Abstract
Rice germplasm is a rich resource for discovering genes associated with salt tolerance. In the current study, a set of 96 accessions were evaluated for seedling stage salinity tolerance and its component traits. Significant phenotypic variation was observed among the genotypes for all the measured traits and eleven accessions with high level of salt tolerance at seedling stage were identified. The germplasm set comprised of three sub-populations and genome-wide association study (GWAS) identified a total of 23 marker–trait associations (MTAs) for traits studied. These MTAs were located on rice chromosomes 1, 2, 5, 6, 7, 9, and 12 and explained the trait phenotypic variances ranging from 13.98 to 29.88 %. Twenty-one MTAs identified in this study were located either in or near the previously reported quantitative trait loci (QTLs), while two MTAs namely, qSDW2.1 and qSNC5 were novel. A total of 18 and 13 putative annotated candidate genes were identified in a genomic region spanning ~200 kb around the MTAs qSDW2.1 and qSNC5, respectively. Some of the important genes underlying the novel MTAs were OsFBA1, OsFBL7, and mTERF which are known to be associated with salinity tolerance in crops. These MTAs pave way for combining salinity tolerance with high yield in rice genotypes through molecular breeding.
Highlights
Rice (Oryza sativa L.) is cultivated in ~114 countries with an annual production of~755 million tons [1]
The present study aims at screening rice germplasm for seedling stage salinity tolerance to identify tolerant cultivars and marker–trait associations (MTAs) governing salinity tolerance
Significant phenotypic variation was observed among the genotypes for all 14 salinity tolerance related traits recorded in the current study (Supplementary Table S1)
Summary
Rice (Oryza sativa L.) is cultivated in ~114 countries with an annual production of. ~755 million tons [1]. Saltol a major QTL for seedling stage salinity tolerance from landrace Pokkali was identified on chromosome 1 which regulates shoot Na+ /K+ under salt stress [17,20,24]. Association mapping was successful in identifying the genomic regions for various salt-tolerance related traits viz., stress susceptibility indices of the vigor index, germination time, Na+ and K+ contents in shoot and root, net photosynthetic rate, seedling length ratio, fresh and dry weight ratio in various growth stages [36,37,38,39,40]. The present study aims at screening rice germplasm for seedling stage salinity tolerance to identify tolerant cultivars and MTAs governing salinity tolerance These donors and MTAs can be utilized in breeding programs to develop varieties with tolerance to salinity through marker assisted selection
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