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Genetic dissection of lint percentage in short-season cotton using combined QTL mapping and RNA-seq

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Abstract

Key message

In total, 17 QTLs for lint percentage in short-season cotton, including three stable QTLs, were detected. Twenty-eight differentially expressed genes located within the stable QTLs were identified, and two genes were validated by qRT-PCR.

Abstract

The breeding and use of short-season cotton have significant values in addressing the question of occupying farmlands with either cotton or cereals. However, the fiber yields of short-season cotton varieties are significantly lower than those of middle- and late-maturing varieties. How to effectively improve the fiber yield of short-season cotton has become a focus of cotton research. Here, a high-density genetic map was constructed using genome resequencing and an RIL population generated from the hybridization of two short-season cotton accessions, Dong3 and Dong4. The map contained 4960 bin markers across the 26 cotton chromosomes and spanned 3971.08 cM, with an average distance of 0.80 cM between adjacent markers. Based on the genetic map, quantitative trait locus (QTL) mapping for lint percentage (LP, %), an important yield component trait, was performed. In total, 17 QTLs for LP, including three stable QTLs, qLP-A02, qLP-D04, and qLP-D12, were detected. Three out of 11 non-redundant QTLs overlapped with previously reported QTLs, whereas the other eight were novel QTLs. A total of 28 differentially expressed genes associated with the three stable QTLs were identified using RNA-seq of ovules and fibers at different seed developmental stages from the parental materials. The two genes, Ghir_A02G017640 and Ghir_A02G018500, may be related to LP as determined by further qRT-PCR validation. This study provides useful information for the genetic dissection of LP and promotes the molecular breeding of short-season cotton.

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Data availability

The data were deposited in the NCBI database. The genome resequencing is under accessions BioProject PRJNA917106 and BioSample SAMN32527284, and the RNA-sequencing is under accessions BioProject PRJNA917106 and BioSample SAMN32546507.

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Funding

This study was funded by the National Natural Science Foundation of China (31671743, 32201763), the Key Research and Development Program of the Xinjiang Production and Construction Corps (2021AB010), and the Fundamental Research Project of Shanxi Province (20210302123081).

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Authors and Affiliations

  1. School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China

    Qiao Liu, Yuanyuan Wang, Yuanzhi Fu, Qinglian Wang & Runrun Sun

  2. Life Science College, Yuncheng University, Yuncheng, 044000, China

    Lei Du, Yilin Zhang & Chengqi Li

  3. Shihezi Academy of Agricultural Sciences, Shihezi, 832000, China

    Nijiang Ai & Guoli Feng

Authors
  1. Qiao Liu
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  2. Yuanyuan Wang
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  4. Lei Du
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  5. Yilin Zhang
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  10. Chengqi Li
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Contributions

CQL designed the experiments. QL, YYW, QLW, LD, NJA, and GLF performed field trials and data analyses. YYW and RRS prepared cotton DNA and RNA samples. YZF and YLZ contributed to performing RNA-seq and qRT-PCR experiments. QL and CQL performed QTL mapping and drafted the manuscript. CQL revised the manuscript. All the authors read and approved the final manuscript.

Corresponding author

Correspondence to Chengqi Li.

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The authors declare that there are no conflicts of interest in the reported research.

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The authors note that this research was performed and reported in accordance with ethical standards of scientific conduct.

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Communicated by Tianzhen Zhang.

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Liu, Q., Wang, Y., Fu, Y. et al. Genetic dissection of lint percentage in short-season cotton using combined QTL mapping and RNA-seq. Theor Appl Genet 136, 205 (2023). https://doi.org/10.1007/s00122-023-04453-4

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