be simply distinguished using flag leaf length and width, panicle branching type and distance from panicle base to lowest spikelet insertion. The dendrogram results indicated that four main clusters are at a similarity level of 98.73, showing the diversely related populations with a high identity based on higher similarity values. P1 and P2 populations grouped together by forming the first cluster. The second, third and fourth clusters consisted of P3, P5 and P4 populations, respectively. One population from the first cluster and P3, P5 and P4 populations can be used for conservation. This study highlights the phenotypic diversity of O. rufipogon populations existing in Sri Lanka across the geographic locations and Knowledge on such morphological diversity provides opportunities to design conservation strategies and the potentials of using particular population based on breeding objectives.
Keywords: Genetic differentiation, Morphological variation, O. rufipogon, Population divergence, Wild rice
... Some new disease and insect resistance, and stress-tolerant cultivars need to be evolved to meet climate changing and pathogen plant co-evolution. The nondomesticated common wild rice (Oryza rufipogon Griff.) has been proved an invaluable resistance genetics resource for rice genetic improvement due to its high level of resistance against various biotic and abiotic stresses (Tanksley and McCouch 1997;Song et al. 2005). ...
Common wild rice (Oryza rufipogon Griff.) is invaluable genetic resource for rice resistance breeding. Whole-genome re-sequencing was conducted to systematically analyze the variations in two new inbred lines (Huaye 3 and Huaye 4) developed from a common wild rice. A total of 4,841,127 SNPs, 1,170,479 InDels, 24,080 structural variations (SVs), and 298 copy number variations (CNVs) were identified in three materials. Approximately 16.24 and 5.64% of the total SNPs and InDels of Huaye 3 and Huaye 4 were located in genic regions, respectively. Together, 12,486 and 15,925 large-effect SNPs, and 12,417 and 14,513 large-effect InDels, which affect the integrity of the encoded protein, were identified in Huaye 3 and Huaye 4, respectively. The distribution map of 194 and 245 NBS-LRR encoding homologs was constructed across 12 rice chromosomes. Further, GO enrichment analysis of the homologs with identical genotype variations in Huaye 3 and Huaye 4 revealed 67, 82, and 58 homologs involved in cell death, response to stress, and both terms, respectively. Comparative analysis displayed that 550 out of 652 SNPs and 129 out of 147 InDels were present in a widely used blast-susceptible rice variety (LTH). Protein-protein interaction analysis revealed a strong interaction between NBS-LRR candidates and several known R genes. One homolog of disease resistance protein (RPM1) was involved in the plant-pathogen interaction pathway. Artificial inoculation of disease/insect displayed resistance phenotypes against rice blast and brown planthopper in two lines. The results will provide allele-specific markers for rice molecular breeding.
Electronic supplementary material
The online version of this article (10.1007/s11105-018-1103-1) contains supplementary material, which is available to authorized users.
... The wild FNPs identified in A.M. Moner et al. Molecular Phylogenetics and Evolution 127 (2018) 475-487 this study represent the original gene pool before domestication and may be useful in developing rice genotypes for cultivation in future environments (Song et al., 2005;Hajjar and Hodgkin, 2007;Henry, 2009;Andersson et al., 2010;Zhongming et al., 2012;Brozynska et al., 2015). Further study of these FNPs is required to determine their significance. ...
Whole chloroplast genome sequence analysis of 58 wild and domesticated rice samples was used to investigate their phylogeny providing more detail on the biogeography of the major groups of wild A genome rices globally. An optimized chloroplast assembly method was developed and applied to extracting high quality whole chloroplast genome sequences from shot gun whole DNA sequencing data. Forty complete high quality chloroplast genome sequences were assembled (including; temperate japonica, tropical japonica and aus). The South American and African wild rice relationships were confirmed, while the Australian chloroplast type was found to extend north to the Philippines. The remainder could be divided into an African (O. barthii and the domesticated O. glaberrima) clade and the Asian taxa. The Asian taxa were placed in two distinct clades including the domesticated O. sativa ssp. indica and O. sativa ssp. japonica respectively. These two groups of wild rices had substantially overlapping distributions with the O. sativa japonica group extending further west into India. The aromatic rices had japonica chloroplasts as expected. A polyphyletic maternal genome origin of the cultivated aus group of rices was suggested by the identification of aus accessions in both the wild indica and japonica clades. The current distribution of the chloroplast types appears to differ significantly to that of the nuclear genome diversity suggesting a complex evolutionary history of the rice progenitors leading to the domestication of rice.
... rufipogon Griff.) (Song et al., 2005;Tian et al., 2011;Zhou et al., 2016) hybridized to a cultivated rice variety (O. sativa ssp. ...
Salt stress causes significant reductions in rice production worldwide; thus, improving salt tolerance is a promising approach to meet the increasing food demand. Wild rice germplasm is considered a valuable genetic resource for improving rice cultivars. However, information regarding the improvement of salt tolerance in cultivated rice using wild rice genes is limited. In this study, we identified a salt-tolerant line Dongxiang/Ningjing 15 (DJ15) under salt-stress field conditions from the population of a salt tolerant Dongxiang wild rice × a cultivated rice variety Ningjing16 (NJ16). Genomic resequencing analysis of NJ16, DJ15 and Dongxiang wild rice revealed that the introgressed genomic fragments were unevenly distributed over the 12 chromosomes (Chr.) and mainly identified on Chr. 6, 7, 10, and 11. Using quantitative trait locus (QTL) mapping, we found 9 QTL for salt tolerance (qST) at the seedling stage located on Chr. 1, 3, 4, 5, 6, 8, and 10. In addition, sequence variant analysis within the QTL regions demonstrated that SKC1/HKT8/HKT1;5 and HAK6 transporters along with numerous transcriptional factors were the candidate genes for the salt tolerant QTL. The DJ15/Koshihikari recombinant inbred lines that contained both qST1.2 and qST6, two QTL with the highest effect for salt tolerance, were more tolerant than the parental lines under salt-stress field conditions. Furthermore, the qST6 near-isogenic lines with IR29 background were more tolerant than IR29, indicating that qST1.2 and qST6 could improve salt tolerance in rice. Overall, our study indicates that wild rice genes could markedly improve the salt tolerance of cultivated rice.
... Some examples include the use of: Oryza rufipogon to confer cold tolerance and other abiotic stress resistance in rice (O. sativa) in China (Song et al., 2005), Thinopyrum intermedium and Th. ponticum to improve wheat (Triticum aestivum) for barley yellow dwarf virus immunity which was released all across the World (Ayala et al., 2001), Arachis batizocoi, A. cardenasii, A. duranensis, A. stenosperma and A. villosa for rust and late leaf spot resistant to peanut (A. ...
This options paper has been prepared as a contribution to the discussion on issues related to on-farm management of plant genetic resources for food and agriculture and in situ conservation of crop wild relatives and wild plants for food, particularly in developing countries.
... The species is ecologically adapted to forest edges, as well as to open vegetation with preference to alluvial or sandy soil on limestone under partial shade to full sunlight. Rapid decline in populations attributed to habitat fragmentation or destruction due to human disturbance has been reported in China (Gao et al. 2001;Gao and Zhang 2005;Song et al. 2005), although O. officinalis has been assessed as of ''least concern'' by the IUCN Red List of Threatened Species (http://www.iucnredlist. org/). ...
This study was conducted to understand variation patterns and establish the population structure in the wild rice species, Oryza officinalis, using accessions collected across the 11 regions/areas of endemism in Asia and Oceania and conserved ex situ in the International Rice Genebank at the International Rice Research Institute. Morphological and microsatellite data detected a tendency for latitudinal divergence in O. officinalis and divided the accessions into (1) Malesian and (2) South and East Asian populations. Cluster and ordination analyses of morphological characters revealed that accessions from Malesia (Regions 1–6), Vietnam (Region 7), and Central Thailand (Region 8) showed short (16.19 ± 3.70 cm) and slender (1.53 ± 2.06 cm) flag leaves that are erect to almost horizontal, short panicles (25.19 ± 3.02 cm) and mainly purple internodes; and (3) accessions from Northern Thailand and Myanmar (Region 9), India (Region 10) and China (Region 11) characterized by long (29.57 ± 4.94 cm) and broad (2.18 ± 3.33 cm) flag leaves that are horizontal to drooping, long panicles (35.26 ± 2.63 cm) and green internodes. With 79.3 % of the SSR markers being polymorphic, molecular analyses detected an average of 5.31 alleles per marker with a total of 154 alleles. Differentiation was evident among the regions with FST = 0.2173, although there is an apparent loss of heterozygosity across regions indicated by an over-all positive FIS. Based on the results, issues related to the management of O. officinalis, specifically filling gaps in the collection and the formulation of seed multiplication practices are addressed.
