Identification of SNP and Analysis of Haplotype for the Salt Tolerant Genes In Rice Mutant Lines.

Single nucleotide polymorphism (SNP) is useful marker for the detection of associations between allelic forms of a gene and phenotypes. The analysis of SNP haplotypes, rather than the individual SNPs, provides a more effective way of associating alleles with traits. In order to identify the sequence variation of salt stress responsive genes related to SSR locus, 20 genes were sequenced in 23 rice mutant lines and their original variety Dongan. The length of genes ranged from 915bp to 7011bp. In the analysis of sequence variations, the total 21 clones generated 516 SNPs. Plasma membrane ATPase 1 generated 90 SNPs and 110 SNPs were discovered in potassium transporter 12. Seventy five SNPs were detected in ATPase/ABC transporter. The highest number of SNPs(134) was generated in peptidyl-prolyl cis-trans isomerase which plays a various roles in plant such as protein folding, calcium modulated signal transduction pathway(s), wound stress and temperature stress. These four genes generated 409 SNPs which accounted for 79% of all. Other 10 genes generated only 107 SNPs. Sequence variations of exon and intron were examined in sequenced genes excluding 5’- and 3’-untranslated region in order to identify the SNPs variation. Five clones displayed SNPs in both exon and intron and 9 clones showed SNPs only in exon or intron. Out of 9 clones concatenated, OSA25 displayed the most various haplotype in all mutant lines. Especially, DM4 and DM5 showed higher variation than any other lines and quietly different haplotype. Out of 516 SNPs, 8 SNPs showed significance based on p-value(<0.05) and R²(>0.1). Although these SNPs were located in intron region, they have a possibility as a marker for detecting salt tolerant traits.

Key words: salt tolerant, SNP, haplotype