Genome-wide association analysis and genomic prediction of salt tolerance trait in soybean germplasm

Rongqing Xu; Qing Yang; Zhi Liu; Xiaolei Shi; Xintong Wu; Yuehan Chen; Xinyu Du; Qiqi Gao; Di He; Ainong Shi; Peijun Tao; Long Yan

doi:10.3389/fpls.2024.1494551

Genome-wide association analysis and genomic prediction of salt tolerance trait in soybean germplasm

Front Plant Sci. 2024 Nov 18:15:1494551. doi: 10.3389/fpls.2024.1494551. eCollection 2024.

Authors

Rongqing Xu^#^{1

2}, Qing Yang^#¹, Zhi Liu¹, Xiaolei Shi¹, Xintong Wu¹, Yuehan Chen¹, Xinyu Du^{1

2}, Qiqi Gao¹, Di He¹, Ainong Shi³, Peijun Tao², Long Yan¹

Affiliations

¹ Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China.
² College of Agronomy, Hebei Agricultural University, Baoding, China.
³ Department of Horticulture, University of Arkansas, Fayetteville, AR, United States.

^# Contributed equally.

Abstract

Introduction: Soybean is an important protein and oil crop, and improving yield has traditionally been a major breeding goal. However, salt stress is an important abiotic factor that can severely impair soybean yield by disrupting metabolic processes, inhibiting photosynthesis, and hindering plant growth, ultimately leading to a decrease in productivity.

Methods: This study utilized phenotypic and genotypic data from 563 soybean germplasms sourced from over 20 countries. Employing four distinct models-we performed a genome-wide association study (GWAS) using four models, including MLM, MLMM, FarmCPU, and BLINK in GAPIT 3, we conducted a Genome-Wide Association Study (GWAS) to identify single nucleotide polymorphism (SNP) associated with salt tolerance in soybean. Subsequently, these identified SNP were further analyzed for candidate gene discovery. Using 34,181 SNPs for genomic prediction (GP) to assess prediction accuracy.

Results: Our study identified 10 SNPs significantly associated with salt tolerance, located on chromosomes 1, 2, 3, 7, and 16. And we identified 11 genes within a 5 kb window upstream and downstream of the QTLs on chromosomes 1, 3, and 16. Utilizing the GWAS-derived SNP marker sets for genomic prediction (GP) yielded r-values greater than 0.35, indicating a higher level of accuracy. This suggests that genomic selection for salt tolerance is feasible.

Discussion: The 10 identified SNP markers and candidate genes in this study provide a valuable reference for screening and developing salt-tolerant soybean germplasm resources.

Keywords: genome-wide association study; genomic prediction; germplasm; salt stress; soybean.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This study is supported by China Agriculture Research System of MOF and MARA (CARS-04-PS06), the National Key Research and Development Program (2023YFD2301505), Hebei Agriculture Research System (HBCT2023040101), Introduction and Screening of Soybean Germplasm Resources in Bashang, coupled with the Breeding of Novel Varieties (2023KJCXZX-LYS-23), Scientific and Technological Innovation Talent Team Construction (C24R0302; C24R0308).