... The cytoplasmic male sterile gene, which was found in one of the germplasms of Chinese wild rice in the early 1970s, facilitates the utilization of heterosis in rice. Wild rice is genetically more diverse than cultivated rice Lu et al, 2002;Song et al, 2005;Gao et al, 2006;Zhu et al, 2007b), and wild rice from China shows greater levels of polymorphism than do those from other countries (Ge et al, 1999). Some studies have shown that the variation present , in cultivated rice, in terms of SSR , RFLP (Sun et al, 2001a) and isozyme (Shahi et al, 1967) markers, account for about 60% of the total found in wild rice. ...
Rice is the major source of food for over half of the world's population. As a model cereal crop, the complete genome sequence of rice has become fundamental for analyzing gene functions and relating them to practical applications in plants. At present, rice researchers devote much effort to generating mutants and tagged lines, or utilizing elite germplasms to clone important genes and identify their functions. Such processes combine different -omic technologies including genomics, transcriptomics and proteomics. In the past decade, Chinese scientists have made great contributions toward integrated analyses of rice omics and biotechnological applications, particularly whole genome shotgun sequencing of Indica rice 9311, and sequencing of chromosome 4 of japonica rice Nipponbare, cloning and identifying 220 functional genes, and using certain identified genes to improve rice agronomic traits through molecular breeding approaches. This review presents a summary of the advances made in rice omics and biotechnology in China, as well as future prospects.
... En parallèle des synthèses et bilan géographique, l'apport de la phylogéographie le plus concret en conservation est de définir de manière objective des unités de conservation au niveau infraspécifique (Song et al., 2005;Watts et al., 2005). Ces unités dites « évolutives » ou ESU (Evolutionary Significant Unit, Moritz, 1994) pourront servir à établir des priorités de conservation dans le cadre des plans de conservation (Small et al., 1998) ...
Diversity patterns represent a temporary state in a dynamic continuum of ecological and evolutionary changes. Thus, conservation policies have to integrate this dynamics to ensure long term conservation of biodiversity. Conservation priorities have to be oriented towards the processes which generate and maintain diversity. An original approach is to assess the capacity of phylogeography as a method to integrate processes of diversification and persistence into conservation. Indeed, the phylogeography allows providing indices for diversification zonation and can be used to delineate the units (e.g. evolutionary significant units) that support diversification at intraspecific level. The main objective of this PhD thesis is to evaluate, in terms of targets and surrogates, the role of phylogeography for conservation of the Mediterranean flora. We based our analyses on two study areas harbouring two endemic plant species with restricted distributions: (i) the coastal ranges of the Maritime Alps where the endemic Acis nicaeensis grows, (ii) the calcareous Provence where the endemic Arenaria provincialis is found. At a sub-regional scale, spatial diversity of Arenaria provincialis showed a spatial distribution of persistence and divergence which reveal the potentials of research on the use of the evolutionary legacy, as a surrogate for biodiversity. Our study highlights the critical role of phylogeography to delineate and assess conservation efficiency of the protected areas as well as in the search for optimal criteria for the defining the conservation strategies. The marked differences in populations of Acis nicaeensis in terms of isolation, size, genetic origin, and ecology but also in terms of its vulnerability to urbanization are highlighted in a local scale. The results demonstrate the important vulnerability of coastal population, whose originality necessitates conservation actions designed for small areas to avoid the loss of Acis nicaeensis evolutionary legacy.
In this chapter, we assess the current status of wild Oryza gene bank collections and in situ protection sites. We have identified O. neocaledonica and O. schlechteri as priority species, and Africa and South America as priority regions for ex situ and in situ conservation. We review recent genetic diversity studies and explained how information on population genetic structure, ecogeographic differentiation within species, and intra- and interspecific gene flow can be used in enhancing the effectivity and efficiency of conservation methods. We emphasize the need for further studies on species-specific dormancy-breaking treatments and on seed longevity of wild rice species under storage conditions. We discuss the potentials of molecular taxonomic markers, tissue culture, and plant-dwelling symbionts in improving gene bank practices. Finally, we present the significant contributions of wild Oryza species to rice improvement.KeywordsWild rice
Oryza
ConservationGene bankCrop wild relative
Genus Oryza consists of two cultivated and 21 related wild species. Cultivated rice is not only the staple food of the majority of the countries in the world, but it also serves as a model crop for genomic studies. The rice germplasm is conserved in different gene banks around the world, which can be accessed for plant breeding programmes aiming to improve rice varieties. However, the ever‐increasing number of accessions poses problem of the phenotypic and genotypic characterization of the germplasm. Therefore, to speed up characterization and utilization of germplasm, the concept of core collection (~10–20% of total base collection) was developed which provides maximum diversity in limited number of accessions. Similarly, a mini core collection (~1–2% of the entire collection) is constructed retaining maximum diversity to provide wider genetic coverage in manageable numbers. The present review summarizes the current information on different core and mini core sets developed for varied purposes from world rice collections using different strategies.
Bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is a common, widespread, and highly devastating disease that affects rice yield. Breeding resistant cultivars is considered the most effective measure for controlling this disease. The introgression line G252 derived from Yuanjiang common wild rice (Oryza rufipogon) was highly resistant to all tested Xoo strains, including C5, C9, PXO99, PB, T7147Y8, Hzhj19, YM1, YM187, YJdp-2, and YJws-2. To identify the BB resistance gene(s) of G252, we developed an F2 population from the cross between G252 and 02428. A linkage analysis was carried out between the phenotype and genotype in the population. A segregation ratio of 3:1 was observed between the resistant and susceptible individuals in F2 progeny, indicating a dominant resistance gene, Xa47(t), in G252. The resistance gene was mapped within an approximately 26.24 kb physical region on chromosome 11 between two InDel markers, R13I14 and 13rbq-71; and moreover, one InDel marker, Hxjy-1, co-segregated with Xa47(t). Three genes were predicted within the target region, including a promising candidate gene encoding a nucleotide-binding domain and leucine-rich repeat (NLR) protein (LOC_Os11g46200) by combining the structure and expression analysis. Physical mapping data suggested that Xa47(t) was a new broad-spectrum BB resistance gene.
The wild rice species in the genus Oryza harbor a large amount of genetic diversity that has been untapped for rice improvement. Pan-genomics has revolutionized genomic research in plants. However, rice pan-genomic studies so far have been limited mostly to cultivated accessions, with only a few close wild relatives. Advances in sequencing technologies have permitted the assembly of high-quality rice genome sequences at low cost, making it possible to construct genus-level pan-genomes across all species. In this review, we summarize progress in current research on genetic and genomic resources in Oryza, and in sequencing and computational technologies used for rice genome and pan-genome construction. For future work, we discuss the approaches and challenges in the construction of, and data access to, Oryza pan-genomes based on representative high-quality genome assemblies. The Oryza pan-genomes will provide a basis for the exploration and use of the extensive genetic diversity present in both cultivated and wild rice populations.
Over the past 30 years, human disturbance and habitat fragmentation have severely endangered the survival of common wild rice (Oryza rufipogon Griff.) in China. A better understanding of the genetic structure of O. rufipogon populations will therefore be useful for the development of conservation strategies. We examined the diversity and genetic structure of natural O. rufipogon populations at the national, provincial, and local levels using simple sequence repeat (SSR) markers. Twenty representative populations from sites across China showed high levels of genetic variability, and approximately 44% of the total genetic variation was among populations. At the local level, we studied fourteen populations in Guangxi Province and four populations in Jiangxi Province. Populations from similar ecosystems showed less genetic differentiation, and local environmental conditions rather than geographic distance appeared to have influenced gene flow during population genetic evolution. We identified a triangular area, including northern Hainan, southern Guangdong, and southwestern Guangxi, as the genetic diversity center of O. rufipogon in China, and we proposed that this area should be given priority during the development of ex situ and in situ conservation strategies. Populations from less common ecosystem types should also be given priority for in situ conservation.
