GWAS Analysis and QTL Identification of Fiber Quality Traits and Yield Components in Upland Cotton Using Enriched High-Density SNP Markers
2018
Ruixian Liu | Ruixian Liu | Juwu Gong | Juwu Gong | Xianghui Xiao | Xianghui Xiao | Zhen Zhang | Junwen Li | Aiying Liu | Quanwei Lu | Quanwei Lu | Haihong Shang | Yuzhen Shi | Qun Ge | Muhammad S. Iqbal | Xiaoying Deng | Shaoqi Li | Jingtao Pan | Li Duan | Qi Zhang | Xiao Jiang | Xianyan Zou | Abdul Hafeez | Quanjia Chen | Hongwei Geng | Wankui Gong | Youlu Yuan | Youlu Yuan
It is of great importance to identify quantitative trait loci (QTL) controlling fiber quality traits and yield components for future marker-assisted selection (MAS) and candidate gene function identifications. In this study, two kinds of traits in 231 F6:8 recombinant inbred lines (RILs), derived from an intraspecific cross between Xinluzao24, a cultivar with elite fiber quality, and Lumianyan28, a cultivar with wide adaptability and high yield potential, were measured in nine environments. This RIL population was genotyped by 122 SSR and 4729 SNP markers, which were also used to construct the genetic map. The map covered 2477.99 cM of hirsutum genome, with an average marker interval of 0.51 cM between adjacent markers. As a result, a total of 134 QTLs for fiber quality traits and 122 QTLs for yield components were detected, with 2.18–24.45 and 1.68–28.27% proportions of the phenotypic variance explained by each QTL, respectively. Among these QTLs, 57 were detected in at least two environments, named stable QTLs. A total of 209 and 139 quantitative trait nucleotides (QTNs) were associated with fiber quality traits and yield components by four multilocus genome-wide association studies methods, respectively. Among these QTNs, 74 were detected by at least two algorithms or in two environments. The candidate genes harbored by 57 stable QTLs were compared with the ones associated with QTN, and 35 common candidate genes were found. Among these common candidate genes, four were possibly “pleiotropic.” This study provided important information for MAS and candidate gene functional studies.
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