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A high-density genetic map and multiple environmental tests reveal novel quantitative trait loci and candidate genes for fibre quality and yield in cotton

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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 whole-genome 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.

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Acknowledgments

This study was financially supported by the Fund of the China Agriculture Research System (CARS15-03) and the Science and Technology Support Program of Hebei Province (16226307D).

Author information

Author notes

  1. Qishen Gu, Huifeng Ke and Zhengwen Liu have contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China

    Qishen Gu, Huifeng Ke, Zhengwen Liu, Xing Lv, Zhengwen Sun, Man Zhang, Liting Chen, Jun Yang, Yan Zhang, Liqiang Wu, Zhikun Li, Jinhua Wu, Guoning Wang, Chengsheng Meng, Guiyin Zhang, Xingfen Wang & Zhiying Ma

Authors
  1. Qishen Gu
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  2. Huifeng Ke
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  3. Zhengwen Liu
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  4. Xing Lv
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  5. Zhengwen Sun
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  6. Man Zhang
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  7. Liting Chen
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  8. Jun Yang
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  9. Yan Zhang
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  10. Liqiang Wu
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  11. Zhikun Li
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  12. Jinhua Wu
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  13. Guoning Wang
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  14. Chengsheng Meng
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  15. Guiyin Zhang
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  16. Xingfen Wang
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  17. Zhiying Ma
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Contributions

Author contributions statement

ZYM designed the research; QSG, XFW, HFK, ZWL, XL, ZWS, MZ, LTC, JY, YZ, LQW, ZKL, JHW, GNW, CSM and GYZ performed experiments; QSG, HFK and ZWL analysed data; QSG wrote the manuscript; ZYM and XFW revised the manuscript. All authors read and approved the manuscript.

Corresponding authors

Correspondence to Xingfen Wang or Zhiying Ma.

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Conflict of interest

The authors declare no competing financial interests.

Ethical standards

The experiments were performed in compliance with the current laws of China.

Additional information

Communicated by Diane E. Mather.

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Gu, Q., Ke, H., Liu, Z. et al. A high-density genetic map and multiple environmental tests reveal novel quantitative trait loci and candidate genes for fibre quality and yield in cotton. Theor Appl Genet 133, 3395–3408 (2020). https://doi.org/10.1007/s00122-020-03676-z

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  • DOI: https://doi.org/10.1007/s00122-020-03676-z

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