QTL Detection of Salt Tolerance at Soybean Seedling Stage Based on Genome-Wide Association Analysis and Linkage Analysis

• Published in: Plants (Basel) Vol. 13; no. 16; p. 2283
• Main Authors: Sun, Maolin, Zhao, Tianxin, Liu, Shuang, Han, Jinfeng, Wang, Yuhe, Zhao, Xue, Li, Yongguang, Teng, Weili, Zhan, Yuhang, Han, Yingpeng
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 16-08-2024; MDPI
• Subjects: Abiotic stress; Association analysis; Biomass; Chlorophyll; Chromosomes; Gene mapping; Genetic analysis; Genomes; Genomic analysis; Genotypes; Germplasm; GWAS; Inbreeding; Land use; Leaves; Linkage analysis; molecular marker; Phenotypic variations; Plant breeding; Population studies; Quantitative trait loci; Salinity tolerance; Salt; Salt tolerance; Seedlings; Single-nucleotide polymorphism; soybean; Soybeans; soybean; salt tolerance; GWAS; linkage analysis; molecular marker
• ISSN: 2223-7747; 2223-7747
• DOI: 10.3390/plants13162283

The utilization of saline land is a global challenge, and cultivating salt-tolerant soybean varieties is beneficial for improving the efficiency of saline land utilization. Exploring the genetic basis of salt-tolerant soybean varieties and developing salt-tolerant molecular markers can effectively promote the process of soybean salt-tolerant breeding. In the study, the membership function method was used to evaluate seven traits related to salt tolerance and comprehensive salt tolerance at the soybean seedling stage; genome-wide association analysis (GWAS) was performed in a natural population containing 200 soybean materials; and linkage analysis was performed in 112 recombinant inbred lines (RIL) population to detect quantitative trait loci (QTLs) of salt tolerance. In the GWAS, 147 SNPs were mapped, explaining 5.28-17.16% of phenotypic variation. In the linkage analysis, 10 QTLs were identified, which could explain 6.9-16.16% of phenotypic variation. And it was found that there were two co-located regions between the natural population and the RIL population, containing seven candidate genes of salt tolerance in soybean. In addition, one colocalization interval was found to contain qZJS-15-1, rs47665107, and rs4793412, all of which could explain more than 10% of phenotypic variation rates, making it suitable for molecular marker development. The physical positions of rs47665107 and rs47934112 were included in qZJS-15-1. Therefore, a KASP marker was designed and developed using Chr. 15:47907445, which was closely linked to the qZJS-15-1. This marker could accurately and clearly cluster the materials of salt-tolerant genotypes in the heterozygous population tested. The QTLs and KASP markers found in the study provide a theoretical and technical basis for accelerating the salt-tolerant breeding of soybean.