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Resistance to cotton blue disease (CBD) was evaluated in 364 F(2.3) families of three populations derived from resistant variety 'Delta Opal'. The CBD resistance in 'Delta Opal' was controlled by one single dominant gene designated Cbd. Two simple sequence repeat (SSR) markers were identified as linked to Cbd by bulked segregant analysis. Cbd resid...
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... For the marker DC20027, three fragments, i.e. 182 bp, 200 bp and 202 bp, were observed (Table 3). The fragment 182 bp was present in all DNA samples. The fragments 200 bp and 202 bp were allelic, and linked to the susceptible and resistance alleles at Cbd locus, respectively. The genetic distance between DC20027 marker locus and Cbd is 0.75 cM (Fig. 2). Similarly, primer BNL3646 generated 3 fragments, i.e. 145 bp, 147 bp, and 155 bp. The fragments 145 bp and 147 bp were allelic, and linked to the susceptible and resistance alleles at Cbd locus, respectively at a distance of 1.65 cM. The fragment 155 bp was present in all DNA ...
Context 2
... 15 SNP markers that are within 5 cM of SSR marker DC20027 on this chromosome were first screened between 'Delta Opal' and 'DP388'. Three of them were polymorphic between two parents, and were analyzed among the 253 F 2 progeny of ''Delta Opal'/'DP388'. These 3 SNP markers, i.e., NG0203671, NG0204310, NG0203481, were found as tightly linked to Cbd (Fig. 2). The primer and probe sequences of all 4 SNP markers are listed in Table 5. The optimum situation for MAS is to select based on marker haplotype which should include SNPs flanking the gene of interest as in this case. The haplotype 'CC-CC-AA-TT' denotes resistance, while 'TT-TT-TT-CC' denotes ...
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Cotton (Gossypium spp.) is an important economic crop and the largest source of textile fiber in the world. However, to date, only a few genes have been identified that exhibit critical roles in fiber development, and few has shown positive effects on fiber yield and quality in transgenic cotton. Here, we report the characterization of a novel sucr...
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... The first association mapping study in cotton focusing on fiber quality was reported in G. arboretum (Kantartzi and Stewart, 2008). Subsequently, association mapping has been extensively applied in upland cotton to investigate crucial economic traits, including fiber quality (Abdurakhmonov et al., 2008;Nie et al., 2016;Liu et al., 2020;Song et al., 2021), seed oil content (Liu G. et al., 2015;Yuan et al., 2018;Zhao et al., 2019), fiber yield (Ademe et al., 2017;Sun et al., 2018;GUO et al., 2021;Niu et al., 2023), and biotic and abiotic stresses (Fang et al., 2010;Bardak et al., 2021;Xu et al., 2021;Zhang et al., 2021;Zhao et al., 2021), as well as those associated with epistasis and environmental interactions (Jia et al., 2014). ...
Upland cotton (Gossypium hirsutum L.) is a major fiber crop that is cultivated worldwide and has significant economic importance. India harbors the largest area for cotton cultivation, but its fiber yield is still compromised and ranks 22nd in terms of productivity. Genetic improvement of cotton fiber yield traits is one of the major goals of cotton breeding, but the understanding of the genetic architecture underlying cotton fiber yield traits remains limited and unclear. To better decipher the genetic variation associated with fiber yield traits, we conducted a comprehensive genome-wide association mapping study using 117 Indian cotton germplasm for six yield-related traits. To accomplish this, we generated 2,41,086 high-quality single nucleotide polymorphism (SNP) markers using genotyping-by-sequencing (GBS) methods. Population structure, PCA, kinship, and phylogenetic analyses divided the germplasm into two sub-populations, showing weak relatedness among the germplasms. Through association analysis, 205 SNPs and 134 QTLs were identified to be significantly associated with the six fiber yield traits. In total, 39 novel QTLs were identified in the current study, whereas 95 QTLs overlapped with existing public domain data in a comparative analysis. Eight QTLs, qGhBN_SCY_D6-1, qGhBN_SCY_D6-2, qGhBN_SCY_D6-3, qGhSI_LI_A5, qGhLI_SI_A13, qGhLI_SI_D9, qGhBW_SCY_A10, and qGhLP_BN_A8 were identified. Gene annotation of these fiber yield QTLs revealed 2,509 unique genes. These genes were predominantly enriched for different biological processes, such as plant cell wall synthesis, nutrient metabolism, and vegetative growth development in the gene ontology (GO) enrichment study. Furthermore, gene expression analysis using RNAseq data from 12 diverse cotton tissues identified 40 candidate genes (23 stable and 17 novel genes) to be transcriptionally active in different stages of fiber, ovule, and seed development. These findings have revealed a rich tapestry of genetic elements, including SNPs, QTLs, and candidate genes, and may have a high potential for improving fiber yield in future breeding programs for Indian cotton.