To evaluate genetic diversity and genetic structure of wild rice (Oryza rufipogon) populations in Myanmar, seven research sites were selected based on various ecological conditions. A large number of samples under natural growth conditions were collected and studied using six simple sequence repeats (SSRs) and two chloroplast DNA markers. A total of 77 alleles were detected from 1559 samples over six SSR loci. The mean number of alleles per population ranged from 3.167 to 8.667, and the mean expected heterozygosity ranged from 0.140 to 0.701. Wild rice populations survived under various environmental conditions and retained different levels of genetic diversity. The large number of samples was effective to confirm the spatial genetic structure of wild rice populations in a relatively small area. Regarding chloroplast DNA polymorphisms, four populations possessed only one pattern, while the other three showed two or five combinations of haplotypes, even within the same population. Additionally, the existence of a new genotype was revealed. Considerable variations in chloroplast DNA exist in the wild rice populations of Myanmar. A high proportion of genetic variation was detected within, rather than among, populations. To ensure maintenance of allelic diversity, it is advisable to preserve many individuals from a large population.
Extinction of traditional crop varieties is becoming a common scenario in the world due to adoption of hybrid/improved varieties. Conservationists are very busy with protection of those verities for novel genes to develop agriculture through molecular breeding. However conservation feasibility is always questionable for traditional seeds because of recalcitrance and low viability in nature. This is the first report on the protection of traditional deep water rice (Oryza sativa L.) cultivar, TNR1 from possible extinction using callus induction and regeneration system. TNR1 is known for its traditional (antidiabetic) and genetic (salinity and submergence resistance genes) importance. The matured embryos were inoculated on LS medium prepared with 2.5 mg L−1 2, 4-D and 0.1 mg L−1 KN showed 74.5% of embryogenic callus induction. The calli was regenerated on MS medium fortified with 1.5 mg L−1 NAA and 3.0 mg L−1 BAP and obtained 83.4% of regeneration. Regenerated plants were successfully acclimatized in the field with 100% survival. The germination percentage of tissue culture derived seeds was found to be high (84.2%) compared to traditional seeds (36.4%). The outcome of this study revealed that, tissue culture enhanced the viability of recalcitrant seeds. In future, this protocol will be an invaluable tool for both transgenic plant production or conservation of threatened traditional rice germplasms.
Cultivated plants are the most important material basis for human survival and development. Growing global human population and personal demands result in increasing consumption of plant resources. The low genetic diversity of cultivated plants is a key factor that restricts production and quality improvements. Wild relatives of cultivated plants have accumulated rich genetic variations and adaptive traits during the process of long-term adaptive evolution, thus can be used as genetic donors in germplasm innovation and improvement of cultivated plants. However, the persistence and evolution of wild relative populations are threatened by habitat destruction and anthropogenic climate change. This review summarizes the progress of in situ and ex situ conservation of wild relatives of cultivated plants and offers conservation suggestions for wild relatives of cultivated plants based on the current situation in China. Moreover, technologies for the utilization of wild relatives of cultivated plants are reviewed and new insights on the sustainable use of genetic resources of wild crop relatives are also discussed. Finally, the status of conservation and utilization of the main cultivated plants that originated from the Yangtze River Basin are investigated, with four plants of different uses used as representatives.
The rainforest of Central Africa belongs to that of the Congo basin. It is the habitat to more than half the wildlife of the continent and is an extremely useful and valuable ecosystem for humanity to feed, shelter, heal, get energy, etc. Unfortunately, this forest wealth is increasingly threatened by abusive exploitation of vast wooded areas before even explore it scientifically and develop effective strategies of conservation and sustainable use. The conservation in situ of species requires prior knowledge of the ecology and genetic data of these species. Two species: Dacryodes buettneri and Dacryodes edulis were chosen for this study. The overall objective of this study is to contribute at the sustainable management of both species. The specific objectives are: to describe the geographical distributions of D. buettneri and D. edulis from the geographic coordinates of available observations and potential distributions modeled with nineteen climate parameters ; to characterize the ecological conditions based on the cover of vegetation, climate (precipitation and temperature) and the altitude ; to isolate and to characterize the D. edulis microsatellite loci ; to describe the genetic diversity within populations and between populations of D. buettneri and D. edulis across the lower Guinea endemism (Cameroon and Gabon) and finally to describe the genetic structure of D. buettneri and D. edulis and the genetic relation between these species.
The actual distributions based on the coordinates assigned to each observation of D. buettneri and of D. edulis have been established using the GIS software (Diva-Gis). The potential distributions of each species were modeled with 19 climatic parameters. The study of the ecological niches was based on vegetation cover, 19 climatic parameters and altitudes. Graphs describing the ecological requirements from the altitude, rainfall and temperature data have been made using the descriptive statistics by Statistica 6 software. The nuclear DNA of 694 individuals across 29 populations (23 populations of D. edulis) was extracted from cambium and leaflets. Five microsatellite loci were isolated from D. edulis and genetic analyses were based on isolated microsatellite polymorphism. Intra-population and inter-population diversity and genetic structure within species were studied.
D. buettneri is a species of wet forests. It can be seen in destroyed vegetation because it is protected by farmers. The centre of Gabon offer more favorable climatic parameters conditions to its growth. The confidence interval of the precipitation ranges from 1500 to 2550 mm/year. Optimal average annual temperatures are between 23.8 to 25.8 °C. The species grows from the level of the sea up to 750 m altitude. D. edulis is a species of humid forests. South of Cameroon and Gabon provide more favorable climatic parameters conditions to its natural growth naturally. The optimal annual precipitation ranges from 1600 to 2600 mm/year. Optimal average annual temperatures range from 23.5 to 25.5 °C while the confidence interval is between 21.8 and 25.8 °C. The species grows naturally from the level of sea up to 750 m altitude. It is domesticated and has widely adapted to ecological conditions. The environmental conditions of the individuals of the plantations represent the fundamental ecological niche while those of wild individuals represent the real or realized ecological niche.
Genetic analysis of populations of D. buettneri has identified populations of Chaillu (P = 100% and Hatt = 0.47), of Casterville (P = 80% and Hatt = 0.36) and of Makoukou (P = 80% and Hatt = 0.36) as the most polymorphic populations. All studied populations were exhibited positive coefficients of consanguinity, ranging from 0.15 (Mt Crystal population) and 0.36 (Casterville population). Regarding D. edulis, the average of intra-population genetic parameters are A = 5.36; P = 90% and Hatt = 0.47. The average of coefficient of consanguinity is F = 0.12. Five populations have showed coefficient of consanguinity significantly less than zero. The establishment of plantations of D. edulis by farmers therefore maintained genetic diversity of the species. The study of the genetic structure has not showed different genetic groups within species that could be associated with varietal demarcations.
The study of the ecological niches of D. buettneri and D. edulis combined with analyses of population genetics parameters is a coherent contribution to optimize the in situ conservation and the sustainable use of these species.
Keywords: Dacryodes buettneri, Dacryodes edulis, geographical distribution, ecological niches, genetic diversity, markers microsatellite, in situ conservation.
Rice cultivated gene pool includes two species. Asian rice, Oryza sativa, displays a very large phenotypic diversity resulting from a long history of domestication driven by human demographic expansion and sympatry with its wild relatives. African rice, Oryza glaberrima, represents a typical case of domestication bottleneck. Recent sympatry of the two species in Africa has given birth to new diversity. Current rice in situ genetic diversity results from the succession of a number of long-standing evolutionary events and the contemporary reversal of the trend of increasing diversity, referred to as genetic erosion. Since the early twentieth century, human demographic growth, agricultural modernisation and the advent of formal breeding systems, have affected the in situ diversity of cultivated rice species and their wild relatives. The evolutionary processes had produced a very large number of Landraces (LV) of which some 500,000 are conserved ex situ. The contemporary changes have resulted in the replacement of a large proportion of LV by a small number of Modern varieties (MV) in more than 70 % of rice-growing areas in Asia and Latin America, 38 % in Africa. The most important feature of rice in situ diversity emerging from our case studies in China, South and Southeast Asian countries, West Africa and Madagascar, is the diversity of situations. Aggregated data suggest massive absolute genetic erosion and sharp reduction of diversity indexes, particularly in irrigated ecosystems. Detailed surveys indicate smoother genetic erosion in rainfed ecosystems. However, the perspectives of rice in situ genetic diversity are gloomy even in rainfed ecosystems. The most realistic and promising option for the future is a dynamic management in the framework of the emerging concept of ecological intensification.
