Identification of single nucleotide polymorphisms in the agouti signaling protein (ASIP) gene in some goat breeds in tropical and temperate climates

Abstract

The agouti-signaling protein (ASIP) plays a major role in mammalian pigmentation as an antagonist to melanocortin-1 receptor gene to stimulate pheomelanin synthesis, a major pigment conferring mammalian coat color. We sequenced a 352 bp fragment of ASIP gene spanning part of exon 2 and part of intron 2 in 215 animals representing six goat breeds from Nigeria and the United States: West African Dwarf, predominantly black; Red Sokoto, mostly red; and Sahel, mostly white from Nigeria; black and white Alpine, brown and white Spanish and white Saanen from the US. Twenty haplotypes from nine mutations representing three intronic, one silent and five missense (p.S19R, p.N35K, p.L36V, p.M42L and p.L45W) mutations were identified in Nigerian goats. Approximately 89 % of Nigerian goats carry haplotype 1 (TGCCATCCG) which seems to be the wild type configuration of mutations in this region of the gene. Although we found no association between these polymorphisms in the ASIP gene and coat color in Nigerian goats, in-silico functional analysis predicts putative deleterious functional impact of the p.L45W mutation on the basic amino-terminal domain of ASIP. In the American goats, two intronic mutations, g.293G>A and g.327C>A, were identified in the Alpine breed, although the g.293G>A mutation is common to American and Nigerian goat populations. All Sannen and Sahel goats in this study belong to haplotypes 1 of both populations which seem to be the wild-type composite ASIP haplotype. Overall, there was no clear association of this portion of the ASIP gene interrogated in this study with coat color variation. Therefore, additional genomic analyses of promoter sequence, the entire coding and non-coding regions of the ASIP gene will be required to obtain a definite conclusion.

Whole-genome sequencing of eight goat populations for the detection of selection signatures underlying production and adaptive traits

“…Mutations in the MC1R gene have been associated with coat colors variation in pigs2324, cattle25, and goats26. As an antagonist to MC1R to stimulate pheomelanin synthesis, ASIP has been implicated as a strong candidate gene that controls coat color patterns in goats and sheep272829. MITF is a key regulator of melanocyte development and is associated with various coat patterns in mammals30.…”

Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data

“…This variation in coat color was highly represented in the 14 Draa samples used in this study (Table S4 ). However, previous studies focussing on this gene identified an important polymorphism in worldwide goat breeds without any clear association with differences in coat color (Badaoui et al, 2011 ; Adefenwa et al, 2013 ). Fontanesi et al ( 2009b ) reported the presence of a copy number variation (CNV) affecting ASIP and AHCY genes, and might be associated to the white color in Girgentana and Saneen breeds.…”

A Review of Challenges to Genetic Improvement of Indigenous Livestock for Improved Food Production in Nigeria

“…In addition, livestock play important roles in religious ceremonies and festivals such as marriages, naming ceremonies and traditional worship activities (Adefenwa et al, 2013a).…”