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Identification of the domestication gene GmCYP82C4 underlying the major quantitative trait locus for the seed weight in soybean

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Abstract

Key message

A major quantitative trait locus (QTL) for the hundred-seed weight (HSW) was identified and confirmed in the two distinct soybean populations, and the target gene GmCYP82C4 underlying this locus was identified that significantly associated with soybean seed weight, and it was selected during the soybean domestication and improvement process.

Abstract

Soybean is a major oil crop for human beings and the seed weight is a crucial goal of soybean breeding. However, only a limited number of target genes underlying the quantitative trait loci (QTLs) controlling seed weight in soybean are known so far. In the present study, six loci associated with hundred-seed weight (HSW) were detected in the first population of 573 soybean breeding lines by genome-wide association study (GWAS), and 64 gene models were predicted in these candidate QTL regions. The QTL qHSW_1 exhibits continuous association signals on chromosome four and was also validated by region association study (RAS) in the second soybean population (409 accessions) with wild, landrace, and cultivar soybean accessions. There were seven genes in qHSW_1 candidate region by linkage disequilibrium (LD) block analysis, and only Glyma.04G035500 (GmCYP82C4) showed specifically higher expression in flowers, pods, and seeds, indicating its crucial role in the soybean seed development. Significant differences in HSW trait were detected when the association panels are genotyped by single-nucleotide polymorphisms (SNPs) in putative GmCYP82C4 promoter region. Eight haplotypes were generated by six SNPs in GmCYP82C4 in the second soybean population, and two superior haplotypes (Hap2 and Hap4) of GmCYP82C4 were detected with average HSW of 18.27 g and 18.38 g, respectively. The genetic diversity of GmCYP82C4 was analyzed in the second soybean population, and GmCYP82C4 was most likely selected during the soybean domestication and improvement process, leading to the highest proportion of Hap2 of GmCYP82C4 both in landrace and cultivar subpopulations. The QTLs and GmCYP82C4 identified in this study provide novel genetic resources for soybean seed weight trait, and the GmCYP82C4 could be used for soybean molecular breeding to develop desirable seed weight in the future.

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Data availability

The datasets in the current study are available in the supplementary information published online or from the corresponding authors on reasonable request.

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Funding

This work was supported by the GDAS' Project of Science and Technology Development (2022GDASZH-2022010102, 2020GDASYL-2020102011), Guangdong Basic and Applied Basic Research Foundation (2022A1515111146), Zhanjiang Science and Technology Plan Project (2022A01009), the Core Technology Development for Breeding Program of Jiangsu Province (JBGS-2021-014), Guangdong Pearl River Talents Program (2021CX02N173), and Zhanjiang innovation and entrepreneurship team ‘pilot plan’ (211207157080997).

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  1. Yang Li, Wenqian Zhao contributed equally to this work.

Authors and Affiliations

  1. Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China

    Yang Li, Jinbao Gu, Biyao Zhao, Cong Li, Yanhang Chen, Jianbo Yuan, Yan Lin & Zhen-Yu Wang

  2. National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China

    Yang Li, Wenqian Zhao, Jiajun Tang, Xiuli Yue, Yan Li & Tuan-Jie Zhao

  3. Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China

    Fanjiang Kong

  4. College of Agriculture, Guizhou University, Guiyang, China

    Jin He

  5. Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, China

    Dong Wang

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  16. Zhen-Yu Wang
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Contributions

ZW, TZ, and YL conceived and designed the research. YL and WZ conducted the experiments, with the assistance of JT, XY, JG, BZ, CL, YC, JY YL; YL, TZ, and WZ analyzed the data. TZ, FK, and ZW contributed reagents/materials; YL, WZ, YL, JH, DW, and ZW wrote and revised the manuscript. All authors read and approved the final manuscript.

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Correspondence to Tuan-Jie Zhao or Zhen-Yu Wang.

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Communicated by Dechun Wang.

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Li, Y., Zhao, W., Tang, J. et al. Identification of the domestication gene GmCYP82C4 underlying the major quantitative trait locus for the seed weight in soybean. Theor Appl Genet 137, 62 (2024). https://doi.org/10.1007/s00122-024-04571-7

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