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Genome resequencing-based high-density genetic map and QTL detection for yield and fiber quality traits in diploid Asiatic cotton (Gossypium arboreum)

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Abstract

Cotton is the most important fiber crop in the world. Asiatic cotton (Gossypium arboreum, genome A2) is a diploid cotton species producing spinnable fibers and important germplasm for cotton breeding and a significant model for fiber biology. However, the genetic map of Asiatic cotton has been lagging behind tetraploid cottons, as well as other stable crops. This study aimed to construct a high-density SNP genetic map and to map QTLs for important yield and fiber quality traits. Using a recombinant inbred line (RIL) population and genome resequencing technology, we constructed a high-density genetic map that covered 1980.17 cM with an average distance of 0.61 cM between adjacent markers. QTL analysis revealed a total of 297 QTLs for 13 yield and fiber quality traits in three environments, explaining 5.0–37.4% of the phenotypic variance, among which 75 were stably detected in two or three environments. Besides, 47 QTL clusters, comprising 131 QTLs for representative traits, were identified. Our works laid solid foundation for fine mapping and cloning of QTL for yield and fiber quality traits in Asiatic cotton.

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Availability of data and material

Sequencing data related to this study has been uploaded to NCBI SRA database, which can be accessed through series of SRA numbers PRJNA649393.

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Funding

This study was partially funded by the Genetically Modified Organisms Breeding Major Project of China (2016ZX08005005-001 to Y.H.X.), the National Natural Science Foundation of China (31871539 and U2003209 to Y.H.X.) and Chongqing Science and Technology Commission (cstc2018jscx-msybX0382 to Y.H.X.).

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Authors and Affiliations

  1. Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Southwest University Southern Campus, Tiansheng Rd No. 2, Beibei, Chongqing, 400716, China

    Yaohua Li, Tong Mo, Lingfang Ran, Jianyan Zeng, Chuannan Wang, Aimin Liang, Yonglu Dai, Yiping Wu, Ziman Zhong & Yuehua Xiao

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  1. Yaohua Li
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  2. Tong Mo
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  3. Lingfang Ran
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  4. Jianyan Zeng
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  5. Chuannan Wang
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  6. Aimin Liang
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  7. Yonglu Dai
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  8. Yiping Wu
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  9. Ziman Zhong
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  10. Yuehua Xiao
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Contributions

YX conceived the study, participated in its design and modified the manuscript. YL contributed to data analysis and manuscript writing. YL, TM, LR, JZ, CW, YD, YW, ZZ collected the data from the field; YX and AL constructed RIL population. All authors have read and approved the final manuscript.

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Correspondence to Yuehua Xiao.

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Communicated by Bing Yang.

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Li, Y., Mo, T., Ran, L. et al. Genome resequencing-based high-density genetic map and QTL detection for yield and fiber quality traits in diploid Asiatic cotton (Gossypium arboreum). Mol Genet Genomics 297, 199–212 (2022). https://doi.org/10.1007/s00438-021-01848-0

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