Genetic architecture and marker-assisted breeding for salt tolerance in soybean

Abstract

Salinity is one of the major abiotic stresses that inhibits plant growth and causes seed yield loss in soybean. Although a major gene for salt tolerance on chromosome (Chr.) 3 was mapped, cloned and characterized, it does not fully explain genetic variability for tolerance in soybean. Two mapping approaches, quantitative trait loci (QTL) mapping and genome-wide association study (GWAS), can complement each other to identify genomic regions and molecular markers associated with traits of interest. QTL mapping is more suitable to map traits governed by rare alleles in a designed population while GWAS is better in mapping traits underlined by few genes of large effect in the natural population. This study was performed to identify additional loci and new sources for salt tolerance by using both approaches. For bi-parental QTL mapping, salt tolerance of 132 F2 families was evaluated by accessing leaf scorch score (LSS), chlorophyll content ratio (CCR), leaf sodium content (LSC), and leaf chloride content (LCC). Their genotypes were obtained using the Illumina Infinium SoySNP6K BeadChip assay to map salt tolerant gene(s). A major locus significantly associated with LSS, CCR, LSC, and LCC was mapped to Chr. 3 with LOD scores of 19.1, 11.0, 7.7, and 25.6, respectively. In addition, a second locus associated with salt tolerance for LSC was also detected and mapped on Chr. 13 with a LOD score of 4.6 and an R2 of 0.115. The evaluation of salt tolerance of an F5 population derived from the same cross showed that combining salt tolerant alleles of major and minor loci significantly increased salt tolerance. On the other hand, GWAS for salt tolerance was conducted using SNPs of two datasets, SoySNP50K iSelect BeadChip and 3.7M SNP dataset (from whole-genome sequencing data), across 305 soybean accessions of a diverse panel. The known gene on Chr. 3 was confirmed by three gene-based markers (GBMs) that integrated into both datasets. Other genomic regions significantly associated with salt tolerance were identified on Chrs. 1, 2, 5, 6, 8, 14, 18, and 19 by analyzing 3.7M SNP dataset, in which the position on Chr. 8 strongly predicted a new minor locus for salt tolerance. The genotype-phenotype correlation using three GBMs discovered six new salt tolerant sources that may carry novel gene(s) for salt tolerance. By complementation tests and segregation analysis of salt tolerance among F2 plants developed from a cross of Fiskeby III and a salt tolerance accession, PI 468908, it was speculated that salt tolerance from PI 468908 was possibly controlled by a new gene instead of the known gene on Chr. 3. These significant loci in new salt tolerant sources coupled with significant SNP markers could be useful for marker-assisted selection in molecular breeding programs to improve salt tolerance in soybean.