... However, it has not been effective (Galbieri et al., 2017;Mahas et al., 2022). A resistant cotton variety was developed with a dominant resistant gene (Cbd) (Fang et al., 2010). Although this variety showed absolute resistance to CLRDV by restricting systemic virus replication, it was not long before a new strain that broke the resistance was identified in South America (Silva et al., 2008). ...
... Upon the rise of CBD in Brazil, deploying cultivars with a single dominant resistance gene, Rghv1, effectively mitigated the disease (Junior et al., 2008). However, varieties carrying a single dominant resistance gene, Cbd (Fang et al., 2010), became susceptible to CLRDV-at in Argentina (Agrofoglio et al., 2019). Furthermore, the BRS-293 cultivar, which is moderately resistant to typical and atypical CLRDVs (Morello et al., 2010), was susceptible to prevalent CLRDV in the southeastern United States . ...
Cotton is a multipurpose crop grown globally, including the United States. Cotton leafroll dwarf virus (CLRDV), a phloem-limited virus (Solemoviridae) transmitted by aphids, causes significant economic losses to cotton cultivation. CLRDV strains (CLRDV-typical and atypical) that were previously prevalent in other countries cause severe symptoms leading to high yield loss. Recently, a new isolate of CLRDV (CLRDV-AL) has been characterized from infected cotton plants in Alabama that are often asymptomatic and difficult to detect, implying a low titer and pathogenicity within the host. Different pathogenicity among certain strains within the same species often correlates with both environmental and molecular factors. Thus, better management and control of the vector-borne disease can be achieved by elucidating host-pathogen interaction, such as host immune response and pathogen counter-response. In this study, we demonstrate the ability of CLRDV-AL to suppress a major host defense response known as RNA silencing and compare the potency of silencing suppression to other strains of the same virus. Also, we discuss the difference in pathogenicity among them by evaluating the observations based on the amino acid variation within the functional domain. Our study provides and suggests a future direction for specifying the strategy to mitigate potential cotton disease severity.
... Young leaves were collected from each F 2 plant in the two populations. Total DNA was extracted from leaf tissues using a CTAB protocol described by D. D. Fang et al. (2010) with a step of RNAase A digestion before DNA precipitation. DNA quality was checked on a 1.5% agarose gel, and DNA quantity was measured using a Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific). ...
A determination of efficiency in the use of marker‐assisted selection (MAS) for improving cotton (Gossypium hirsutum L.) fiber quality is critical for a successful utilization of MAS in cotton breeding. This study was designed to determine selection responses and realized heritability (h2) of fiber strength selected by MAS in comparison with phenotype selections by traditional breeding. Previously identified single‐sequence repeats markers, CGR6764 and DPL0852, flanking a fiber strength quantitative trait locus on chromosome A07 were used in MAS. Two genetic populations, MD15/TAM98D‐99ne (Pop 1) and TAM98D‐99ne/UA48 (Pop 2), were developed. F2 plants were selected by three methods based on (1) phenotype, (2) combined marker‐genotype and phenotype (MAS‐1), and (3) marker‐genotype alone (MAS‐2) in Pop 1 and two methods based on phenotype and MAS‐1 in Pop 2. F3 progeny rows derived from the selected F2 plants were planted with two replicates in 2019. In Pop 1, the fiber strength mean of the selected F3 progenies was in an order of MAS‐1 > MAS‐2 > phenotype selection. In Pop 2, there was no significant difference in strength between F3 progenies derived from selections by MAS‐1 and phenotypic breeding. In Pop 1, h2 of MAS selections was higher than phenotype selections. In Pop 2, h2 of MAS selections was similar to the phenotype selections. The results indicate that selection efficiency by MAS for fiber strength is better than or equivalent to phenotype selection.
