Identification and genotyping of SNPs in RKM1 and RKM4 genes of Sordaria fimicola

Single nucleotide polymorphisms (SNPs) are one of the most common and abundant class of molecular markers present in the genome of many organisms. The current study represents the first attempt to investigate the natural variations in the RK-MTases genes; Ribosomal N-lysine methyltransferase1 (RKM1) and Ribosomal N-lysine methyltransferase4 (RKM4) in Sordaria fimicola using SNP markers. A total seven SNPs in the RKM1 gene and nine in RKM4 gene were identified. A subset of SNPs were unique in SFS strains and others were fixed in the NFS strains of S. fimicola. These polymorphisms might be adaptive in stressful environmental conditions. Genotyping of eight SNPs of RK-MTases genes of S. fimicola was accomplished by designing allele specific primers via amplification refractory mutation system–PCR (ARMS-PCR) yielding amplicons of different sizes. This study concluded that SNP markers are an efficient and informative marker system in S. fimicola. Most of the studied SNPs are non-synonymous substitutions, which might underpin functional differences in their protein products.