![mRNA levels of Ehd1, RFT1 and Hd3a in control, #3098-2-1-1 and Nona Bokra growing under LD conditions. Graphical genotypes around RFT1 and Hd3a are shown below (for graphical genotypes of the whole genomes, see Figure S1). White and black boxes represent Koshihikari and Nona Bokra origin, respectively. All lines have functional Hd1 and Hd16. Hd1* indicates strong allele [52]. Ehd1, RFT1 and Hd3a expression was below the detection limit in Nona Bokra.](https://www.researchgate.net/profile/Eri-Ogiso-Tanaka/publication/257464834/figure/fig14/AS:669705710878740@1536681692547/mRNA-levels-of-Ehd1-RFT1-and-Hd3a-in-control-3098-2-1-1-and-Nona-Bokra-growing-under_Q320.jpg)
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Natural variation of the RICE FLOWERING LOCUS T 1 contributes to flowering time divergence in rice
PLOS ONE
Abstract and Figures
In rice (Oryza sativa L.), there is a diversity in flowering time that is strictly genetically regulated. Some indica cultivars show extremely late flowering under long-day conditions, but little is known about the gene(s) involved. Here, we demonstrate that functional defects in the florigen gene RFT1 are the main cause of late flowering in an indica cultivar, Nona Bokra. Mapping and complementation studies revealed that sequence polymorphisms in the RFT1 regulatory and coding regions are likely to cause late flowering under long-day conditions. We detected polymorphisms in the promoter region that lead to reduced expression levels of RFT1. We also identified an amino acid substitution (E105K) that leads to a functional defect in Nona Bokra RFT1. Sequencing of the RFT1 region in rice accessions from a global collection showed that the E105K mutation is found only in indica, and indicated a strong association between the RFT1 haplotype and extremely late flowering in a functional Hd1 background. Furthermore, SNPs in the regulatory region of RFT1 and the E105K substitution in 1,397 accessions show strong linkage disequilibrium with a flowering time-associated SNP. Although the defective E105K allele of RFT1 (but not of another florigen gene, Hd3a) is found in many cultivars, relative rate tests revealed no evidence for differential rate of evolution of these genes. The ratios of nonsynonymous to synonymous substitutions suggest that the E105K mutation resulting in the defect in RFT1 occurred relatively recently. These findings indicate that natural mutations in RFT1 provide flowering time divergence under long-day conditions.
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Supplementary resources (3)
Data
March 2015
... Kitazawa, Shomura, Mizubayashi, Ando, Hayashi, Yabe, Matsubara, Ebana, Yamanouchi and Fukuoka LOC_Os06g06300.1 Ogiso-Tanaka et al. (2013) [16] ...
Heading date (HD) is a crucial agronomic trait, controlled by multiple loci, that conditions a range of geographical and seasonal adaptations in rice (Oryza sativa L.). Therefore, information on the HD genotypes of cross parents is essential in marker-assisted breeding programs. Here, we used the Fluidigm 96-plex SNP genotyping platform to develop genotyping assays to determine alleles at 41 HD loci (29 previously characterized genes and 12 quantitative trait loci [QTLs], including a newly detected QTL). The genotyping assays discriminated a total of 144 alleles (defined on the basis of the literature and publicly available databases) and QTLs. Genotyping of 377 cultivars revealed 3.5 alleles per locus on average, a higher diversity of Hd1, Ghd7, PRR37, and DTH8 than that of the other loci, and the predominance of the reference (‘Nipponbare’) genotype at 30 of the 41 loci. HD prediction models using the data from 200 cultivars showed good correlation (r > 0.69, P < 0.001) when tested with 22 cultivars not included in the prediction models. Thus, the developed assays provide genotype information on HD and will enable cost-effective breeding.
... RDRS varieties are classified into three genotype groups based on RFLP data, with "Nipponbare" and "Kasalath" as reference varieties [24][25][26] Group A is a "japonica (J) group" with the "Nipponbare" allele, while Group B is an "India-1" group with aus varieties from India, Bangladesh, Bhutan, Nepal, and Sri Lanka, and Group C is an "Indica-2" group with Indica varieties from Madagascar to China. The "Kasalath" allele is predominant in Groups B and C, with a higher ratio in Group B. The RDRS collection has been used for the evaluation of several agricultural traits, such as heading date, seed cadmium concentration, and seed dormancy [27][28][29][30][31][32]. Suggesting that this set is a powerful tool for investigating and finding useful potential breeding materials in rice. ...