... Leaves were stored at -80 °C. Total DNA was extracted from the frozen leaves following a protocol described before (Fang et al. 2010) with an additional RNAase A digestion step before binding DNA to a column. DNA quantity and quality was measured using a Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA) as well as on a 1.5% agarose gel. ...
Introgression of superior fiber traits from Pima cotton (Gossypium barbadense, GB) into high yield Upland cotton (G. hirsutum) has been a breeding objective for many years in a few breeding programs in the world. However, progress has been very slow due to introgression barriers resulting from whole genome hybridization between the two species. To minimize such barriers, chromosome substitution lines (CS-B) from Pima cotton 3–79 in an Upland cotton cultivar TM-1 were developed. A multiparent advanced generation inter-cross (MAGIC) population consisting of 180 recombinant inbred lines (RILs) was subsequently made using the 18 CS-B lines and three Upland cotton cultivars as parents. In this research, we sequenced the whole genomes of the 21 parents and 180 RILs to examine the G. barbadense introgression. Of the 18 CS-B lines, 11 contained the target GB chromosome or chromosome segment, two contained more than two GB chromosomes, and five did not have the expected introgression. Residual introgression in non-target chromosomes was prevalent in all CS-B lines. A clear structure existed in the MAGIC population and the 180 RILs were distributed into three groups, i.e., high, moderate, and low GB introgression. Large blocks of GB chromosome introgression were still present in some RILs after five cycles of random-mating, an indication of recombination suppression or other unknown reasons present in the population. Identity by descent analysis revealed that the MAGIC RILs contained less introgression than expected. This research presents an insight on understanding the complex problems of introgression between cotton species.
... Virus resistance in cotton is conferred by a single locus (Pupim et al., 2008). Single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) markers linked to the resistance gene Cbd have been identified (Fang et al., 2010). The presence of atypical symptoms has been observed in cotton fields and may be related to the variability of the virus (Silva et al., 2008). ...
... After some initial tests with labeled goat anti-rabbit antiserum, the polyclonal α-GQE and the monoclonal α-NKF were conjugated to the enzyme alkaline phosphatase. Cotton plants grown in a greenhouse, covered with an aphid-proof screen, were used for DNA extraction and PCR to verify the presence of the SSR marker DC20027 and assess the presence of the resistance gene, expected in the CLRDV-resistant cotton varieties (Delta Opal and BRS 293), and absent on those reported as susceptible (Fibermax 966, CNPA GO33, and CNPA 809) (Pupim et al., 2008;Fang et al., 2010;Menezes et al., 2014). For cotton plant inoculation, A. gossypii, fed on diseased cotton plants for 3-5 days, was transferred to the resistant or susceptible plants with a brush. ...
The cotton blue disease, caused by the cotton leafroll dwarf virus (CLRDV), leads to dwarfism, leaf rolling, and production loss in susceptible cotton varieties. To develop an enzyme-linked immunosorbent assay (ELISA) test to detect the virus in cotton and weeds, peptides based on the coat protein were used to produce polyclonal (α-GQE, α-PRN, and α-INK) and monoclonal (α-GQE, α-PRN, and α-NKF) antibodies. All six were tested as capture antibodies, and polyclonal α-GQE and the monocle onal α-NKF were labeled with the enzyme alkaline phosphatase and used as detection antibodies for a double antibody sandwich (DAS) ELISA method, in which p-nitrophenyl phosphate was added and measured by absorbance at 405 nm. The DAS-ELISA sandwich was efficient in discriminating between healthy and diseased plant extracts. The ELISA methodology detected the virus in the weeds Commelina sp., which was confirmed by RT-PCR. The monoclonal antibodies may be used to develop other diagnostic procedures.
