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Genetic dissection of ten photosynthesis-related traits based on InDel- and SNP-GWAS in soybean

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Abstract

Key message

A total of 416 InDels and 112 SNPs were significantly associated with soybean photosynthesis-related traits. GmIWS1 and GmCDC48 might be related to chlorophyll fluorescence and gas-exchange parameters, respectively.

Abstract

Photosynthesis is one of the main factors determining crop yield. A better understanding of the genetic architecture for photosynthesis is of great significance for soybean yield improvement. Our previous studies identified 5,410,112 single nucleotide polymorphisms (SNPs) from the resequencing data of 219 natural soybean accessions. Here, we identified 634,106 insertions and deletions (InDels) from these 219 accessions and used these InDel variations to perform principal component and linkage disequilibrium analysis of this population. The genome-wide association study (GWAS) were conducted on six chlorophyll fluorescence parameters (chlorophyll content, light energy absorbed per reaction center, quantum yield for electron transport, probability that a trapped exciton moves an electron into the electron transport chain beyond primary quinone acceptor, maximum quantum yield of photosystem II primary photochemistry in the dark-adapted state, performance index on absorption basis) and four gas-exchange parameters (intercellular carbon dioxide concentration, stomatal conductance, net photosynthesis rate, transpiration rate) and revealed 416 significant InDels and 112 significant SNPs. Based on GWAS results, GmIWS1 (encoding a transcription elongation factor) and GmCDC48 (encoding a cell division cycle protein) with the highest expression in the mapping region were determined as the candidate genes responsible for chlorophyll fluorescence and gas-exchange parameters, respectively. Further identification of favorable haplotypes with higher photosynthesis, seed weight and seed yield were carried out for GmIWS1 and GmCDC48. Overall, this study revealed the natural variations and candidate genes underlying the photosynthesis-related traits based on abundant phenotypic and genetic data, providing valuable insights into the genetic mechanisms controlling photosynthesis and yield in soybean.

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Data availability

The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

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Funding

This work was supported in partly by the Major Project in Agricultural Biological Breeding (2022ZD0400701), the National Natural Science Foundation of China (32090065, 32301831, 31871649, 32072080, 32101742), the National Key Research and Development Program of China (2021YFF1001204), Jiangsu Agriculture Science and Technology Innovation Fund [CX(22)2003], Hainan Yazhou Bay Seed Lab (B23YQ1503, B23CQ153P), the China Postdoctoral Science Foundation (2022M721656) and the Bioinformatics Center of Nanjing Agricultural University.

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Authors and Affiliations

  1. National Center for Soybean Improvement, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China

    Dezhou Hu, Yajun Zhao, Lixun Zhu, Xiao Li, Xuan Cui, Wenlong Li, Zhongyi Yang, Fei Wu, Shupeng Dong, Xiaoyue Su, Fang Huang & Deyue Yu

  2. College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China

    Dezhou Hu

  3. Henan Collaborative Innovation Center of Modern Biological Breeding, School of Agriculture, Henan Institute of Science and Technology, Xinxiang, 453003, China

    Jinyu Zhang

  4. Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, 226012, China

    Derong Hao

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  1. Dezhou Hu
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  2. Yajun Zhao
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  3. Lixun Zhu
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  4. Xiao Li
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  12. Xiaoyue Su
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  13. Fang Huang
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  14. Deyue Yu
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Contributions

DY and FH designed this research; D Hu and XL conducted the GWAS; D Hu, YZ, LZ, JZ, XC, WL, D Hao and ZY performed the field experiments and collected the phenotypic data; D Hu, FW, SD and XS conducted the haplotype analysis; D Hu, XL and DY wrote this manuscript. All authors approved this manuscript.

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Correspondence to Fang Huang or Deyue Yu.

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Hu, D., Zhao, Y., Zhu, L. et al. Genetic dissection of ten photosynthesis-related traits based on InDel- and SNP-GWAS in soybean. Theor Appl Genet 137, 96 (2024). https://doi.org/10.1007/s00122-024-04607-y

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