Ecological impact caused by transgene flow from genetically engineered (GE) crops to their wild relatives is largely determined by the fitness effect brought by a transgene. To estimate such impact is critical for the ecological risk assessment prior to the commercialization of GE crops. We produced F1 and F2 hybrid descendants from crosses of two insect-resistant GE rice lines (Bt, Bt/CpTI) and their non-GE rice parent with a wild rice (Oryza rufipogon) population to estimate the transgenic fitness. Insect damages and life-cycle fitness of GE and non-GE crop–wild hybrid descendants as well as their wild parent were examined in a common-garden experiment. No significant differences in insect damages were observed between the wild rice parent and GE hybrid descendants under high-insect pressure. The wild parent showed significantly greater relative survival-regeneration ratios than its GE and non-GE hybrid descendants under both high- and low-insect pressure. However, more seeds were produced in GE hybrid descendants than their non-GE counterparts under high-insect pressure. Given that the introduction of Bt and Bt/CpTI transgenes did not provide greater insect resistance to crop–wild hybrid descendants than their wild parent, we predict that transgene flow from GE insect-resistant rice to wild rice populations may not cause considerable ecological risks.
Oryza rufipogon Griff. is a valuable reservoir of useful traits for rice genetic improvement. We evaluated the genetic diversity of six populations of O. rufipogon from Kerala using random amplified polymorphic DNA (RAPD) markers. Various estimates revealed high genetic diversity in the populations. However, gene flow between the populations was low and 47% of the total genetic diversity was partitioned between populations, suggesting moderate differentiation between them. Clustering of all individuals from the same populations under distinct nodes supported the population differentiation. Considering its outbreeding behaviour, the low gene flow and moderate differentiation recorded in this study indicate that the recent habitat destruction and fragmentation have had an impact on the genetic characteristics of O. rufipogon populations in Kerala. The high genetic diversity observed in this study, contrary to expectations for fragmented populations, is presumably contributed by the recurring gene flow from cultivated rice grown in nearby fields. We recommend immediate conservation of a large number of populations of this species, including establishment of isolated conservatories away from rice fields to maintain the purity of the wild gene pool.
With the extensive environment release and large scale cultivation of genetically modified (GM) crops, the ecological environment security problems, caused by transgene escape from GM crop to its non-GM counterpart and wild relatives, have appeared gradually. During the early years of breeding and seed increase, there are some uncertainty among regulators about containment measures needed to prevent the movement of regulated GM traits into adjacent fields and possibly into the human or animal food chain. Cotton, one of the wind-pollinated and highly outcrossing cash crops, is planted on millions of hectares annually and is the third most abundant GM crop. This study investigated the occurrence of gene flow from transgenic cotton to non-transgenic cottons under closed conditions using an insect-resistant gene as a tracer marker. The selectable marker used in this study was the synthetic GFM CryIA(C)gene which encoded Bt insecticidal protein with resistance to cotton bollworm. In order to determine the impacts of wind direction on pollen-mediated gene flow (PGF), two greenhouse experiments under different wind conditions (directed and indirected) were establishied. The growth area for each treatment was 480m2, and the row and plant spacing was 80cm×30cm. To observe the frequency and distance of gene flow, the transgenic cotton, SGK321 (Gossypium hirsutum L.), was used as a pollen donor, and conventional varieties Shiyuan321 (Gossypium hirsutum L.), Zhongmian35 (Gossypium hirsutum(L.) and Jizha1 (Gossypium barbadense L.) were applied as pollen recipients, separately. Following natural pollination under the wind conditions, the seeds were collected from each conventional varieties at varying distances and sown in pot culture. DNAs were extracted by the CTAB procedure during cotyledon period, then screened for Cry I A (C) gene by PCR assays. The positive samples in the PCR assays were identified for Bt insecticidal protein by dipstick assay. The results showed that there was a variation of PGF with increasing distances from the donor plots. The highest frequencies of gene flow were (33.33±12.02)% at 6.4m in thg directed-wind treatment and (36.67±6.67)% at 12.8 m in the indirected-wind treatment. The maximal gene flow distance observed were 25.6m in the directed-wind treatment and 36m in the indirected-wind treatment. PGF to the island cotton (Jizha1) was higher under the indirected-wind treatment than that under the directed-wind treatment, associated with the possibility that the gargantuan island cotton could hinder the wind, leading to cross pollination. PGF to non-transgenic counterpart (Shiyuan321) was obviously higher than those to the island cotton (Jizha1) and the upland cotton (Zhongmian35), indicating that genetic relationship played an important role in cross-pollination with non-GM crops. Such control by individual factor (wind direction) under closed conditions in affecting the occurrence of gene flow rather than open-field trial designs could also be proved very useful in studying the influence of a certain factor on the gene flow. Our research may provide some reference value for the ecological safety assessment of transgenic cotton with the aim of establishing strategies to prevent pollen dispersal.
Iron (Fe) and zinc (Zn) contents in hexaploid wheat are very low and are further reduced
because of the removal of micronutrient-rich bran of wheat grains during milling and processing.
Therefore, hexaploid wheat, its wild species and wheat–Aegilops kotschyi substitution
lines were evaluated to identify the genome(s) carrying gene(s) for high Fe and Zn concentrations
in bran and endosperm fractions of grains. It is reflected from the results that Triticum
monococcum (acc. W463) may serve as a promising donor for biofortification of Fe, and
Aegilops speltoides (acc. 3804) may serve as a promising donor for biofortification of Zn in
the endosperm of cultivated wheat. Further, among the three wheat–Ae. kotschyi substitution
lines, the higher concentration of Fe and Zn in endosperm fraction was observed in BC2F4
63-2-13-1. The work on precise transfer of useful gene(s) from 7Uk chromosome of this line
is in progress to reduce linkage drag.
The mode of inheritance and allelic relationships of the genes for resistance to bacterial blight caused by Xanthomonas campestris pv oryzae (Ishiyama 1922) Dye 1978 in 58 rice (Oryza saliva L.) cultivars were studied in the field. The analysis of F 1 and F 2 populations from the crosses of resistant cultivars and susceptible 'TN1' revealed that single dominant genes conditioned resistance in each of 48 cultivars whereas single recessive genes conveyed resistance in 10 remaining cultivars. The allele tests indicated that the 48 cultivars have the Xa 4 gene for resistance. The recessive genes for resistance in eight cultivars are allelic to xa 5. However, the recessive genes for resistance in 'Khao Lay Nhay' and 'Sateng' are allelic to each other but are nonallelic to and segregate independently of Xa 3, Xa 4, xa 5, Xa 7, and xa 8. This new recessive gene is linked with Xa 6 with a crossover value of 5.9%. Thus cultivars Khao Lay Nhay and Sateng have a new gene for resistance, which was designated xa 9.
As one of important original centers of Asian cultivated rice Oryza sativa L., China is abundant in genetic resources of rice and its wild relatives. They are not only useful for mountainous farmers to cope with heterogeneous microclimates, but also of extremely significance for rice genetic improvement programs in the future. Unfortunately, the combination of new conditions, including rapid population growth, new agricultural technology and swift economic & cultural changes produces a new environment. As a result, most of wild populations have disappeared, and others are at the edge of the extinction. Moreover, widespread adoption of high-yielding rice varieties (HYVs) have led to biological impoverty of rice germplasms, as local rice varieties are abandoned for modern varieties. These processes, known as genetic erosion, are generally summarized as two types in Chinese rice genetic resources. Based on our recent studies on the conservation of Chinese rice biodiversity, this paper reviews the biodiversity, ethnobotany and genetic erosion of rice and its wild relatives in China. Finally, some suggestions for the ways to enhance efforts to conserve rice genetic resources, including investigation of genetic erosion, studies on population genetics and conservation genetics using molecular approaches, settings of in situ & ex situ conservation priorities, significance of ethnobotanical knowledge for taking in situ conservation, and necessities of extensive participation in the conservation activities, are given.
The pollen flow pattern of a cultivated rice variety, Minghui-63, was studied at horizontal and vertical levels under experimental conditions. Data obtained from pollen traps for six designed populations (as pollen sources) at different intervals showed that the dispersal of rice pollen decreased with the increase of distance from pollen sources and that the rice pollen flow was significantly influenced by weather conditions, particularly by wind direction and speed. For a mean wind speed of 2.52 m/s in a downwind direction, the observed distance of rice pollen dispersal was 38.4 m, indicating that rice pollen grains normally disperse at a relatively small range. However, the maximum distance of rice pollen flow could be up to 110 m, using regression analysis of pollen flow and wind speed, when the wind speed reached 10 m/s in this study. The frequency of pollen flow was positively correlated with pollen source size within a given range, suggesting that pollen flow will occur effectively at a considerable rate in rice fields with sufficiently large pollen sources. In addition, many more pollen grains were detected at the height of 1.0–1.5 m than at 2.0 m, indicating that rice pollen mainly disperses at relatively low heights. Results from this study are useful both for minimizing transgene escape from transgenic rice and in situ conservation of wild relatives of rice, as well as for hybrid seed production, where an effective isolation buffer zone needs to be established.
