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The key to plant survival under NaCl salt stress is maintaining a low Na +  level or Na + /K +  ratio in the cells. A population of recombinant inbred lines (RILs, F 2∶9 ) derived from a cross between the salt-tolerant  japonica  rice variety Jiucaiqing and the salt-sensitive  indica  variety IR26, was used to determine Na +  and K +  concentrations in the roots and shoots under three different NaCl stress conditions (0, 100 and 120 mM NaCl). A total of nine additive QTLs were identified by QTL Cartographer program using single-environment phenotypic values, whereas eight additive QTLs were identified by QTL IciMapping program. Among these additive QTLs, five were identified by both programs. Epistatic QTLs and QTL-by-environment interactions were detected by QTLNetwork program in the joint analyses of multi-environment phenotypic values, and one additive QTL and nine epistatic QTLs were identified. There were three epistatic QTLs identified for Na +  in roots (RNC), three additive QTLs and two epistatic QTLs identified for Na +  in shoots (SNC), four additive QTLs identified for K +  in roots (RKC), four additive QTLs and three epistatic QTLs identified for K +  in shoots (SKC) and one additive QTL and one epistatic QTL for salt tolerance rating (STR). The phenotypic variation explained by each additive, epistatic QTL and QTL×environment interaction ranged from 8.5 to 18.9%, 0.5 to 5.3% and 0.7 to 7.5%, respectively. By comparing the chromosomal positions of these additive QTLs with those previously identified, five additive QTLs,  qSNC9 ,  qSKC1 ,  qSKC9 ,  qRKC4  and  qSTR7 , might represent novel salt tolerance loci. The identification of salt tolerance in selected RILs showed that a major QTL  qSNC11  played a significant role in rice salt tolerance, and could be used to improve salt tolerance of commercial rice varieties with marker-assisted selection (MAS) approach.

QTL Analysis of Na+ and K+ Concentrations in Roots and Shoots under Different Levels of NaCl Stress in Rice (Oryza sativa L.)