Quantitative Trait Loci, Candidate Genes, and Breeding Lines to Improve Salt Tolerance at the Flowering and Seedling Stages in Rice

Abstract Salinity is a major environmental constraint that limits growth and productivity of rice all over the world. Although rice plants are vulnerable to salt stress at both seedling and flowering stages, genetic dissection of salt tolerance at the flowering stage is challenging due to non‐uniformity of stress application at the appropriate growth stage. The present study was conducted to identify quantitative trait loci (QTLs) and candidate genes associated with the flowering stage salt tolerance and compare with those associated with the seedling stage using a high‐resolution genetic map. A population of advanced generation introgression lines with uniform flowering time was evaluated for salt tolerance at the seedling and flowering stages. A genetic map was constructed using 14,230 polymorphic single nucleotide polymorphism markers between donor parents (TCCP and FL478) and the recurrent parent (RP) (Jupiter). Seventeen and 28 QTLs were identified for traits associated with salt tolerance at the seedling and flowering stage, respectively. Important candidate genes present in the flowering stage salt responsive QTL regions were OsHAK13, OsCYP21‐4, GIF1, and OsRGG20, whereas the seedling stage QTL intervals harbored genes such OsHAK20, STRK1, and OsMADS25. Gene expression analysis revealed upregulation of OsHAK13 and OsCYP21‐4 in TCCP, 3 days after exposure to salt stress at the flowering stage. Similarly, expression of OsHAK20, STRK1, and OsMADS25 was highly upregulated in TCCP under salt stress at the seedling stage. Due to differences in genetic control of salt tolerance at both seedling and flowering stages, stacking of genes/QTLs for salt tolerance at both stages will be needed. Since some beneficial QTLs were also contributed by the RP, emphasis should be on targeting the desirable QTLs from donors while retaining the beneficial QTLs of the RP to improve salinity tolerance in rice using marker‐assisted selection.