... Young leaves were collected from 10 plants of each RIL or parent and stored at −80°C. Genomic DNA was extracted from the frozen leaves using a CTAB method with an additional RNAase A digestion steps as described previously 52,55 . Genomic DNA was sent to Novogene (Chula Vista, CA, USA) for library preparation and the whole genome was sequenced using Illumina HiSeq 2500 with 150 bp end-paired reads. ...
Cotton ( Gossypium hirsutum L.) fiber is the most important resource of natural and renewable fiber for the textile industry. However, the understanding of genetic components and their genome-wide interactions controlling fiber quality remains fragmentary. Here, we sequenced a multiple-parent advanced-generation inter-cross (MAGIC) population, consisting of 550 individuals created by inter-crossing 11 founders, and established a mosaic genome map through tracing the origin of haplotypes that share identity-by-descent (IBD). We performed two complementary GWAS methods—SNP-based GWAS (sGWAS) and IBD-based haplotype GWAS (hGWAS). A total of 25 sQTLs and 14 hQTLs related to cotton fiber quality were identified, of which 26 were novel QTLs. Two major QTLs detected by both GWAS methods were responsible for fiber strength and length. The gene Ghir_D11G020400 (GhZF14) encoding the MATE efflux family protein was identified as a novel candidate gene for fiber length. Beyond the additive QTLs, we detected prevalent epistatic interactions that contributed to the genetics of fiber quality, pinpointing another layer for trait variance. This study provides new targets for future molecular design breeding of superior fiber quality.
... In the future, sustainable control of CBTD in commercial cotton crops may be underpinned by incorporating the recently characterized genetic resistance to it conferred by the putative single dominant locus Cbt into new cotton cultivars [294]. The Cbt locus was found to be located on chromosome A10 close to resistance gene Cbd to CLRDV mapped by Fang et al. [295]. Ellis et al. [294] noted that while their mapping indicated that Cbt was close to, but distinct from, Cbd, they could not rule out the possibility that the same gene is responsible for resistance to both viruses. ...
This review summarizes research on virus diseases of cereals and oilseeds in Australia since the 1950s. All viruses known to infect the diverse range of cereal and oilseed crops grown in the continent’s temperate, Mediterranean, subtropical and tropical cropping regions are included. Viruses that occur commonly and have potential to cause the greatest seed yield and quality losses are described in detail, focusing on their biology, epidemiology and management. These are: barley yellow dwarf virus, cereal yellow dwarf virus and wheat streak mosaic virus in wheat, barley, oats, triticale and rye; Johnsongrass mosaic virus in sorghum, maize, sweet corn and pearl millet; turnip yellows virus and turnip mosaic virus in canola and Indian mustard; tobacco streak virus in sunflower; and cotton bunchy top virus in cotton. The currently less important viruses covered number nine infecting nine cereal crops and 14 infecting eight oilseed crops (none recorded for rice or linseed). Brief background information on the scope of the Australian cereal and oilseed industries, virus epidemiology and management and yield loss quantification is provided. Major future threats to managing virus diseases effectively include damaging viruses and virus vector species spreading from elsewhere, the increasing spectrum of insecticide resistance in insect and mite vectors, resistance-breaking virus strains, changes in epidemiology, virus and vectors impacts arising from climate instability and extreme weather events, and insufficient industry awareness of virus diseases. The pressing need for more resources to focus on addressing these threats is emphasized and recommendations over future research priorities provided.
... Cotton leafroll dwarf virus (CLRDV; family Solemoviridae, genus Polerovirus) is known to cause cotton blue disease (CBD), and its occurrence was first reported in Africa in 1949, followed by reports of the disease in Asia and South America (Fang et al., 2010). Cotton yield losses up to 80% have been observed from CLRDV in South America (Silva et al., 2008), and the virus is now an emerging threat to cotton production in the United States (Avelar et al., 2019). ...