Seed longevity is a crucial trait for the seed industry and genetic resource preservation. To develop excellent cultivars with extended seed lifespans, it is important to understand the mechanism of keeping seed germinability long-term and to find useful genetic resources as prospective breeding materials. This study was conducted to identify the best cultivars with a high and stable seed longevity trait in the germplasm of rice (Oryza sativa L.) and to analyse the correlation between seed longevity and embryonic RNA integrity. Seeds from 69 cultivars of the world rice core collection selected by the NIAS in Japan were harvested in different years and subjected to long-term storage or controlled deterioration treatment (CDT). The long-term storage (4 °C, RH under 35%, 10 years) was performed on seeds harvested in 2010 and 2013. The seeds harvested in 2016 and 2019 were used for CDT (36 °C, RH of 80%, 40 days). Seed longevity and embryonic RNA integrity were estimated by a decrease in germination rate and RNA integrity number (RIN) after long-term storage, or CDT. The RIN value was obtained by electrophoresis of total RNA extracted from seed embryos. Seeds of ‘Vandaran (Indica)’, ‘Tupa 729 (Japonica)’, and ‘Badari Dhan (Indica)’ consistently showed higher seed longevity and embryonic RNA integrity both under long-term storage and CDT conditions, regardless of the harvest year. A strong correlation (R2 = 0.93) was observed between germination rates and RIN values of the seeds after long-term storage or CDT among nine cultivars selected based on differences in their seed longevity. The study findings revealed the relationship between rice seed longevity and embryo RNA stability and suggested potential breeding materials, including both Japonica and Indica cultivars, for improving rice seed longevity.
... Previous studies on heading dates focused on genotypic photoperiod-sensitive rice cultivars [6]. The heading date is regulated by multiple quantitative trait loci (QTLs) [7] Biology 2024, 13, 358 2 of 12 with several well-known QTLs identified to date, including se-1 [8,9], Hd1 [10], Hd6 [11], Hd3a [12], Ehd1 [13], Ghd7 [14], DTH8 [15], Ghd8 [16], dth3 [17], Hd17 [18], Ehd4 [19], Hd16 [20], RFT1 [21], DTH2 [22], and DTH7 [23]. Furthermore, the intricate regulation of strong photoperiod sensitivity involves collaborative and competitive interactions among Hd1, Ghd7, and DTH8 in rice heading [3]. ...
The current study aims to identify candidate insertion/deletion (INDEL) markers associated with photoperiod sensitivity (PS) in rice landraces from the Vietnamese Mekong Delta. The whole-genome sequencing of 20 accessions was conducted to analyze INDEL variations between two photoperiod-sensitivity groups. A total of 2240 INDELs were identified between the two photoperiod-sensitivity groups. The selection criteria included INDELs with insertions or deletions of at least 20 base pairs within the improved rice group. Six INDELs were discovered on chromosomes 01 (5 INDELs) and 6 (1 INDEL), and two genes were identified: LOC_Os01g23780 and LOC_Os01g36500. The gene LOC_Os01g23780, which may be involved in rice flowering, was identified in a 20 bp deletion on chromosome 01 from the improved rice accession group. A marker was devised for this gene, indicating a polymorphism rate of 20%. Remarkably, 20% of the materials comprised improved rice accessions. This INDEL marker could explain 100% of the observed distinctions. Further analysis of the mapping population demonstrated that an INDEL marker associated with the MADS-box gene on chromosome 01 was linked to photoperiod sensitivity. The F1 population displayed two bands across all hybrid individuals. The marker demonstrates efficacy in distinguishing improved rice accessions within the indica accessions. This study underscores the potential applicability of the INDEL marker in breeding strategies.
... The PdFT gene of peony (Paeonia suffruticosa) is related to its floral organ development (Zhu et al., 2014). Studies on flowering regulation in rice (Oryza sativa) (Kojima et al., 2002;Ogiso-Tanaka et al., 2013) and sorghum (Sorghum bicolor) (Nuñez and Yamada, 2017) found that RFT protein and Hd3a protein work together to promote flowering, and Hd3a gene and Arabidopsis thaliana ELF3 gene belong to FT homologous genes. In addition, a large number of FT homologous genes have been cloned in plants, such as Jili (Tribulus terrestris) (Putterill et al., 2013), wheat (Triticum aestivum) (Yan et al., 2006), chrysanthemum (Dendranthema morifolium) (Pan et al., 2010), camellia (Camellia japonica) (Sun et al, 2014;Fan et al, 2015;Lei et al, 2017) and cotton (Gossypium) (Guo et al., 2015). ...
