Identification of genes involving in salt tolerance using GWAS data based on Na+ content in local Thai rice leaves
DOI:
https://doi.org/10.14456/gag.2017.5Keywords:
Genome-Wide Association Study, Na /K ratio, Salt stress, QTL, Arabidopsis mutant linesAbstract
High salinity is one of the most abiotic stresses that can adversely affect plant growth, development and productivity in rice for rice grown in the Northeastern part of Thailand. To overcome this problem and improve crop yield under salt stress conditions, it is important to improve salt tolerance in crops. This research aims to validate if the SNPs predicted by Genome-Wide Association Study (GWAS) is consistent with the QTL for salt tolerant trait that was previously reported. GWAS based on Na+ content in leaf tissues of local Thai rice varieties after six days of salt stress revealed the involvement of SNPs from 10 loci, located on chromosome 1, 2, 5, 10, 11 and 12. Five loci are in the reported salt tolerant QTL. To determine if these loci contributing to salt tolerant phenotype, the orthologous genes in Arabidopsis were used as the representatives. Homozygous Arabidopsis mutant lines, each of which contains the T-DNA in the orthologous genes of the predicted loci, were analyzed in comparison with wild type for the physiological responses, fresh weight, dry weight, chl a, chl b and carotenoids contents, after 7 days of 250 mM NaCl treatment. All of the mutant lines had the significant lower level of chl a and chl b content in normal condition, while under salt stress condition, all of them showed the significant difference in stability index of photosynthetic pigment contents. These indicate that all of these genes are involved in salt tolerance, which implies the impact of the predicted loci from GWAS in salt tolerant ability of rice. Our data show the consistency between GWAS and QTL studies and GWAS can be used to identify the precise loci that are responsible for the trait of interest.References
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