Genetic structure, linkage disequilibrium and association mapping of salt tolerance in japonica rice germplasm at the seedling stage

Soil salinity is a major constraint to rice production. Understanding the genetic basis of salt tolerance is crucial for the improvement of salt tolerance through breeding. Previous quantitative trait locus (QTL) studies for salt tolerance were mainly derived from bi-parental segregating populations and relatively little is known about the results from natural populations. Understanding the genetic diversity, population structure and linkage disequilibrium (LD) in an association panel can effectively avoid spurious associations in association mapping. In this study, 341 japonica rice (Oryza sativa L. subsp. japonica) accessions worldwide were genotyped with 160 simple sequence repeat (SSR) markers to identify marker-trait associations with salt tolerance at the seedling stage. Salt tolerance was evaluated by survival days of seedlings and shoot K+/Na+ ratio. A total of 872 alleles ranging from 2 to 9 per locus were identified from all collections. Population structure analysis identified three main subpopulations for the accessions. Of the SSR pairs in these accessions, 40.05 % marker pairs showed significant LD (P < 0.01). The LD level for linked markers is significantly higher than that for unlinked markers, and LD level was elevated when the panel was classified into subpopulations. The LD decayed to the background at approximately 20-50 cM within the total panel and each subpopulation. A total of ten marker loci associated with salt tolerance were identified using MLM (Q + K) models in TASSEL 3.0. Among which nine marker loci confirmed or narrowed the genomic region reported to harbor QTLs for salt tolerance by linkage mapping in previous reports, and four salt tolerance-related genes were located in the QTL regions in the present study. According to phenotypic effects for alleles of the detected QTLs, favorable alleles were mined. These favorable alleles could be used to design parental combinations and the expected results would be obtained by pyramiding or substituting the favorable alleles per QTL (apart from possible epistatic effects). Our results demonstrate that association mapping can complement and enhance previous QTL information for marker-assisted selection and breeding by design.