Cotton leafroll dwarf disease (CLRDD) caused by cotton leafroll dwarf virus (CLRDV) is an emerging threat to cotton production in the United States. The disease was first reported in Alabama in 2017 and subsequently has been reported in 10 other cotton producing states in the United States, including Georgia. A field study was conducted at field sites near Tifton, Georgia in 2019 and 2020 to evaluate leaf gas exchange, chlorophyll fluorescence, and leaf temperature responses for a symptomatic cultivar (diseased plants observed at regular frequency) at multiple stages of disease progression and for asymptomatic cultivars (0% disease incidence observed). Disease-induced reductions in net photosynthetic rate (An, decreased by 63–101%), stomatal conductance (gs, decreased by 65–99%), and efficiency of the thylakoid reactions (32–92% decline in primary photochemistry) were observed, whereas leaf temperature significantly increased by 0.5–3.8°C at advanced stages of the disease. Net photosynthesis was substantially more sensitive to disease-induced declines in gs than the thylakoid reactions. Symptomatic plants with more advanced disease stages remained stunted throughout the growing season, and yield was reduced by 99% by CLRDD due to reductions in boll number per plant and declines in boll mass resulting from fewer seeds per boll. Asymptomatic cultivars exhibited more conservative gas exchange responses than apparently healthy plants of the symptomatic cultivar but were less productive. Overall, it is concluded that CLRDV limits stomatal conductance and photosynthetic activity of individual leaves, causing substantial declines in productivity for individual plants. Future studies should evaluate the physiological contributors to genotypic variation in disease tolerance under controlled conditions.
... Young leaves were collected from each individual F 2 plant within the segregating population. DNA was isolated as previously described (Fang et al. 2010). The concentration of DNA samples was measured using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA). ...
Cotton fiber mutants are valuable resources for studying functions of altered genes and their roles in fiber development. The n4t is a recessive tufted-fuzzless seed mutant created through chemical mutagenesis with ethyl methanesulfonate. Genetic analysis indicated that the tufted-fuzzless phenotype is controlled by a single recessive locus. In this study, we developed an F2 population of 602 progeny plants and sequenced the genomes of the parents and two DNA bulks from F2 progenies showing the mutant phenotype. We identified DNA sequence variants between the tufted-fuzzless mutant and wild type by aligning the sequence reads to the reference TM-1 genome and designed subgenome-specific SNP markers. We mapped the n4t locus on chromosome D04 within a genomic interval of about 411 kb. In this region, seven genes showed significant differential expression between the tufted-fuzzless mutant and wild type. Possible candidate genes are discussed in this study. The utilization of the n4t mutant along with other fiber mutants will facilitate our understanding of the molecular mechanisms of cotton fiber cell growth and development.
... There is no host-resistance against CLRDV established, reported, or deployed in the USA; however, cotton blue disease (CBD) resistance has been reported in a cotton variety (Delta Opal) with a single dominant gene (cbd) (Fang et al., 2010). Preventive management by destroying alternative hosts that harbor CLRDV is an option to manage the disease. ...
In 2018-19, cotton leafroll dwarf virus (CLRDV) was reported from several cotton-producing states in the southern United States. An extensive survey was conducted in the spring, summer, and fall of 2019 to identify weeds and overwintering cotton as sources for primary inoculum for the next season crop. Foliage samples of 57 different weed species were collected from fields formerly planted to cotton and analyzed using RT-PCR with CLRDV specific primers. CLRDV was detected from 23 weed species belonging to 16 different botanical families. Overwintering cotton stalks (48%) and regrowth leaves (75%) both harbored CLRDV. A phylogenetic analysis conducted using nucleotide and amino acid sequences of complete ORF 0, ORF 3, and ORF 4 determined that the CLRDV from all weeds and overwintered cotton stalks from Georgia clustered with CLRDV isolates collected in the USA but differed from isolates reported from South America and Asia. Pairwise nucleotide and amino acid identity showed 91-100% sequence similarity for complete ORF3. For ORF4, pairwise identity among the nucleotide ranged from 92-100%, while amino acids ranged from 90.2-100% with isolates reported from the USA and South America, with the exception of three Asian CLRDV isolates and two weed isolates from Georgia. Similarly, CLRDV isolates from Georgia weeds shared 91.6-93% nucleotide and 88-90.8% amino acid for silencing suppressor compared to most of the isolates from North America and South America. The role of alternative hosts on disease incidence and spread has not been studied in cotton-producing countries where the disease is prevalent. This is the first comprehensive study that identifies weeds and overwintering cotton as a potential green bridge for the year-round survival of CLRDV.