Griff., allozyme analysis was conducted using 22 loci on a typical population from Yunnan Province, China. Non-random distribution
of genotypes and/or genetic variability was found among three subpopulations, and the result was further demonstrated by considerable
genetic differentiation observed (F
ST
=0.206) within the population. Microhabitat selection may not be an important factor in shaping intra-population genetic structure,
and restricted gene flow (N
m
=0.964<1) and genetic drift act together towards a genetic subdivision within the population. This genetic subdivision may
enhance inbreeding and will ultimately lead to genetic depletion within the predominantly outcrossing (t=0.830) perennial population, and therefore, more attention should be paid to the conservation and genetic management of the
population.
In order to determine the genetic diversity and genetic structure of populations in common wild rice Oryza rufipogon, an endangered species, allozyme diversity was analyzed using 22 loci in 607 individuals of 21 natural populations from the
Guangxi, Guangdong, Hainan, Yunnan, Hunan, Jiangxi and Fujian provinces in China. The populations studied showed a moderate
allozyme variability (A=1.33, P=22.7%, Ho=0.033 and He=0.068), which was relatively high for the genus Oryza. The levels of genetic diversity for Guangxi and Guangdong were significantly higher than those for the other regions, and
thus South China appeared to be the center of genetic diversity of O. rufipogon in China. A moderate genetic differentiation (FST=0.310, I=0.964) was found among the populations studied. Interestingly, the pattern of population differentiation does not
correspond to geographic distance. An estimate of the outcrossing rate (t=0.324) suggests that the species has a typical mixed-mating
system. The deficit of heterozygotes (F=0.511) indicates that some inbreeding may have taken place in outcrossing asexual
populations because of intra-clone outcrossing events and ”isolation by distance” as a result of human disturbance. In order
to predict the long-term genetic survival of fragmented populations, further studies on gene flow among the remaining populations
and the genetic effects of fragmentation are proposed. Finally, some implications for the conservation of endangered species
are suggested.
In order to reveal levels and distribution of genetic variation within Oryza rufipogon Griff. of Yunnan, China, where one of the centers of genetic diversity for Asian cultivated rice O. sativa L. is located, allozyme variation encoded by 22 loci was electrophoretically analyzed in 149 individuals of all three existing
populations as well as five from other regions (Guangxi, Hainan and Jiangxi provinces) of China. As compared to the level
of genetic diversity (the mean A = 1.2, P = 24.1%, Ho = 0.045 and He = 0.079) for the populations from other regions, a rather
low genetic diversity (the mean A = 1.1, P = 7.6%, Ho = 0.007 and He = 0.011) was found in Yunnan, which may originate from
marginal nature of these populations, recent reduction of populations and consequent drift. The result suggests that the current
center of genetic diversity for O. rufipogon fail to agree with that for cultivated rice in China. The genetic differentiation for all the eight populations(FST = 0.254) was slightly lower than that for three populations from Yunnan (FST = 0.302), indicating a fairly high genetic differentiation in the region. Finally, a conservation plan for sampling/preserving
fewer populations but more individuals from each population for the species was given, and an appropriate strategy for conserving
the three surviving populations from Yunnan was proposed.
Genetic variation within and between eight natural populations of Oryza rufipogon from China and Brazil was investigated at the DNA level by analysis of RAPD fragments. Out of 60 random primers, which were initially screened against DNA from four individuals, 20 generated highly reproducible RAPD fragments which were then used for further population analysis. With these primers, 95 discernible DNA fragments were produced and 78 (82.1%) were polymorphic, which indicated that high levels of genetic variation existed in these natural populations. In addition, the Chinese populations showed greater polymorphism than those from Brazil at both the population and regional levels. This is noteworthy considering that the Chinese populations are from a relatively restricted area of China. The factors responsible for these findings include the contrasting mating systems in the Brazilian and Chinese populations, and gene flow from annual cultivated rice to perennial natural populations in China. An Analysis of Molecular Variance (AMOVA) was used to apportion the variation between individuals within populations, between populations within regions, and between regions. Results showed that 61.8% of the total genetic diversity resided between the two continents, whereas only 14.9% and 23.3% was attributable to population differences within regions and to individual differences within a population, respectively. The great genetic differentiation between the Chinese and Brazilian populations is in agreement with recent treatment of the American form of O. rufipogon as a separate species, O. glumaepatula.
In order to monitor genetic erosion within the northern marginal population of common wild rice Oryza rufipogon Griff. from Dongxiang, Jiangxi Province, China, allozyme diversity encoded by 22 loci was analyzed electrophoretically from all the existing subpopulations in 1980, 1985 and 1994. The sample collected from the nine large subpopulations in 1980 showed the highest levels of genetic diversity (A = 1.27, P = 18.20%, Ho = 0.042 and He = 0.049) and a slight deviation from Hardy-Weinberg expectation (F = 0.143), the sample from five moderate ones in 1985 displayed medium levels of genetic diversity (A = 1.14, P = 13.60%, Ho = 0.008 and He = 0.049) and a great deviation from Hardy-Weinberg expectation (F = 0.837), and the sample from two small ones in 1994 demonstrated the lowest levels of genetic diversity (A = 1.09, P = 9.10%, Ho = 0.000 and He = 0.043) and the largest deviation from Hardy-Weinberg expectation (F = 1.000). The results not only documented the genetic erosion stemmed from the extinction of the subpopulations, but also revealed the drastic change of the population genetic structure due to the reduction of the population. Finally, some conservation strategies for the population are proposed.
The genetic structure of five natural populations of common wild rice Oryza rufipogon Griff. from China, was investigated with 21 microsatellite loci and compared to estimates of genetic diversity and genetic differentiation detected by 22 allozyme loci. Microsatellite loci, as expected, have much higher levels of genetic diversity (mean values of A = 3.1, P = 73.3%, Ho = 0.358 and He = 0.345) than allozyme loci (mean values of A = 1.2, P = 12.7%, Ho = 0.020 and He = 0.030). Genetic differentiation detected by microsatellite loci ( FST = 0.468, mean I = 0.472) was higher than that for allozyme loci ( FST =0.388, mean I = 0.976). However, microsatellite markers showed less deviation from Hardy-Weinberg expectation (Wright's inbreeding coefficient FIS = -0.069) than do allozymes ( FIS = 0.337). These results suggest that microsatellite markers are powerful high-resolution tools for the accurate assessment of important parameters in population biology and conservation genetics of O. rufipogon, and offer advantages over allozyme markers.
Genetic diversity and population genetic structure of natural Oryza rufipogon populations in China were studied based on ten microsatellite loci. For a total of 237 individuals of 12 populations collected from four regions, a moderate to high level of genetic diversity was observed at population levels with the number of alleles per locus (A) ranging from 2 to 18 (average 10.6), and polymorphic loci (P) from 40.0% to 100% (average 83.3%). The observed heterozygosity (H
O
) varied from 0.163 to 0.550 with the mean of 0.332, and the expected heterozygosity (H
E
) from 0.164 to 0.648 with the mean of 0.413. The level of genetic diversity for Guangxi was the highest. These results are in good agreement with previous allozyme and RAPD studies. However, it was unexpected that high genetic differentiation among populations was found (R
ST
= 0.5199, θ = 0.491), suggesting that about one-half of the genetic variation existed between the populations. Differentiation (pairwise θ) was positively correlated with geographical distance (r = 0.464), as expected under the isolation by distance model. The habitat destruction and degradation throughout the geographic range of O. rufipogon may be the main factor attributed to high genetic differentiation among populations of O. rufipogon in China.