... Diversification of florigen-antiflorigen components can result in phenotypic variation (i.e., on flowering and/or plant architecture), providing alternative choices for crop breeding (Eshed and Lippman, 2019). For example, single amino acid substitution (E105K) in florigen gene RFT1 contributed to the late-flowering trait in 'Nona Bokra' rice (Ogiso-Tanaka et al., 2013). Deletion in the 5' cis-regulatory region of LanFTc1 led to vernalization-insensitive and early-flowering traits in Lupinus angustifolius (Nelson et al., 2017;Taylor et al., 2019). ...
Litchi (Litchi chinensis) was a royal tribute in ancient China. Today, it is still regarded as one of the most luxurious fresh fruits in summer because of the short harvest season. Floral induction in litchi is promoted by the expression of the FLOWERING LOCUS T (FT), LcFT1, when the leaves sense cool temperatures in winter.
Moreover, two alleles of the LcFT1 promoter affect the sensitivity and expression level of the gene, resulting in early-flowering or late-flowering traits in litchi of Chinese origin. Some litchi cultivars are able to flower and produce in the tropical region of central Thailand, so called “tropical litchi”, but their flowering mechanism is less understood. In this study, we cloned and investigated the expression of the LcFT homolog from the early-season cultivar ‘Sanyuehong’, the mid-season cultivar ‘Hak Ip’, the late-season cultivar ‘Rose Red’ and the tropical litchi ‘Khom’. Our results revealed a duplication of the partial promoter in the first intron of LcFT1 of tropical litchi ‘Khom’, resulting in a 676 bp insertion. The ‘Khom’-type LcFT1 produces identical transcripts as other cultivars. Although this allele seems to be derived from the late-flowering-type, its expression is earlier than the late-flowering-type. On the other hand, the sequence and expression of LcFT2 was conserved in the cultivars we examined. Today, ‘Khom’ is
used in litchi breeding in Taiwan to generate new cultivars that can flower and bear fruit under increasing global warming conditions. Our first findings on the ‘Khom’-type LcFT1 identified a selective target for introgression of the flowering trait in litchi.
Photoperiod sensitivity in rice cultivars is defined when the cultivar begins anthesis on a relatively invariant date, varying by < 7days, regardless of the date of sowing or germination. While the date of flowering in photoperiod sensitive (PPS) rice cultivars is characteristically determined by the day length, especially during the short-day season (September–December), the response of the flower opening time (FOT) to photoperiod remains hitherto unexplored. This paper examines whether day length restrains year-to-year variation in FOT in PPS cultivars. We examined 105 PPS and 173 photoperiod insensitive (PPI) cultivars grown in different years and estimated their year-to-year FOT difference (or FOTD) and the year-to-year difference of sunrise to anthesis duration (or SADD). Wilcoxon signed rank test and bootstrap test were then performed to test whether these descriptors significantly differed between PPS and PPI groups of cultivars. The means of FOTD and SADD were detected to be significantly less in the PPS group than in the PPI group of cultivars, indicating significantly lesser variability of FOT in PPS than in PPI cultivars. This is the first report of a strong restraining influence of photoperiod on FOT variability in PPS cultivars.
Plant species have evolved different requirements for environmental/endogenous cues to induce flowering. Originally, these varying requirements were thought to reflect the action of different molecular mechanisms. Thinking changed when genetic and molecular analysis in Arabidopsis thaliana revealed that a network of environmental and endogenous signalling input pathways converge to regulate a common set of ‘floral pathway integrators’. Variation in the predominance of the different input pathways within a network can generate the diversity of requirements observed in different species. Many genes identified by flowering time mutants were found to encode general developmental and gene regulators, with their targets having a specific flowering function. Studies of natural variation in flowering were more successful at identifying genes acting as nodes in the network central to adaptation and domestication. Attention has now turned to mechanistic dissection of flowering time gene function and how that has changed during adaptation. This will inform breeding strategies for climate-proof crops and help define which genes act as critical flowering nodes in many other species.
Introduction
Over four billion people around the world rely on bread wheat (Triticum aestivum L.) as a major constituent of their diet. The changing climate, however, threatens the food security of these people, with periods of intense drought stress already causing widespread wheat yield losses. Much of the research into the wheat drought response has centred on the response to drought events later in development, during anthesis or grain filling. But as the timing of periods of drought stress become increasingly unpredictable, a more complete understanding of the response to drought during early development is also needed.
Methods
Here, we utilized the YoGI landrace panel to identify 10,199 genes which were differentially expressed under early drought stress, before weighted gene co-expression network analysis (WGCNA) was used to construct a co-expression network and identify hub genes in modules particularly associated with the early drought response.
Results
Of these hub genes, two stood out as novel candidate master regulators of the early drought response – one as an activator (TaDHN4-D1; TraesCS5D02G379200) and the other as a repressor (uncharacterised gene; TraesCS3D02G361500).
