Soil salinization is one of the significant factors limiting high crop yields and expansion of arable land, seriously affecting global agricultural production. Rice is an essential food crop throughout the world, and its seedlings are particularly susceptible to salt stress, which can directly affect the growth and development of rice and its final yield. We used the natural population as the material for genome-wide association study (GWAS) and the recombinant inbred line (RIL) population from CD (salt sensitive)/WD20342 (salt tolerant) hybridization as the material for linkage analysis.
The degree of salt tolerance was evaluated by using the relative root length (RRL), relative root number (RRN), relative root fresh weight (RRFW), and relative root dry weight (RRDW) as indicators. Fifteen and six major quantitative trait loci (QTLs) were identified by GWAS and linkage analysis, respectively. Meanwhile, the GWAS identified the lead SNP (Chr2_22340368), which was located within qRRL2 and qRRDW2 identified by linkage analysis. GWAS, combined with linkage analysis, selected a 196-kb overlapping region on chromosome 2, including 22 candidate genes.
The phenotypic validation indicated that