To estimate genetic diversity of the residual northern populations of Oryza rufipogon, a total of 232 individuals from six populations were analyzed using microsatellites (SSRs). The O. rufipogon populations with different status included three from Dongxiang (Jiangxi Province) and three from Chaling (Hunan Province) in China. The 23 rice SSR primer pairs selected from the RiceGenes Database detected a total of 115 alleles, indicating that all the SSR loci were polymorphic in this study. The total gene diversity was 0.919 in the six O. rufipogon populations, and the Donxiang populations showed higher diversity than the Chaling populations. More significant genetic differentiation and less gene flow were found among the Dongxiang populations than those from Chaling. The two putative introgressed populations showed relatively high genetic variation. One in situ conserved population from Dongxiang had the lowest level of genetic diversity. The re-introduced population from Chaling restored about 90% of the genetic variation, compared with the original source population. It is concluded from these results that a relatively high level of genetic variation resided in the northern O. rufipogon populations and continued efforts of conservation of these populations are needed; and that the conservation of some Chaling and Dongxiang populations has been effective in preventing gene flow from cultivated rice. Introgression of cultivated rice demonstrated significant impacts on genetic variability of the O. rufipogon populations, and should be carefully considered in conserving this wild rice. This study also suggested that re-introduction to its original habitats is an effective approach to restore O. rufipogon populations.
Introgression of crop genes into populations of wild relatives has important implications for germplasm conservation as well as for the persistence of novel transgenes in wild populations. Studies of hybrid fitness can be used to evaluate the potential for introgression to occur following episodes of interspecific hybridization.
This study estimated relative fitness of interspecific hybrids through performance comparison of F(1) hybrids with their parental species, a cultivated rice (Oryza sativa) Minghui-63 and perennial common wild rice (O. rufipogon) under the cultivation conditions.
Compared with their parents, the hybrids had the lowest values of seedling survival ability, pollen viability and seed production; intermediate values of seed germination, spikelet production and flag leaf areas; and the highest values of plant height, number of tillers and panicles. The hybrids performed poorly at the stage of sexual reproduction, although they had a slightly higher hybrid vigour at the vegetative growth stage and better tillering ability than their wild parent. There were no significant differences in composite fitness across the whole life-history between the hybrids and their wild parental species.
Rice genes, including transgenes, might persist in wild rice populations through vegetative and sexual reproduction. Further studies are needed to examine whether the extent of gene flow from rice is sufficiently significant to influence genetic diversity in wild populations of O. rufipogon, a species that has become endangered in some regions of south-east Asia.
Oryza rufipogon Griff. is the most agriculturally important but seriously endangered wild rice species. To better estimate how genetic structure can be used to obtained a conservation perspective of the species, genetic variability at six polymorphic microsatellite DNA loci was examined. High levels of genetic variability were detected at six loci in 1245 individuals of 47 natural populations covering most of the species' range in China (overall RS = 3.0740, HO = 0.2290, HS = 0.6700). Partitioning of genetic variability (FST = 0.246) showed that most microsatellite variation was distributed within populations. Significant departures from Hardy-Weinberg expectations and very strong linkage disequilibrium indicate a high degree of inbreeding in the species and severe subdivision within populations. A mean Nm value of 0.7662 suggested a limited gene flow among the assayed populations. Our study suggests that conservation and restoration genetics should focus in particular on the maintenance of historically significant processes such as high levels of outbreeding and gene flow and large effective population size in the species.
There are two cultivated and twenty-one wild species of genus Oryza. O. sativa, the Asian cultivated rice is grown all over the world. The African cultivated rice, O. glaberrima is grown on a small scale in West Africa. The genus Oryza probably originated about 130 million years ago in Gondwanaland and different species got distributed into different continents with the breakup of Gondwanaland. The cultivated species originated from a common ancestor with AA genome. Perennial and annual ancestors of O. sativa are O. rufipogon and O. nivara and those of O. glaberrima are O. longistaminata, O. breviligulata and O. glaberrima probably domesticated in Niger river delta. Varieties of O. sativa are classified into six groups on the basis of genetic affinity. Widely known indica rices correspond to group I and japonicas to group VI. The so called javanica rices also belong to group VI and are designated as tropical japonicas in contrast to temperate japonicas grown in temperate climate. Indica and japonica rices had a polyphyletic origin. Indicas were probably domesticated in the foothills of Himalayas in Eastern India and japonicas somewhere in South China. The indica rices dispersed throughout the tropics and subtropics from India. The japonica rices moved northward from South China and became the temperate ecotype. They also moved southward to Southeast Asia and from there to West Africa and Brazil and became tropical ecotype. Rice is now grown between 55 degrees N and 36 degrees S latitudes. It is grown under diverse growing conditions such as irrigated, rainfed lowland, rainfed upland and floodprone ecosystems. Human selection and adaptation to diverse environments has resulted in numerous cultivars. It is estimated that about 120,000 varieties of rice exist in the world. After the establishment of International Rice Research Institute in 1960, rice varietal improvement was intensified and high yielding varieties were developed. These varieties are now planted to 70% of world's riceland. Rice production doubled between 1966 and 1990 due to large scale adoption of these improved varieties. Rice production must increase by 60% by 2025 to feed the additional rice consumers. New tools of molecular and cellular biology such as anther culture, molecular marker aided selection and genetic engineering will play increasing role in rice improvement.
This chapter reviews the progress made in developing rice that is resistant to diseases and insects. Among cereal crops, rice is the host of the largest number of diseases and insect pests. These cause serious yield loss annually. The magnitude of loss caused by diseases and insects, increases as the level of rice production per unit area increases. The chapter discusses the nature of the disease or insect, its distribution, genetic variability of the pathogen, host resistance, genetics of resistance, and breeding for resistance. Fungal diseases attack the plant foliage, stems, roots, leaf sheath, or inflorescence, and grains. Four fungal diseases: blast, sheath blight, brown spot, and narrow brown leaf spot; two bacterial diseases: bacterial blight and bacterial streak; and five virus diseases: tungro, grassy stunt, stripe, dwarf, and hoja blanca have been discussed in the chapter. To minimize yield loss from disease and insect attacks, varieties with multiple resistances to most major diseases and insects are required. Also, a systematic international survey of races or biotypes of major diseases and insects should be carried out with the use of differential varieties.
Sterile AC hybrids between cultivated Oryza sativa (AA) and a distant wild species, O. officinalis (CC), were backcross to O. sativa. Most of the BC1 progenies were allotriploid (AAC), a few were hypotriploid. AAC progenies were again backcrossed to O. sativa. BC2 progenies consisting of disomic or aneuploid individuals were examined for the presence of O. officinalis traits. Eleven different traits from O. officinalis were identified in these progenies. Segregation data in the subsequent generations suggest that these traits are monogenic in nature. Two of these genes - for resistance to BPH and WBPH - are of value in rice improvement. The extremely low recovery of recombinant progenies is in agreement with the very low amount of pairing between A and C genomes. Because of this restricted recombination, the genotype of the recurrent parent was reconstituted after two backcrosses only. Thus, the BC2 progenies look remarkably similar to O. sativa. Most of them are stable and fertile and also interfertile with other O. sativa breeding lines. Some of the BPH-and WBPH-resistant progenies are comparable in yield to the best O. sativa parents and are being evaluated as varietal possibilities.
There are two cultivated and twenty-one wild species of genus Orvza. O. saliva, the Asian cultivated rice is grown all over the world. The African cultivated rice, O. glaberrima is grown on a small scale in West Africa. The genus Oriyza probably originated about 130 million years ago in Gondwanaland and different species got distributed into different continents with the breakup of Gondwanaland. The cultivated species originated from a common ancestor with AA genome. Perennial and annual ancestors of O. saliva are O. rufipogon and O. nivara and those of O. glaberrima are O. longistaminata, O. breviligulata and O. glaberrima probably domesticated in Niger river delta. Varieties of O. sativa are classified into six groups on the basis of genetic affinity. Widely known indica rices correspond to group I and japonicas to group VI. The so called javanica rices also belong to group VI and are designated as tropical japonicas in contrast to temperate japonicas grown in temperate climate. Indica and japonica rices had a polyphyletic origin. Indicas were probably domesticated in the foothills of Himalayas in Eastern India and japonicas somewhere in South China. The indica rices dispersed throughout the tropics and subtropics from India. The japonica rices moved northward from South China and became the temperate ecotype. They also moved southward to Southeast Asia and from there to West Africa and Brazil and became tropical ecotype. Rice is now grown between 55°N and 36°S latitudes. It is grown under diverse growing conditions such as irrigated, rainfed lowland, rainfed upland and floodprone ecosystems. Human selection and adaptation to diverse environments has resulted in numerous cultivars. It is estimated that about 120 000 varieties of rice exist in the world. After the establishment of International Rice Research Institute in 1960, rice varietal improvement was intensified and high yielding varieties were developed. These varieties are now planted to 70% of world’s riceland. Rice production doubled between 1966 and 1990 due to large scale adoption of these improved varieties. Rice production must increase by 60% by 2025 to feed the additional rice consumers. New tools of molecular and cellular biology such as anther culture, molecular marker aided selection and genetic engineering will play increasing role in rice improvement.
