A high-density genetic map and multiple environmental tests reveal novel quantitative trait loci and candidate genes for
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ORIGINAL ARTICLE
A high‑density genetic map and multiple environmental tests reveal novel quantitative trait loci and candidate genes for fibre quality and yield in cotton Qishen Gu1 · Huifeng Ke1 · Zhengwen Liu1 · Xing Lv1 · Zhengwen Sun1 · Man Zhang1 · Liting Chen1 · Jun Yang1 · Yan Zhang1 · Liqiang Wu1 · Zhikun Li1 · Jinhua Wu1 · Guoning Wang1 · Chengsheng Meng1 · Guiyin Zhang1 · Xingfen Wang1 · Zhiying Ma1 Received: 16 January 2020 / Accepted: 21 August 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Key message A high-density linkage map of an intraspecific RIL population was constructed using 6187 bins to identify QTLs for fibre quality- and yield-related traits in upland cotton by whole-genome resequencing. Abstract Good fibre quality and high yield are important production goals in cotton (Gossypium hirsutum L.), which is a leading natural fibre crop worldwide. However, a greater understanding of the genetic variants underlying fibre quality- and yield-related traits is still required. In this study, a large-scale population including 588 F7 recombinant inbred lines, derived from an intraspecific cross between the upland cotton cv. Nongdamian13, which exhibits high quality, and Nongda601, which exhibits a high yield, was genotyped by using 232,946 polymorphic single-nucleotide polymorphisms obtained via a wholegenome resequencing strategy with 4.3-fold genome coverage. We constructed a high-density bin linkage map containing 6187 bin markers spanning 4478.98 cM with an average distance of 0.72 cM. We identified 58 individual quantitative trait loci (QTLs) and 25 QTL clusters harbouring 94 QTLs, and 119 previously undescribed QTLs controlling 13 fibre quality and yield traits across eight environments. Importantly, the QTL counts for fibre quality in the Dt subgenome were more than two times that in the At subgenome, and chromosome D02 harboured the greatest number of QTLs and clusters. Furthermore, we discovered 24 stable QTLs for fibre quality and 12 stable QTLs for yield traits. Four novel major stable QTLs related to fibre length, fibre strength and lint percentage, and seven previously unreported candidate genes with significantly differential expression between the two parents were identified and validated by RNA-seq. Our research provides valuable information for improving the fibre quality and yield in cotton breeding.
Introduction Communicated by Diane E. Mather. Qishen Gu, Huifeng Ke and Zhengwen Liu have contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00122-020-03676-z) contains supplementary material, which is available to authorized users. * Xingfen Wang [email protected] * Zhiying Ma [email protected] 1
State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China
Cotton is one of the most important cash crops, providing natural and renewable fibre to the textile industry in more than 80 countries worldwide, wit
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