Discussion
As well as appearing to coordinate the transcriptional early drought response, we propose that these hub genes may be able to regulate the physiological early drought response due to potential control over the expression of members of gene families well-known for their involvement in the drought response in many plant species, namely dehydrins and aquaporins, as well as other genes seemingly involved in key processes such as, stomatal opening, stomatal closing, stomatal morphogenesis and stress hormone signalling.
Correct measurement of environmental parameters is fundamental for plant fitness and survival, as well as for timing developmental transitions, including the switch from vegetative to reproductive growth. Important parameters affecting flowering time include day length (photoperiod) and temperature. Their response pathways have been best described in Arabidopsis, that currently offers a detailed conceptual framework and serves as term of comparison also for other species. Rice, the focus of this review, also possesses a photoperiodic flowering pathway, but 150M years of divergent evolution in very different environments have diversified its molecular architecture. The ambient temperature perception pathway is strongly intertwined with the photoperiod pathway and essentially converges on the same genes to modify flowering time. When observing network topologies it is evident that the rice flowering network is centered on EARLY HEADING DATE 1, a rice-specific transcriptional regulator. Here, we summarize the most important features of the rice photoperiodic flowering network, with an emphasis on its uniqueness, and discuss its connections with hormonal, temperature perception and stress pathways.
Grain yield and growth period are two critical agronomic traits for a rice cultivar to be used in field production. The growth period is mainly determined by the flowering time, which also greatly affects grain yields. An Arabidopsis gene, AtNF-YB1 , was introduced into rice, including inbred Kasalath and two hybrids, Jinfeng × Chenghui 727 and Jinfeng × Chuanhui 907. All the transgenic rice showed flowering early under both natural long-day (NLD) and natural short-day (NSD). Kasalath with expression of the gene also showed shorter plant height and less grain yield with the decrease in spike length and grain number but more productive panicles. But, for the hybrids, much smaller or even no reduction of spike length, grain number, and more productive panicle were observed so that grain yields were kept or even increased underNLD. Transcript analysis of the major flowering-time genes suggested that suppression of the Ghd7 transcription activated flowering transition early in the transgenic rice. RNA-Seq further demonstrated that three pathways related to plant photosynthesis were markedly up-regulated in both Jinfeng B and hybrid Jinfeng ×Chuanhui 907. Accordingly, up-regulated photosynthetic rates in the transgenic plants were then observed in the subsequent experiments. All these results suggest that expression of AtNF-YB1 in rice may be useful for creating variety with early ripening, particularly for hybrid rice.
An early heading time gene tentatively designated as 'v' and nonallelic to E1, E2, E3 and Ef-1 was detected in the Taiwanese rice cultivar Taichung 65 (T65) (Okumoto et al. 1992b). This gene remarkably accelerated heading time. The allelism test of this gene to a photoperiod insensitivity gene Se-1e at the Se-1 Iocus was performed using the progenies from reciprocal crosses between T65 and a heading time tester line ER. The role of this gene in the rice cultivation in Taiwan was also discussed on the basis of photoperiod responses of T65, ER and a heading time tester line LR. T65 was found to have the genotype E1E1E2E2E3E3 vv ef-1ef-1, while ER and LR had the genotypes E1E1e2e2E3E3Se-1eSe-1eEf-1Ef-1 and E1E1e2e2E3E3Se-1uSe-1uEf-1Ef-1, respectively. ER also carried a rice blast resistance gene Pi-zt closely linked to Se-1e on chromosome 6. E1, E2, E3 and Se-1u were all photoperiod sensitivity genes, and ef-1 at the Ef-1 Iocus remarkably increased the duration of the basic vegetative growth period (BVG). In the F2, rio distinct transgressive segregants appeared, and the three genotypes (Pi-zt Pi-zt, Pi-zt+, ++) for the Pi-z locus in the F2 exhibited almost the same range and the same mean for heading time. These facts imply that 'v' is identical with Se-1e. T65 exhibited a far longer BVG than the two tester lines. The critical day-lengths (CDLs) of T65 and ER were longer than 16 h, while the CDL of LR ranged between 14 h and 15 h : the CDL of LR was shorter than those of T65 and ER. When compared to LR, T65 and ER exhibited a small retarding effect under super optimum photoperiod (RES), and did not differ in RES. These results indicate that the low photoperiod sensitivity of T65 is due to the action of 'v' (=Se-1e). Since the long BVG of T65 is attributed to the action of ef-1, it is considered that 'v' (=Se-1e) and ef-1 are very important genes for rice cultivation in Taiwan, where natural day-length is short even in summer and seasonal changes are negligible.
