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. 2025 Jul 23;15(1):26826.
doi: 10.1038/s41598-025-08702-y.

Mining genetic loci and candidate genes related to salt tolerance traits in soybean

Rui Tian  1   2 , Dai Han  1   3 , Xiaolei Shi  1   2 , Qimike Shan  1   2 , Sunlei Ding  1   2 , Yucheng Wu  1   3 , Jinbo Zhang  4   5 , Yongliang Yan  6   7
Affiliations

Mining genetic loci and candidate genes related to salt tolerance traits in soybean

Rui Tian et al. Sci Rep. .

Abstract

Soybean is an important crop worldwide that provides ~ 50% oil for humans. Salinity is a major abiotic stress that inhibits soybean growth and yield. Dissecting the genetic basis of salt tolerance is an effective way for soybean plants to combat salt-related yield losses. In this study, the variety salt tolerance index (STIv) of a natural population of 140 soybean germplasms was calculated in terms of plant height (PH), leaf area (LA), shoot fresh weight (SFW) and shoot dry weight (SDW), which were measured under normal condition and in a 1.50% NaCl solution. GWAS analysis was subsequently conducted on the basis of STIv and 150 K SNP markers of "Zhongdouxin-1". The results revealed that 365 significant SNPs located on 19 chromosomes (excluding Gm03) were associated with STIv. Among them, 108 SNPs were associated with LA-STIv, 71 SNPs associated with PH-STIv, 95 SNPs associated with SDW-STIv and 91 SNPs associated with SFW-STIv. A total of 333 genes were identified according to the flanking region (150 kb) of the significant SNPs. 333 genes were identified. Based on gene functional annotations, SNP mutations, and RNA expressions, nine causal genes responsible for soybean salt tolerance were identified. Thus, the significantly associated SNPs and candidate genes detected in this study might provide novel insights into soybean salt tolerance in breeding programs.

Keywords: Candidate genes; GWAS; Salt tolerance-related traits; Soybean.

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Conflict of interest statement

Declarations. Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Population structure analysis of soybean. (a) delta K analysis. (b) LD decay analysis of the genome-wide average. (c) Phylogenetic tree analysis. (d) PCA plot of the first two components (PC1 and PC2). (e) Stack figure analysis of the population.
Fig. 2
Fig. 2
GWAS analysis of soybean salt tolerance in natural population. (a) Manhattan and QQ plots of LA-STIv. (b) Manhattan and QQ plots of PH-STIv. (c) Manhattan and QQ plots of SDW-STIv. (d) Manhattan and QQ plots of SFW-STIv.
Fig. 3
Fig. 3
Haplotype analysis of candidate genes. (a) Glyma.04G044900. (b) Glyma.10G058300. (c) Glyma.11G242200. (d) Glyma.15G263700. (e) Glyma.16G199100. (f) Glyma.19G159400. (g) Glyma.19G161100. (h) Glyma.20G128100. (i) Glyma.20G129600. Green violin: LA-STIv; blue violin: SH-STIv; red violin: SDW-STIv; purple violin: SFW-STIv. Statistical significance was assessed via a two-tailed t-test.
Fig. 4
Fig. 4
Expression pattern analysis of candidate genes. (a) Expressions levels of Glyma.04G044900 in different accessions at 0, 2, 4 and 8 h after salt stress. (b) Expressions levels of Glyma.10G058300 in different accessions at 0, 2, 4 and 8 h after salt stress. (c) Expressions levels of Glyma.11G242200 in different accessions at 0, 2, 4 and 8 h after salt stress. (d) Expressions levels of Glyma.15G263700 in different accessions at 0, 2, 4 and 8 h after salt stress. (e) Expressions levels of Glyma.16G199100 in different accessions at 0, 2, 4 and 8 h after salt stress. (f) Expressions levels of Glyma.19G159400 in different accessions at 0, 2, 4 and 8 h after salt stress. (g) Expressions levels of Glyma.19G161100 in different accessions at 0, 2, 4 and 8 h after salt stress. (h) Expressions levels of Glyma.20G128100 in diffrent accessions at 0, 2, 4 and 8 h after salt stress. (i) Expressions levels of Glyma.20G129600 in different accessions at 0, 2, 4 and 8 h after salt stress.
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