Fifteen Shades of Grey: Combined Analysis of Genome-Wide SNP Data in Steppe and Mediterranean Grey Cattle Sheds New Light on the Molecular Basis of Coat Color

Abstract

Coat color is among the most distinctive phenotypes in cattle. Worldwide, several breeds share peculiar coat color features such as the presence of a fawn pigmentation of the calf at birth, turning over time to grey, and sexual dichromatism. The aim of this study was to search for polymorphisms under differential selection by contrasting grey cattle breeds displaying the above phenotype with non-grey cattle breeds, and to identify the underlying genes. Using medium-density SNP array genotype data, a multi-cohort FST-outlier approach was adopted for a total of 60 pair-wise comparisons of the 15 grey with 4 non-grey cattle breeds (Angus, Limousin, Charolais, and Holstein), with the latter selected as representative of solid and piebald phenotypes, respectively. Overall, more than 50 candidate genes were detected; almost all were either directly or indirectly involved in pigmentation, and some of them were already known for their role in phenotypes related with hair graying in mammals. Notably, 17 relevant genes, including SDR16C5, MOS, SDCBP, and NSMAF, were located in a signal on BTA14 convergently observed in all the four considered scenarios. Overall, the key stages of pigmentation (melanocyte development, melanogenesis, and pigment trafficking/transfer) were all represented among the pleiotropic functions of the candidate genes, suggesting the complex nature of the grey phenotype in cattle.

Variants at the ASIP locus contribute to coat color darkening in Nellore cattle

“…A recent genetic divergence analysis conducted by Senczuk et al [ 10 ] compared 15 white/grey Central and Eastern European B. taurus breeds with four non-grey northwestern cattle populations and identified three loci that displayed substantial divergence between the two groups, namely CHR2:6,510,630–7,010,630, CHR14:22,531,305–25,722,332 and CHR26:22,789,524–23,289,524. However, in our study, none of these loci were associated with DHC in Nellore cattle, which could be explained by one of the following alternative hypotheses: (a) the trait investigated differed between the studies, i.e.…”

“…Senczuk and colleagues [ 10 ] performed a genetic divergence analysis in which the above-mentioned B. taurus breeds were contrasted with four non-grey northwestern cattle populations (Angus, Charolais, Limousin, and Holstein), and suggested that three loci may be linked to white/grey hair-coat: CHR2:6,510,630–7,010,630, CHR14:22,531,305–25,722,332 and CHR26:22,789,524–23,289,524 based on the ARS-UCD1.2 bovine genome assembly [ 11 ]. Holland [ 12 ] also mapped white/grey coat color in a Nellore-Angus crossbred population to chromosome 6, within a segment that harbors genes known to impact coat color such as v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog ( KIT ).…”

Genome‐wide assessment of diversity and differentiation between original and modern Brown cattle populations

“…2019; Senczuk et al . 2020a). However, although the method is the basis of many tests for genetic differentiation, it is prone to produce false positives when the populations have an unequal effective population size (Fariello et al .…”

Molecular characterization of coat color gene in Sahiwal versus Karan Fries bovine

“…These two breeds showed the intense allele frequency divergence in the MC1R region was observed by [ 51 ], which recently reported that the MC1R gene (c.871G>A) SNP can cause the mutation in brown Japanese cattle [ 52 ]. Senczuk et al reported that different grey and non-grey coat color cattle breeds [ 53 ]. The MC1R gene variant is associated with black color in Swiss Holstein cattle breed [ 54 ].…”