A number of genetic stocks of Oryza perennis Moench, collected from various tropical countries of the world, were investigated regarding various characters related to the breeding system of the species. O. breviligulata A. Chev. et Roehr. and cultivated rice species, O. sativa L. and O. glaberrima Steud. were observed for comparison. Two variation axes were assumed, one concerning the pollination system, and the other concerning the relative extent of seed and vegetative propagation. The former was expressed by a combination of measurements for the time interval from flowering to pollen emission, stigma and style size, and pollen-grain number per anther; the latter from the regenerative ability of excised stem segments, seed number per plant, "awn-development index," and "seed-dormancy index." Variations in all these characters were intercorrelated, and it was concluded from the correlations that strains propagated mainly by seeds tend to be relatively autogamous. Three methods for vegetative propagation were found; cespitose growth, rhizome formation, and tiller separation. Most African and a few Asian as well as Oceanian strains were rhizomatous, while some Amazonian strains showed tiller separation.
Alien transgene escape from genetically engineered rice to non-transgenic varieties or close wild relatives ( including weedy rice) may lead to unpredictable ecological risks. However, for transgene escape to occur three conditions need to be met: (i) spatially, transgenic rice and its non-transgenic counterparts or wild relatives should have sympatric distributions; (ii) temporally, the flowering time of transgenic rice and the non-transgenic varieties or wild relatives should overlap; and (iii) biologically, transgenic rice and its wild relative species should have such a sufficiently close relationship that their interspecific hybrids can have normal generative reproduction. This paper presents research data on the geographic distribution, flowering habits, interspecific hybridization, and gene flow of cultivated rice ( Oryza sativa) and its closely related wild relatives containing the AA genome. The objective is to estimate the possibility of transgene escape to non-transgenic rice varieties and wild relatives of rice, which may result in unpredictable ecological risks.
Studying the process of population restoration is helpful for managing and preserving endangered species. A population of Oryza rufipogon (wild rice), an endangered species, was reintroduced in 1993 into Huli Marsh. We conducted a detailed survey over a 5-year period (1997–2001) to evaluate the present status of the population and to further our understanding of its habitat requirements and the population model. The population was surveyed using 2 × 2–m quadrats in mid-September of each year. In total, 2,683 quadrats were surveyed covering the whole O. rufipogon reserve during each survey. The population's spatial distribution was mapped, and the maps were used to examine the relationship between patch replacement and water depth. The individual number of O. rufipogon increased steadily from 1993 to 2001. The patch number, patch area, mean patch size, and largest patch size increased over this time period, and Korcak patchiness exponents decreased. On average, 83% of the patches persisted from one year to the next. There was a significant positive correlation between the initial patch size and the size the following year. The probability of patch disappearance decreased as patch size increased. Fifty-eight percent of the patches were located at water depths between 20 and 30 cm. Water depth had no significant effect on the patch transition from O. rufipogon to other species. The loss and gain of O. rufipogon patches were statistically correlated with the patch areas in different water depths. Our results show that the population of O. rufipogon can successfully be reintroduced to the original habitat after appropriate environmental conditions have been restored. We recommend the following transplantation practices: transplant many smaller patches rather than a few larger patches, use transplant patch sizes of at least 20 m2, and transplant into sites vegetated with species with different regeneration niches from the transplanted species.
Abstract Variation in mating system in the common wild rice Oryza rufipogon was studied in relation to life-history traits to examine its effect on the genetic structure of natural populations. Results of general survey in Asian populations and of a detailed population study carried out in Thailand are presented. Estimated outcrossing rates of Asian wild rices ranged from 5 to 60%, though cultivated rices are predominantly selfing. Interpopulational comparison showed mating system is associated with life-history traits, resulting in the differentiation into two ecotypes; predominantly selfing annuals having high reproductive effort and mixed-mating perennials having low reproductive effort. Resource allocation to pollen production vs. seed production (pollination effort) proved to be correlated with outcrossing rate. Isozyme study showed that both mating system and reproductive system jointly influence genetic structure of populations such as the level of intrapopulational variability and the extent of interpopulational differentiation. Evolution of selfing in this plant group might have been promoted by selection for seed propagation which was brought by environmental change and/or habitat disturbance.
Summary • Here, the gene flow from a cultivated rice variety (Minghui-63) to common wild rice (Oryza rufipogon) was investigated to assess the biosafety risk associated with the environmental release of transgenic varieties. • Four experimental designs differing in the spatial arrangement of the Minghui-63 and O. rufipogon plants were used in experiments conducted in an isolated rice field in Hunan Province, southern China, where O. rufipogon occurs naturally. • Natural hybridization events between the two species were detected by scoring a simple sequence repeat (SSR) molecular marker. A total of 296 hybrids were identified from 23 776 seedlings that were randomly germinated from > 80 000 seeds collected from O. rufipogon. The occurrence of the crop-to-wild gene flow was significantly associated with wind direction and frequencies of the gene flow, which decreased significantly with distance from the pollen sources. The maximum observed distance of gene flow was 43.2 m. • The results indicated that gene flow from cultivated rice to O. rufipogon occurred at a considerable rate. Therefore, isolation measures should be considered when deploying transgenic rice in the sympatric regions of the wild rice, and when establishing in situ conservation of O. rufipogon. The experimental system in this study can be used for biosafety assessment of transgene escape of other wind-pollinated crops.
Post‐pollination competition is reported here in cultivated rice ( Oryza sativa ) and a perennial wild rice ( O. rufipogon ) to investigate the occurrence of crop‐to‐wild gene flow.
Wild and cultivated rice (variety Minghui‐63) were grown in a common garden in Hunan province, China, and crop‐specific genetic markers were used to detect hybridization following hand‐pollinations. Using 11 sequential pollination treatments, the effects of the relative timing of pollination on the success of foreign pollen was investigated.
Foreign pollen from the crop resulted in lower pollen germination, fewer pollen tubes per style, and a significant reduction of seed set, demonstrating a disadvantage of foreign pollen even in the absence of pollen competition. When 1 : 1 pollen mixtures were applied, only 2% of the resulting seeds were hybrids, revealing a much stronger disadvantage of foreign pollen when competing with conspecific pollen. Testing the effects of the relative timing of pollination on the success of foreign pollen suggested that conspecific pollen is often more successful than foreign pollen. Nonetheless, hybridization is possible following the deposition of pollen mixtures, especially when foreign pollen arrives earlier than conspecific pollen.
Pollen competition between wild and cultivated rice could slow the rate of crop‐to‐wild gene flow, but even if pollen competition was ubiquitous it would not prevent gene flow from the crop.
Natural populations of wild rice, Oryza rufipogon Griff., are now threatened with the disturbance of their natural habitats by various human activities. To obtain basic information on genetic erosion or loss of genetic diversity in wild rice, we investigated how environmental changes of habitat affected the genetic structure of its natural population at a study site in the central plain of Thailand. During 10 years from 1985 to 1994, the wild-rice population at this site was seriously destroyed and fragmented. Using two sets of seed sample collected in 1985 and 1994 from the same population, allozyme variability at 17 loci of 11 enzymes were examined. Isozyme genotypes of mother plants of seed samples were estimated by the segregation in each progeny, and we calculated genetic parameters for the population. Gene diversity severely decreased in the 1994 sample compared with the 1985 sample. It is supposed that declining and fragmentation of the wild rice population, which happened during the 10 years, caused loss of genetic variability and forced the habitually outbreeding plants to inbreed, accelerating a reduction in gene variability. Pgi1-1 allele which was common in Indica rice cultivars of this region was found in the wild rice plants growing at the side of rice fields. Probably, introgression has occurred between wild and cultivated rice plants, and consequently the intrinsic nature of wild rice was gradually blurred by cultivar genes. We must realize that the genetic erosion of wild rice is rapidly proceeding and that an action for their conservation in natural environment, so called in situ conservation, is urgently needed.
