Genetic dissection of low-sulfur tolerance via linkage and genome-wide association analyses in soybean [Glycine max (L.) Merr.] seedlings

Kaixin Zhang, Yanning Chen, Sujing Wang, Yu’e Zhang, Yudan Chen, Kaili Ren, Xiao Li, Guizhen Kan, Deyue Yu & Hui Wang

Theoretical and Applied Genetics; October 31 2025; vol. 138; article 288

Key message

Seven co-localized QTLs that control low-sulfur tolerance in soybean seedlings were identified. Two putative candidate genes and 3 promising parental cross combinations were further predicted.

Abstract

Low-sulfur nutrient stress severely affects yield and quality in soybean production. However, genetic studies related to soybean tolerance to low-sulfur conditions are insufficient. Here, soybean tolerance to low-sulfur conditions was evaluated according to ten traits at the seedling stage. A total of 72 quantitative trait loci (QTLs) and 103 quantitative trait nucleotides (QTNs) related to low-sulfur tolerance in soybean seedlings were detected via linkage analysis and genome-wide association analysis (GWAS) in a recombinant inbred line (RIL) population and a natural population, respectively. Among these loci, 7 co-localized QTLs were identified via two methods across chromosomes 1, 6, 8, 9, 14, and 17. Glyma.17G167100, which includes two significant SNPs (AX-93862060 and AX-93862061), and Glyma.14G169300 were suggested as putative candidate genes on the basis of transcriptome data, haplotype analysis and real-time quantitative PCR. In addition, 3 promising parental cross combinations with the aim of improving low-sulfur tolerance have been designed across favorable alleles, which were determined on the basis of the co-localized QTLs and relative values of trait phenotypes in three environments. These results provide important evidence for understanding the genetic basis of low-sulfur tolerance in soybean and may be helpful in the breeding of new soybean varieties with high tolerance to low-sulfur soil.

See https://link.springer.com/article/10.1007/s00122-025-05078-5