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, 22 (2), 133-45

Genome-wide Association Mapping of Salinity Tolerance in Rice (Oryza Sativa)

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Genome-wide Association Mapping of Salinity Tolerance in Rice (Oryza Sativa)

Vinod Kumar et al. DNA Res.

Abstract

Salinity tolerance in rice is highly desirable to sustain production in areas rendered saline due to various reasons. It is a complex quantitative trait having different components, which can be dissected effectively by genome-wide association study (GWAS). Here, we implemented GWAS to identify loci controlling salinity tolerance in rice. A custom-designed array based on 6,000 single nucleotide polymorphisms (SNPs) in as many stress-responsive genes, distributed at an average physical interval of <100 kb on 12 rice chromosomes, was used to genotype 220 rice accessions using Infinium high-throughput assay. Genetic association was analysed with 12 different traits recorded on these accessions under field conditions at reproductive stage. We identified 20 SNPs (loci) significantly associated with Na(+)/K(+) ratio, and 44 SNPs with other traits observed under stress condition. The loci identified for various salinity indices through GWAS explained 5-18% of the phenotypic variance. The region harbouring Saltol, a major quantitative trait loci (QTLs) on chromosome 1 in rice, which is known to control salinity tolerance at seedling stage, was detected as a major association with Na(+)/K(+) ratio measured at reproductive stage in our study. In addition to Saltol, we also found GWAS peaks representing new QTLs on chromosomes 4, 6 and 7. The current association mapping panel contained mostly indica accessions that can serve as source of novel salt tolerance genes and alleles. The gene-based SNP array used in this study was found cost-effective and efficient in unveiling genomic regions/candidate genes regulating salinity stress tolerance in rice.

Keywords: genome-wide association study; infinium genotyping assay; rice; salt tolerance; single-nucleotide polymorphism.

Figures

Figure 1.
Figure 1.
Distribution of 6,000 SNPs in known abiotic and biotic stress-responsive and unknown expressed rice genes on 12 rice chromosomes. Physical distance (kb) between adjacent SNP loci varied from 16 kb in chromosome 3 to 98 kb in chromosome 11 with an average of 51 kb.
Figure 2.
Figure 2.
Functional annotation of 6,000 SNPs in known abiotic and biotic stress-responsive and unknown expressed rice genes distributed over 12 rice chromosomes.
Figure 3.
Figure 3.
Population structure of current association panel which consisted mostly of the indica accessions. (A) Scree plot from GAPIT showing the selection of PCs for association study. (B) PCA plot of first two components. (C) Bayesian clustering of 220 rice accessions using STRUCTURE program.
Figure 4.
Figure 4.
Comparison of LD patterns and LD decay in the whole panel and subgroups. The whole genome r2 values from PLINK are first sorted considering distance, and then divided into 100 blocks of 20 kb. The r2 values in each block are averaged and plotted against the genetic distance for different subgroups.
Figure 5.
Figure 5.
Summary of percentage of variance explained by significant loci in the study. The x-axis represents the trait, and the y-axis shows the contribution (%) of significant loci. The label on the top of average bar is the total number of significant SNPs for respective trait.
Figure 6.
Figure 6.
Manhattan plot (A) and corresponding quantile–quantile plots (B) of P-values analysed using CMLM approach for Na+/K+ ratio under stress.
Figure 7.
Figure 7.
Chromosome view of significant associations, identified for Na+/K+ ratio under stress. The alongside colour-coded graphs are representing MAF, P-value and r2 of significant SNPs from the respective chromosomes.

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