QTL analysis of Na+ and K+ concentrations in shoots and roots under NaCl stress based on linkage and association analysis in japonica rice

Soil salinity is a major constraint to rice production. Na+ and K+ concentrations and ion balance play important roles in the salt tolerance of rice. In the present study, linkage mapping and association mapping were used to identify the QTLs for the visual tolerance score (SES), and the concentrations of Na+ and K+ in shoots (SNC and SKC) and roots (RNC and RKC). A BC2F2:3 population with 137 SSR markers derived from Dongnong425 (a salt-sensitive and widely cultivated variety) as the recurrent parent and Changbai10 (a salt-tolerant variety) as the donor parent was used for linkage mapping. A total of 13 QTLs were identified by the inclusive composite interval mapping method, including 2 for SES, 4 for SNC, 3 for SKC, 3 for RNC, and 1 for RKC. This study was supplemented with association mapping, which was conducted using a panel of 341 japonica rice accessions from different geographical origins with 160 selected SSR markers. A total of 24 significant marker-trait associations (P ≤ 0.01) involving 20 markers were identified using the GLM (Q) and MLM (Q+K) models in TASSEL2.1. Among them, 10 of the SSR markers confirmed or narrowed the genomic regions for salt tolerance that were reported in linkage studies, including six QTLs identified during the present study. The QTLs identified through linkage and association mapping may be useful for marker-assisted selection in rice breeding programs and may accelerate the development of salt-tolerant rice varieties.