Available evidences drawn from biosystematics, evolutionary biology, biogeography, archaeology, history, anthropology, paleo-geology and paleo-meteorology are pooled to reconstruct the series of events that led to the cosmopolitan cultivation of the Asian cultivated rice (O. sativa) and the regionalized planting of the African cultigen (O. glaberrima) in West Africa. The genus Oryza originated in the Gondwanaland continents and, following the fracture of the supercontinent, became widely distributed in the humid tropics of Africa, South America, South and Southeast Asia, and Oceania. The two cultivated species have had a common progenitor in the distant past. Parallel and independent evolutionary processes occurred in Africa and in Asia, following the sequence of: wild perennialwild annualcultivated annual. The weed races also contributed to the differentiation of the cultivated annuals. The corresponding members of the above series are O. longistaminata
Chev. et Roehr., O. barthii
A. Chev., O. glaberrima
Steud., and the stapfii forms of O. glaberrima in Africa; O. rufipogon
Griff., O. nivara
Sharma et Shastry, O. sativa L., and the spontanea forms of O. sativa in Asia.The differentiation and diversification of the annuals in South Asia were accelerated by marked climatic changes following the last glacial age, dispersal of plants over latitude or altitude, human selection, and manipulation of the cultural environment.Cultivation of rice began in many parts of South and Southeast Asia, probably first in Ancient India. Cultural techniques such as puddling and transplanting were first developed in north and central China and later transmitted to Southeast Asia. Wetland culture preceded dryland culture in China, but in hilly areas of Southeast Asia, dryland cultivation is older than lowland culture. The planting method progressed from shifting cultivation to direct sowing in permanent fields, then to transplanting in bunded fields.Widespread dispersal of the Asian cultigen led to the formation of three eco-geographic races (Indica. Sinica or Japonica, and Javanica) and distinct cultural types in monsoon Asia (upland, lowland, and deep water). Varietal types changed readily within the span of a millenium, largely due to cultivators' preferences, socio-religious traditions, and population pressure. Genetic differentiation developed parallel to the ecologic diversification process.The African cultigen developed later than the Asian cultigen and has undergone less diversification. The wild races in South America and Oceania retain their primitive features mainly due to lack of cultivation pressure or dispersal.Both the African and Asian rices are still undergoing evolutionary changes at habitats where the wild, weed, and cultivated races co-exist.
The present study represents a long-term investigation of polytetrafluoroethylene (PTFE) vascular microprostheses implanted in the right common iliac artery of rats, with the aim of evaluating the degree of intimal hyperplasia and the changes produced in the vascular prosthesis. A follow-up study was performed between 3 months and 1 year post-implantation, using immunohistochemical techniques, light, and electron microscopy. Three months after implantation, the PTFE segment appeared sandwiched between two cell layers. A general endothelialization was observed on the luminal surface. The underlying myointima appeared as an irregular lining of decreasing thickness, from the distal anastomosis with the receptor artery to the proximal suture. A large number of white blood cells were found adherent to and infiltrating the endothelium. A neoformed adventitia covered the prosthesis on the external surface. At 4 months post-implantation, a destabilization of the luminal surface was observed induced by white blood cells. A progressive reduction in the thickness of the myointimal layer was also apparent, so that 1 year after implantation, the luminal surface of the PTFE prosthesis was fully lined by a thin cell covering. There is good long-term tolerance to implanted PTFE microprostheses. The white blood cells present in the implant region appeared to play an important role in the long-term regression of intimal hyperplasia.
Correlations were examined between habitat characters and clonal structures determined by the RAPD (random amplified polymorphic DNA) assay in five populations of Oryza rufipogon in China. Nine of 175 decameric primers were used in the study because they reproducibly amplified polymorphisms. The extent of clonality together with the clonal and sexual reproductive strategies varied greatly among the five populations and correlated with the habitats where they occur. The populations under serious disturbance or seasonal drought tended to have small clones with relatively high clonal diversity caused by sexual reproduction, whereas the populations with little disturbance and sufficient supply of water were prone to have large clones with relatively low clonal variation and low sexual reproduction. Therefore, the dynamics of sexual vs. clonal reproduction of this species depended mainly on environmental factors, such as external disturbance and water supply, rather than latitudes indicated by previous study. These results have important implications for in situ conservation of O. rufipogon. Adequate external disturbance and water supply control are essential for maintaining high clone diversity of in situ conserved populations. According to the extent of clonality of the populations examined, we recommend that an interval of >12 m should be required for collecting samples for ex situ conservation and for population genetic studies to capture possible genetic diversity for O. rufipogon in China.
A study on genetic variation of three wild rices (Oryza spp.) in China and their conservation biology. PhD Dissertation. Institute of Botany
- L Z Gao
Gao L. Z. (1997) A study on genetic variation of three wild rices
(Oryza spp.) in China and their conservation biology. PhD
Dissertation. Institute of Botany, Chinese Academy of Sciences, Beijing. (In Chinese with English abstract.)
Need to wild rice species in Nepal
- Lu B. R.
Lu B. R. (1999) Need to wild rice species in Nepal. International
Rice Research Notes 24: 41.
Ecology of wild rice planted in Taiwan: I. Sequential distribution of species and their interactions in weed communities
- Oka H. I.
Oka H. I. (1991) Ecology of wild rice planted in Taiwan: I.
Sequential distribution of species and their interactions in
weed communities. Botany Bulletin of the Academia Sincica 32:
287-293.
Hybrid rice: Achievements and further outlook
- L P Yuan
- S S Virmani
- C X Mao
Yuan L. P., Virmani S. S. & Mao C. X. (1989) Hybrid rice: Achievements and further outlook. In: Progress in Irrigated Rice
Research. International Rice Research Institute, Manila, pp.
219-223.
Studies on conservation biology of three northern populations of common wild rice (Oryza rufipogon)
- J Zhou
- J Zhou
Diversity of the rice genepool and its sustainable utilization
- B R Lu
Lu B. R. (1996) Diversity of the rice genepool and its sustainable
utilization. In: Zhang A. & Wu S. (eds). Proceedings of the
International Symposium on Florestic Characteristics and Diversity
of East Asian Plants; Kunming City, China. China Higher Education Press, Beijing and Springer-Verlag, Berlin, pp. 454-460.
Gene exchange between Oryza rufipogon and cultivated rice O. sativa under controlled conditions
- Z P Song
- Z P Song
The Wild Relatives of Rice: A Genetic Resources Handbook Origin and Differentiation of Chinese Cultivation Rice Genes from wild rice improve yield
- Vaughan D A J H Xiao
- S Grandillo
- S N Ahn
Vaughan D. A. (1994) The Wild Relatives of Rice: A Genetic Resources Handbook. International Rice Research Institute, Manila. Wang X. K. & Sun C. Q. (1996) Origin and Differentiation of Chinese Cultivation Rice. China Agricultural University Press, Beijing. (In Chinese.) Wu M. S. (1990) Proceedings of Wild Rice Resources Researches. China Science and Technology Press, Beijing. (In Chinese.) Xiao J. H., Grandillo S., Ahn S. N. et al. (1996) Genes from wild rice improve yield. Nature 384: 223–224.
SSR marker detected genetic variations of common wild rice (Oryza rufipogon Griff.) in Guangdong Province
- Z P Song
- J Rong
- W Zhu
- B R Lu
Song Z. P., Rong J., Zhu W. & Lu B. R. (2004a) SSR marker detected
genetic variations of common wild rice (Oryza rufipogon Griff.)
in Guangdong Province. In: Proceedings of the First National
Conference on Wild Rice in China: Studies and Applications of Wild
Rice in China; September 2003, Nanchang. Meteorology Press,
Beijing, pp. 19-25. (In Chinese with English abstract.)
Collection, evaluation and conservation of wild rice resources in China
- W X Zhang
- Q W Yang
Zhang W. X. & Yang Q. W. (2004) Collection, evaluation and
conservation of wild rice resources in China. In: Proceedings
of the First National Conference on Wild Rice in China: Studies
and Applications of Wild rice in China. Meteorology Press,
Beijing, pp. 19-25. (In Chinese with English abstract.)
Sustainability of Rice in the Global Food System
- M R Bellon
- D S Brar
- B R Lu
- J L Pham
Bellon M. R., Brar D. S., Lu B. R. & Pham J. L. (1998) Rice genetic
resources. In: Dwoling N. G., Greenfield S. M. & Fischer K. S.
(eds). Sustainability of Rice in the Global Food System, Chapter
16. Pacific Basin Study Center and International Rice
Research Institute, Manila, pp. 251-283.