Structure, evolution, and comparative genomics of tetraploid cotton based on a high-density genetic linkage map

Li, Ximei; Jin, Xin; Wang, Hantao; Zhang, Xianlong; Lin, Zhongxu

doi:10.1093/dnares/dsw016

Cited by 30 publications

(29 citation statements)

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“…SD has previously been reported in interspecific populations of cotton (Guo et al, 2007; Blenda et al, 2012; Byers et al, 2012; Liang et al, 2012; Yu et al, 2013; Diouf et al, 2014; Zhang et al, 2014; Li et al, 2016), intraspecific populations of G. barbadense (Wang et al, 2013), intraspecific populations of G. hirsutum (Lin et al, 2009; Zhang et al, 2012, 2016; Ning et al, 2014), and intraspecific populations of G. arboreum (Li et al, 2007); however, the genetic mechanism of SD in cotton remains unclear.…”

Section: Discussionmentioning

confidence: 98%

Identification and Characterization of Segregation Distortion Loci on Cotton Chromosome 18

et al. 2017

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Segregation distortion is commonly detected via genetic mapping and this phenomenon has been reported in many species. However, the genetic causes of the segregation distortion regions in a majority of species are still unclear. To genetically dissect the SD on chromosome 18 in cotton, eight reciprocal backcross populations and two F2 populations were developed. Eleven segregation distortion loci (SDL) were detected in these ten populations. Comparative analyses among populations revealed that SDL18.1 and SDL18.9 were consistent with male gametic competition; whereas SDL18.4 and SDL18.11 reflected female gametic selection. Similarly, other SDL could reflect zygotic selection. The surprising finding was that SDL18.8 was detected in all populations, and the direction was skewed towards heterozygotes. Consequently, zygotic selection or heterosis could represent the underlying genetic mechanism for SDL18.8. Among developed introgression lines, SDL18.8 was introgressed as a heterozygote, further substantiating that a heterozygote state was preferred under competition. Six out of 11 SDL on chromosome 18 were dependent on the cytoplasmic environment. These results indicated that different SDL showed varying responses to the cytoplasmic environment. Overall, the results provided a novel strategy to analyze the molecular mechanisms, which could be further exploited in cotton interspecific breeding programs.

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Section: Discussionmentioning

confidence: 98%

Identification and Characterization of Segregation Distortion Loci on Cotton Chromosome 18

et al. 2017

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“…The CottonSNP63K array, the first SNP chip for cotton, was developed from discovery sets that represent a diverse range of G. hirsutum germplasm, including G. hirsutum , G. barbadense , G. tomentosum , G. mustelinum , G. armourianum and G. longicalyx (Hulse‐Kemp et al ., ). This array showed high polymorphism (49.27%) in an upland cotton panel compared with biparental recombinant populations or SSR markers (Li et al ., ; Wang et al ., ). The average density of polymorphic SNPs was 1SNP/0.32 cM, equal to ~200 kb in the physical map, which achieved the requirement for GWAS mapping.…”

Section: Discussionmentioning

confidence: 99%

Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome‐wide association study using high‐density SNPs

Huang

Nie

Shen

et al. 2017

Plant Biotechnology Journal

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Summary Gossypium hirsutum L. represents the largest source of textile fibre, and China is one of the largest cotton‐producing and cotton‐consuming countries in the world. To investigate the genetic architecture of the agronomic traits of upland cotton in China, a diverse and nationwide population containing 503 G. hirsutum accessions was collected for a genome‐wide association study (GWAS) on 16 agronomic traits. The accessions were planted in four places from 2012 to 2013 for phenotyping. The CottonSNP63K array and a published high‐density map based on this array were used for genotyping. The 503 G. hirsutum accessions were divided into three subpopulations based on 11 975 quantified polymorphic single‐nucleotide polymorphisms (SNPs). By comparing the genetic structure and phenotypic variation among three genetic subpopulations, seven geographic distributions and four breeding periods, we found that geographic distribution and breeding period were not the determinants of genetic structure. In addition, no obvious phenotypic differentiations were found among the three subpopulations, even though they had different genetic backgrounds. A total of 324 SNPs and 160 candidate quantitative trait loci (QTL) regions were identified as significantly associated with the 16 agronomic traits. A network was established for multieffects in QTLs and interassociations among traits. Thirty‐eight associated regions had pleiotropic effects controlling more than one trait. One candidate gene, Gh_D08G2376, was speculated to control the lint percentage (LP). This GWAS is the first report using high‐resolution SNPs in upland cotton in China to comprehensively investigate agronomic traits, and it provides a fundamental resource for cotton genetic research and breeding.

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“…Similarly, the introgression line populations were constructed in our laboratory with Gh_E22 as the receptor and the other tetraploid species as donors. Currently, only 5,152 gel-based loci were identified between Gh_E22 and Gb_3–79 [39]. As is known, the gel-based markers are time-consuming and have low efficiency.…”

Section: Discussionmentioning

confidence: 99%

Uncovering SNP and indel variations of tetraploid cottons by SLAF-seq

et al. 2017

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BackgroundCotton (Gossypium spp.), as the world’s most utilized textile fibre source, is an important, economically valuable crop worldwide. Understanding the genomic variation of tetraploid cotton species is important for exploitation of the excellent characteristics of wild cotton and for improving the diversity of cotton in breeding. However, the discovery of DNA polymorphisms in tetraploid cotton genomes has lagged behind other important crops.ResultsA total of 111,795,823 reads, 467,735 specific length amplified fragment (SLAF) tags and 139,176 high-quality DNA polymorphisms were identified using specific length amplified fragment sequencing (SLAF-seq), including 132,880 SNPs and 6,296 InDels between the reference genome (TM-1) and the five tetraploid cotton species. Intriguingly, gene ontology (GO) enrichment analysis revealed that a number of significant terms were related to reproduction in G. barbadense acc. 3–79. Based on the new data sets, we reconstructed phylogenetic trees that showed a high concordance to the phylogeny of diploid and polyploid cottons. A large amount of interspecific genetic variations were identified, and some of them were validated by the single-strand conformation polymorphism (SSCP) method, which will be applied in introgression genetics and breeding with G. hirsutum cv. Emian22 as the receptor and the other species as donors.ConclusionsUsing SLAF-seq, a large number of DNA polymorphisms were identified. The comprehensive analysis of DNA polymorphisms provided invaluable insights into the different tetraploid cotton species. More importantly, the identification of numerous interspecific genetic variations provides the basis and is very practical for future introgression breeding. The results presented herein provide a valuable genomic resource for new insights into the genetics and breeding of cotton.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3643-4) contains supplementary material, which is available to authorized users.

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Structure, evolution, and comparative genomics of tetraploid cotton based on a high-density genetic linkage map

Cited by 30 publications

References 45 publications

Identification and Characterization of Segregation Distortion Loci on Cotton Chromosome 18

Identification and Characterization of Segregation Distortion Loci on Cotton Chromosome 18

Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome‐wide association study using high‐density SNPs

Uncovering SNP and indel variations of tetraploid cottons by SLAF-seq

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