Quantitative Trait Loci Mapping, Genome-wide Association Analysis, and Gene Expression of Salt Tolerance in Soybean

Salt stress is a common abiotic stress causing yield reduction in soybean. There are differential responses, namely tolerance (excluder) and intolerance (includer), among soybean germplasm. However, the genetic and physiological mechanism for salt tolerance is not clear. Identification of novel QTL for salt tolerance and genes that are differentially expressed under salt stress would help elucidate the salt tolerance mechanism and facilitate the development of salt tolerant cultivars through marker assisted selection (MAS). The objectives of this study were to identify new QTL or genes responsible for salt tolerance using three approaches: QTL mapping, association analysis, and RNA sequencing (RNA-seq). A salt-sensitive cultivar, RA-452, was crossed with a salt-tolerant cultivar, Osage, to develop an F4-derived QTL mapping population. Composite interval mapping (CIM) analysis indicated that a major chloride (Cl-)-tolerant QTL was confirmed and narrowed down on Chr. 3 in both NaCl and KCl treatments, a novel Cl--tolerant QTL on Chr. 15 was identified in NaCl treatment, and a novel Cl--tolerant QTL on Chr. 13 was identified in KCl treatment. Based on the results from the screening of the RA-452 x Osage mapping population, two F4:6 lines with extreme responses, most tolerant and most sensitive, were selected for a time-course gene expression study. A total of 2374, 998, 1746, and 630 differentially expressed genes (DEGs) between salt-tolerant line and salt-sensitive line, were found at 0, 6, 12, and 24 h, respectively. The gene expression profiles of six genes including Glyma.02G228100, Glyma.03G031400, Glyma.04G180300, Glyma.04G180400, Glyma.05G204600, and Glyma.17G173200 were verified by qRT-PCR. In addition, a total of 283 diverse germplasm lines were obtained from the Germplasm Resource Information Network (GRIN) and screened for salt stress response in greenhouse. A total of 33,009 SNPs across 283 genotypes were employed in the association analysis with leaf chloride concentration and leaf chlorophyll concentration. Association analysis results confirmed the salt-tolerance QTL on Chr. 3 and revealed eight new putative QTL on Chr. 2, 7, 8, 10, 13, 14, 16, and 20. These QTL and linked SNP markers will be useful for MAS in breeding salt-tolerant soybean varieties.