A backcross population (BC4F2) was developed from a cross between japonica rice variety Taichung 65, used as a recurrent parent, and the wild species Oryza glumaepatula, used as a donor parent. BC4F2 254 (n = 72) and BC4F2 222 (n = 78) populations varied widely in days to heading. The number of days to heading of Taichung 65 ranged from 95 to 100, whereas BC4F2 254 and BC4F2 222 ranged from 95 to 114 d and 95 to 111 d, respectively. Using linkage analysis, we found two late heading genes, Lhd1(t) in BC4F2 254 and Lhd2(t) in BC4F2 222. The Lhd1(t) gene was located between RFLP markers C474 and R1962 on chromosome 6; it was linked to C474 and R1962, with a map distance of 1.4 and 1.5 cM, respectively. Lhd2(t) was located between RFLP markers G338 and R1440 on chromosome 7; it was linked to G338 and R1440, with a map distance of 1.3 and 1.3 cM, respectively. Lhd1(t) showed a good correspondence with that of EnSe1(t) and Hd3b, whereas the position of Lhd2(t) on chromosome 7 might be identical to the region of the previously reported gene E1 and QTL Hd4. Both the Lhd1(t) and Lhd2(t) genes resulted in late flowering under natural daylength conditions during May to September in Fukuoka, Japan. The dominant allele of O. glumaepatula at Lhd1(t) and the partially dominant allele of O. glumaepatula at Lhd2(t) were responsible for the delayed heading. The linked markers could be used for the isolation of late heading genes through map-based cloning.
We developed new binary vectors, pPZP2H-lac and pPZP2Ha3, for the transformation of rice plants. These binary vectors contain multiple cloning sites and the hygromycin B phosphotransferase gene as a plant - selectable marker. After Agrobacterium - mediated transformation, transgenic plants containing a T-DNA could be tightly selected by hygromycin B. The vectors are powerful tools for the functional analysis of genes.
Many genetic studies have so far revealed a number of genes responsible for heading-time of rice. However, the knowledge about these respective genes has yet been of little use for actual breeding program. For saving this situation, it is necessary to detect and identify the genes controlling the heading-time of presently grown varieties, to clarify the relationships among known, detected and identified genes, and thus to systematize the information about heading-time genes. From these points of view, gene analysis of the heading time of Japanese rice varieties was undertaken with the aid of 7 tester lines named EG lines, which are different from one another in the genotype for three late-heading-time genes E1. E2 and E3.
A major quantitative trait locus (QTL) controlling response to photoperiod, Hd1 , was identified by means of a map-based cloning strategy. High-resolution mapping using 1505 segregants enabled us to define a genomic region of ∼12 kb as a candidate for Hd1 . Further analysis revealed that the Hd1 QTL corresponds to a gene that is a homolog of CONSTANS in Arabidopsis. Sequencing analysis revealed a 43-bp deletion in the first exon of the photoperiod sensitivity 1 ( se1 ) mutant HS66 and a 433-bp insertion in the intron in mutant HS110. Se1 is allelic to the Hd1 QTL, as determined by analysis of two se1 mutants, HS66 and HS110. Genetic complementation analysis proved the function of the candidate gene. The amount of Hd1 mRNA was not greatly affected by a change in length of the photoperiod. We suggest that Hd1 functions in the promotion of heading under short-day conditions and in inhibition under long-day conditions.
A rice diversity research set of germplasm (RDRS) was developed based on a genome-wide RFLP polymorphism survey of 332 accessions of cultivated rice (Oryza saliva L.). The accessions used in the initial survey were selected based on the passport data from the whole collection maintained at the Genebank of the National Institute of Agrobiological Sciences (NIAS). These accessions were analyzed using 179 nuclear RFLP markers. A total of 554 alleles were detected, and the number of alleles per locus ranged from 2 to 8 (mean 3.1). Principal coordinate analysis using RFLP data enabled to classify the accessions into three major groups, one Japonica and other two Indica. To develop a rice diversity research set of germplasm, the RFLP data on the 332 accessions were subjected to cluster analysis and 67 groups were recognized at a similarity index of 0.915. A single accession from each of the 67 groups was selected. These 67 accessions retained 91% of the alleles detected in the original 332 accessions, and covered the variation of the initial set of accessions in terms of several agro-morphological traits. The 69 accessions including varieties from 19 countries and the reference varieties, Nipponbare and Kasalath, were selected for the development of a rice diversity research set of germplasm. This collection which is presently well characterized at the molecular level will be used for the detailed genetic studies and rice improvement.
