SNP mining in transcripts and concomitant estimation of genetic variation in Macrobrachium rosenbergii stocks

Macrobrachium rosenbergii is an aquaculture species of global importance whose production has sharply declined since 2005. Single nucleotide polymorphisms (SNPs) in transcribed sequences are likely to have high association with economic traits and are important for marker assisted selection. SNPs were mined in 34 reported transcripts from 4 wild M. rosenbergii stocks of India using the amplicon approach and high-throughput sequencing platforms. Out of 320 SNPs detected, 134 were common to all stocks while 3 were diagnostic. Pair-wise Nei’s genetic distances (0.304–0.469) showed phylogeny consistent with geographical distribution. AMOVA analysis revealed estimated variance of 21.5 among populations. The transition to transversion ratio was 2.20. Changes in amino acid classes and peptide stability were recorded for 80 non-synonymous SNPs while change in codon preference was noted for 138 synonymous ones. Four pathogen defence genes were highly polymorphic, of which lectin 3 had the highest SNP rate (6 SNPs/100 bp). This approach for mining SNPs and using them for population differentiation in a single step is reported for the first time.