Analyzing allelic variation, association mapping and development of gene specific markers for salinity tolerance in rice (Oryza sativa L.)
2012
Thein, S.Z.M.
Through screening of more than 260 Oryza sativa accession under salinity stress (NaCl 120mM for two weeks) at young seedling stage, a diverse spectrum of genotypes towards salt stress was observed. GoldenGate genotyping of the rice accessions using a 384 SNP set identified two distinct clusters of genotypes and several subgroups within indica. A moderate level of genetic diversity and varying levels of salt tolerance were observed among the accessions, indicating their usefulness for association mapping. Candidate gene analysis for Na sup +/Ca sup 2+ exchanger, K sup + efflux antiporter and potassium channel by EcoTILLING identified SNP haplotypes among contrasting genotypes. Sequencing results suggest that the gene encoding Na sup +/Ca sup 2+ exchanger is important for salinity tolerance. Candidate gene association mapping with trait specific markers using Fluidigm SNP genotyping assays revealed that SKCI and the potassium transporter are significantly associated with standard evaluation score (SES) for salinity. Genome-wide association mapping also showed unlinked marker id3011383 followed by SKC1H184R (SKC1) and TBGU384396 (potassium transporter) as being significantly associated with SES. Moreover, markers id3011383 and SKC1 are significantly associated with SES in all subpopulations. Thus, these markers should be useful in marker-assisted selection. Validation of candidate genes using PT-PCR reveals that SKC1 and Na sup +/Ca sup 2+ exchanger are highly expressed in shoots of a salt tolerant genotype over time. This suggests that SKC1 and Na sup +/Ca sup 2+ exchanger are highly important for salinity tolerance in rice.
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