Identification of polymorphisms in melanocortin 1 receptor gene and their association with coat color variants in Black Bengal goat

Abstract

The aim of this study was to identify polymorphisms in the entire coding regions of the Melanocortin 1 Receptor (MC1R) gene and their possible associations with coat color variants of the Black Bengal goat (BBG) of Bangladesh. Forty blood samples representing five distinct color variants of BBG (Solid Black, Toggenburg, Dutch Belt, White and Brown) were collected from Bangladesh Livestock Research Institute, Savar, Dhaka. Two PCR amplicons that harbored entire coding region were sequenced both forward and reverse directions. Multiple sequence alignment identified four single nucleotide polymorphisms (SNPs) based on Capra hircus reference sequence (MT186778.1). Among them, only one was identified as synonymous type (c.183C>T; p.61A) and the remaining three were non-synonymous in nature (c.676A>G, c.748G>T, and c.801C>G), causing amino acid substitutions as p.K226E, p.V250F, and p.C267W, respectively. Twelve haplotypes were defined by four substitutions where four haplotypes (Hap6, Hap7, Hap8, and Hap9) were found white-color goat-specific involving c.801C>G mutation that might be associated with white coat color phenotype of BBG. Furthermore, white goats had the highest haplotype (0.879±0.08) and nucleotide diversity (0.0017±0.0002). The UPGMA phylogenetic tree revealed two separate clusters, one of which included all color variants of BBG and major domestic goat populations (Capra hircus) from various countries. The haplotype sharing features suggest that the coat color phenotypes of BBG were not solely attributable to the MC1R gene. However, more detailed investigation with large samples from diverse populations across the country was required to draw a precise conclusion.