Genome-Wide Association Study Reveals Marker-Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice

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.

Keywords: GWAS; MTAs; SNP; rice; salinity tolerance; salt stress.

Figure 1

Variation in rice germplasm for traits associated with seedling stage salinity tolerance. SL, shoot length (cm); RL, root length (cm); SFW, shoot fresh weight (g); RFW, root fresh weight (g); SDW, shoot dry weight (g); RDW, root dry weight (g); RNC, root Na⁺ content (mmol/g); SNC, shoot Na⁺ content (mmol/g); RKC, root K⁺ content (mmol/g); SKC, shoot K⁺ content (mmol/g); RNK, root Na⁺/K⁺ ratio; SNK, shoot Na⁺/K⁺ ratio.

Figure 2

Phenogram of 96 rice genotype based on salt tolerance score and 13 morpho-physiological characters recorded under salt stress.

Figure 3

Correlation coefficients among various morpho-physiological parameters under salt stress condition. Positive correlations are displayed in blue and negative correlations in red color. Color intensity and the size of the circle are proportional to the correlation coefficients. In the right side of the correlogram, the legend color shows the correlation coefficients and the corresponding colors. STS, Salinity tolerance score; SL, shoot length (cm); RL, root length (cm); SFW, shoot fresh weight (g); RFW, root fresh weight (g); SEW, seedling weight (g); SDW, shoot dry weight (g); RDW, root dry weight (g); RNC, root Na⁺ content (mmol/g); SNC, shoot Na⁺ content (mmol/g); RKC, root K⁺ content (mmol/g); SKC, shoot K⁺ content (mmol/g); RNK, root Na⁺/K⁺ ratio; SNK, shoot Na⁺/K⁺ ratio.

Figure 4

STRUCTURE analysis. (a) The ΔK value was highest for the model parameter K = 3 than for other values of K. (b) The bar plot showing each rice variety belonging to three subpopulations.

Figure 5

Manhattan plots and Q–Q plots representing the significant marker trait associations for 12 seedling salt tolerance related traits. SL, shoot length (cm); RL, root length (cm); SFW, shoot fresh weight (g); RFW, root fresh weight (g); SEW, seedling weight (g); SDW, shoot dry weight (g); RDW, root dry weight (g); RNC, root Na⁺ content (mmol/g); SNC, shoot Na⁺ content (mmol/g); SKC, shoot K⁺ content (mmol/g); RNK, root Na⁺/K⁺ ratio; SNK, shoot Na⁺/K⁺ ratio.