Genome‐wide association study discovered genetic variation and candidate genes of fibre quality traits in <i>Gossypium hirsutum</i> L.

Sun, Zhengwen; Wang, Xingfen; Liu, Zhengwen; Gu, Qishen; Zhang, Yan; Li, Zhikun; Ke, Huifeng; Yang, Jun‐Bo; Wu, Jing; Wu, Liqiang; Zhang, Guiyin; Zhang, Caiying; Ma, Zhiying

doi:10.1111/pbi.12693

Cited by 143 publications

(174 citation statements)

References 85 publications

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“…The PIC values of markers ranged from 0.246 to 0.309 among chromosomes, and the mean PICs of the A and D subgenomes were 0.282 and 0.281, respectively. Our results were similar to those reported by Sun et al (), in which the PIC values ranged from 0.208 to 0.312, and the mean PICs of the A and D subgenomes were, respectively, 0.287 and 0.283. Sun et al conducted a successful GWAS for fiber‐quality‐related traits using 719 diverse accessions of upland cotton and 10,511 polymorphic SNPs.…”

Section: Discussionsupporting

confidence: 92%

A genome‐wide association study of early‐maturation traits in upland cotton based on the CottonSNP80K array

Wang

et al. 2018

JIPB

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Genome-wide association studies (GWASs) efficiently identify genetic loci controlling traits at a relatively high resolution. In this study, variations in major early-maturation traits, including seedling period (SP), bud period (BP), flower and boll period (FBP), and growth period (GP), of 169 upland cotton accessions were investigated, and a GWAS of early maturation was performed based on a CottonSNP80K array. A total of 49,650 high-quality single-nucleotide polymorphisms (SNPs) were screened, and 29 significant SNPs located on chromosomes A6, A7, A8, D1, D2, and D9, were repeatedly identified as associated with early-maturation traits, in at least two environments or two algorithms. Of these 29 significant SNPs, 1, 12, 11, and 5 were related to SP, BP, FBP, and GP, respectively. Six peak SNPs, TM47967, TM13732, TM20937, TM28428, TM50283, and TM72552, exhibited phenotypic contributions of approximately 10%, which could allow them to be used for marker-assisted selection. One of these, TM72552, as well as four other SNPs, TM72554, TM72555, TM72558, and TM72559, corresponded to the quantitative trait loci previously reported. In total, 274 candidate genes were identified from the genome sequences of upland cotton and were categorized based on their functional annotations. Finally, our studies identified Gh_D01G0340 and Gh_D01G0341 as potential candidate genes for improving cotton early maturity.

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Section: Discussionsupporting

confidence: 92%

A genome‐wide association study of early‐maturation traits in upland cotton based on the CottonSNP80K array

Wang

et al. 2018

JIPB

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“…In total, 19 QTLs for fibre quality and 10 QTLs for fibre yield were identified (Figures S12–S25; Table S17). Compared with the published GWAS results for cotton ( G. hirsutum ) (Huang et al ., ; Sun et al ., ; Wang et al ., ), many new QTLs responsible for fibre quality and yield were discovered in this new panel including 100 brown fibre accessions.…”

Section: Resultsmentioning

confidence: 99%

Linkage and association mapping reveals the genetic basis of brown fibre (Gossypium hirsutum)

Wen

Shen

et al. 2018

Plant Biotechnology Journal

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SummaryBrown fibre cotton is an environmental‐friendly resource that plays a key role in the textile industry. However, the fibre quality and yield of natural brown cotton are poor, and fundamental research on brown cotton is relatively scarce. To understand the genetic basis of brown fibre cotton, we constructed linkage and association populations to systematically examine brown fibre accessions. We fine‐mapped the brown fibre region, Lc 1, and dissected it into 2 loci, qBF‐A07‐1 and qBF‐A07‐2. The qBF‐A07‐1 locus mediates the initiation of brown fibre production, whereas the shade of the brown fibre is affected by the interaction between qBF‐A07‐1 and qBF‐A07‐2. Gh_A07G2341 and Gh_A07G0100 were identified as candidate genes for qBF‐A07‐1 and qBF‐A07‐2, respectively. Haploid analysis of the signals significantly associated with these two loci showed that most tetraploid modern brown cotton accessions exhibit the introgression signature of Gossypium barbadense. We identified 10 quantitative trait loci (QTLs) for fibre yield and 19 QTLs for fibre quality through a genome‐wide association study (GWAS) and found that qBF‐A07‐2 negatively affects fibre yield and quality through an epistatic interaction with qBF‐A07‐1. This study sheds light on the genetics of fibre colour and lint‐related traits in brown fibre cotton, which will guide the elite cultivars breeding of brown fibre cotton.

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“…When the recent developments in the field are considered altogether, it appears that the incorporation of various genomic approaches and genotyping will pave the way to increase fiber production and they will be the source of food security at global level. [190] AFLP, amplified fragment length polymorphism; SSR, simple sequence repeat; SNP, single nucleotide polymorphism, ILP, intron length polymorphism. …”

Section: Resultsmentioning

confidence: 99%

Genetic Mapping in Cotton

Bardak¹,

Hayat²,

Erdoğan³

et al. 2018

Past, Present and Future Trends in Cotton Breeding

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The genus Gossypium provides natural fiber for textile industry worldwide. Genetic improvement in cotton for traits of interest is not up to mark due to scarcity of adequate information about fiber production and quality. Use of DNA markers for overcoming the issues of selection associated with complex traits is the ultimate choice which may lead to initiate breeding by design. Numerous marker-trait associations have been identified for economical traits using linkage analysis in cotton. Currently there is need for developing high-density genetic maps using next-generation sequencing approaches together with genome-wide association studies (GWAS). Efforts have been started in this direction and several QTLs including fiber quality, yield traits, plant architecture, stomatal conductance and verticillium wilt resistance were identified. This chapter narrates genetic diversity, QTL mapping, association mapping and QTLs related to fiber quality traits. The incorporation of various genomic approaches and previously described marker strategies will pave the way for increase in fiber production.

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Genome‐wide association study discovered genetic variation and candidate genes of fibre quality traits in Gossypium hirsutum L.

Cited by 143 publications

References 85 publications

A genome‐wide association study of early‐maturation traits in upland cotton based on the CottonSNP80K array

A genome‐wide association study of early‐maturation traits in upland cotton based on the CottonSNP80K array

Linkage and association mapping reveals the genetic basis of brown fibre (Gossypium hirsutum)

Genetic Mapping in Cotton

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