Genetic diversity, population structure of seven Indian domestic goat breeds based SNPs identified in CAPN1 gene

Abstract

The micromolar calcium-activated neutral protease (CAPN1) gene encodes μ-calpain that degrades myofibril proteins under the post-mortem conditions which appears to be the primary enzyme in the postmortem tenderization process, hence affecting the meat quality. Objective of this study was to analyze genetic polymorphism of the CAPN1 gene in seven diverse Indian goat breeds. Direct DNA sequencing was carried out to identify the genetic polymorphisms in 84 unrelated goats representing seven different goat breeds (Barbari, Beetal, Ganjam, Sirohi, Black Bengal, Osmanabadi and Malabari). Six single nucleotide polymorphisms (SNPs) were identified in CAPN1 gene intron 17. The observed heterozygosity (Ho) was highest (0.50) in Sirohi and Osmanabadi (0.42) breeds and lowest in Black Bengal (0.06) breed. The expected heterozygosity (He) was highest (0.45) in Sirohi followed by Osmanabadi (0.37), Barbari (0.34) and Beetal (0.37). The allele frequencies ranged from 0.083 to 0.917 and the major allele frequencies ranged from 0.595 (locus 6499 T/C) to 0.917 (locus 6529 T/C). In Black Bengal, polymorphism at all theloci was fixed with the exception of 6417 T/G and 6533C/G. The identity values oscillated from 0.7866 to 0.9593. The Nei's genetic distances were below 0.0294. Genetic diversity among different goat meat breeds indicates possible role in meat quality trait. Allelic diversity at this locus could be used in further for the association between gene polymorphism and enzyme activity as well as caprine meat quality traits.