QTL mapping for root traits and shoot photosynthesis under salinity stress in rice seedling

To increase the yield production, the crops may have to grow in the harsh environment. Salinity is one of the major abiotic stresses, and rice is very sensitive to increasing salts. In this study, we evaluated three different root types performance in South East Asia rice varieties, total sixteen loci were detected using genome-wide association mapping (GWAS), and two were found in previous study. In addition, chlorophyll fluorescence was used to measure the leaf photosynthesis rate under salt stress. The pilot experiment showed the effective PSII quantum yield (ΦPSII) on day 9 and Injury score (IS) on day 11 was moderately correlated (r = -0.588), suggesting the damage level of leaf photosynthesis rate and its repairing mechanism may be crucial for salinity tolerance in rice. Total 32 significant loci were detected by GWAS in five chlorophyll fluorescence related traits. Among these loci, two genes OsNHX3 and OsCBL4 related to salinity tolerance mechanisms were detected in the candidate regions. Finally, we analyzed root and shoot traits in diverse accessions and found that performance of shoot and root is independent under salt stress We expect these varieties could be used to improve salt tolerance through QTLs pyramiding approach in rice breeding program.