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An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

文献类型： 外文期刊

作者： Su, Junji 1 ; Wang, Caixiang 1 ; Ma, Qi 2 ; Zhang, Ai 1 ; Shi, Chunhui 1 ; Liu, Juanjuan 1 ; Zhang, Xianliang 3 ; Yang, Delong 1 ; Ma, Xiongfeng 4 ;

作者机构： 1.Gansu Agr Univ, Coll Life Sci & Technol, Gansu Prov Key Lab Aridland Crop Sci, Lanzhou 730070, Peoples R China

2.Xinjiang Acad Agr & Reclamat Sci, Cotton Res Inst, Shihezi 832000, Peoples R China

3.Chinese Acad Agr Sci, Inst Cotton Res, State Key Lab Cotton Biol, Anyang 455000, Peoples R China

4.Zhengzhou Univ, Sch Agr Sci, Zhengzhou 450001, Peoples R China

关键词： Upland cotton; Yield trait; RTM-GWAS; QTL alleles; Candidate genes

期刊名称：BMC PLANT BIOLOGY （ 影响因子：4.215； 五年影响因子：4.96 ）

ISSN： 1471-2229

年卷期： 2020 年 20 卷 1 期

页码：

收录情况： SCI

摘要： Background Cotton (Gossypiumspp.) fiber yield is one of the key target traits, and improved fiber yield has always been thought of as an important objective in the breeding programs and production. Although some studies had been reported for the understanding of genetic bases for cotton yield-related traits, the detected quantitative trait loci (QTL) for the traits is still very limited. To uncover the whole-genome QTL controlling three yield-related traits in upland cotton (Gossypium hirsutumL.), phenotypic traits were investigated under four planting environments and 9244 single-nucleotide polymorphism linkage disequilibrium block (SNPLDB) markers were developed in an association panel consisting of 315 accessions. Results A total of 53, 70 and 68 significant SNPLDB loci associated with boll number (BN), boll weight (BW) and lint percentage (LP), were respectively detected through a restricted two-stage multi-locus multi-allele genome-wide association study (RTM-GWAS) procedure in multiple environments. The haplotype/allele effects of the significant SNPLDB loci were estimated and the QTL-allele matrices were organized for offering the abbreviated genetic composition of the population. Among the significant SNPLDB loci, six of them were simultaneously identified in two or more single planting environments and were thought of as the stable SNPLDB loci. Additionally, a total of 115 genes were annotated in the nearby regions of the six stable SNPLDB loci, and 16 common potential candidate genes controlling target traits of them were predicted by two RNA-seq data. One of 16 genes (GH_D06G2161) was mainly expressed in the early ovule-development stages, and the stable SNPLDB locus (LDB_19_62926589) was mapped in its promoter region. Conclusion This study identified the QTL alleles and candidate genes that could provide important insights into the genetic basis of yield-related traits in upland cotton and might facilitate breeding cotton varieties with high yield.

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