PCR optimization and allele distribution of SNAC1 gene coding region in rice (Oryza sativa L.)

Abstract

Drought is the most serious abiotic stress that limits crop production in rain-fed environments. In this study genetic diversity of SNAC1 gene investigated in a collection of 83 diverse rice accessions from different geographical origins. Amplification of SNAC1 gene exons was performed by combined hot start-touchdown PCR protocol. The average number of alleles was 9.5 alleles. A total of 6 rare alleles were identified from exons of SNAC1. The average gene diversity index, PIC (Polymorphism information content) and Shannon value were 0.8518, 0.8343 and 2.0469, respectively. Evolutionary study based on Ewens-Watterson test showed that exon 1 of SNAC1 gene was probability under genetic drift. To identify potential SSR markers in SNAC1 gene sequence, SSR distributions within rice SNAC1 gene sequence were mined. Totally 15 microsatellite loci were detected which tri-nucleotide motifs (8) was being most abundant, followed by di- (6) and tetra-nucleotide (1) motifs. Maximum loci were found in 3′ UTR (5) (Untranslated regions), followed by in 5′ UTR (4) and coding sequences (3 for each exon). The present study revealed genetic divergence of SNAC1 gene coding regions and also mined SSR distributions within SNAC1 gene sequence and introduced an optimized PCR method. This information can be used for the development of drought tolerant rice varieties.