Abstract
BackgroundNellore cattle (Bos indicus) are well-known for their adaptation to warm and humid environments. Hair length and coat color may impact heat tolerance. The Nellore breed has been strongly selected for white coat, but bulls generally exhibit darker hair ranging from light grey to black on the head, neck, hump, and knees. Given the potential contribution of coat color variation to the adaptation of cattle populations to tropical and sub-tropical environments, our aim was to map positional and functional candidate genetic variants associated with darkness of hair coat (DHC) in Nellore bulls.ResultsWe performed a genome-wide association study (GWAS) for DHC using data from 432 Nellore bulls that were genotyped for more than 777 k single nucleotide polymorphism (SNP) markers. A single major association signal was detected in the vicinity of the agouti signaling protein gene (ASIP). The analysis of whole-genome sequence (WGS) data from 21 bulls revealed functional variants that are associated with DHC, including a structural rearrangement involving ASIP (ASIP-SV1). We further characterized this structural variant using Oxford Nanopore sequencing data from 13 Australian Brahman heifers, which share ancestry with Nellore cattle; we found that this variant originates from a 1155-bp deletion followed by an insertion of a transposable element of more than 150 bp that may impact the recruitment of ASIP non-coding exons.ConclusionsOur results indicate that the variant ASIP sequence causes darker coat pigmentation on specific parts of the body, most likely through a decreased expression of ASIP and consequently an increased production of eumelanin.
Highlights
Nellore cattle (Bos indicus) are well-known for their adaptation to warm and humid environments
Since coat color variation may contribute to the adaptation of cattle populations to tropical and sub-tropical environments, and given the interesting complexity of the coat color phenotype in the Nellore breed, our aim was to map positional and functional candidate genetic variants associated with darkness of hair coat (DHC) in Nellore bulls
The most significant single nucleotide polymorphism (SNP), namely g.13:63,629,244A>G, had an alternative allele frequency of 48.1% in our sample, and was located approximately 33.5 kb upstream of the agouti signaling protein gene (ASIP) gene (Fig. 1b). This genome-wide association study (GWAS) hit disappeared when we repeated the analysis by including this SNP as a fixed effect, which indicated that the signal was most likely driven by a single underlying causal variant or haplotype
Summary
Nellore cattle (Bos indicus) are well-known for their adaptation to warm and humid environments. The Nellore breed has been strongly selected for white coat, but bulls generally exhibit darker hair ranging from light grey to black on the head, neck, hump, and knees. Given the potential contribution of coat color variation to the adaptation of cattle populations to tropical and sub-tropical environments, our aim was to map positional and functional candidate genetic variants associated with darkness of hair coat (DHC) in Nellore bulls. Nellore cattle have black skin with cows presenting a near-white hair coat and bulls generally exhibiting darker hair ranging from light grey to black, especially on the head, neck, hump, and knees. This observation points to sex as a first source of phenotypic variation. Given the potential complexity of coat color patterns in Nellore cattle and the putative existence of different molecular pathways governing each one of the three mentioned sources of variation, we hypothesize that they are better understood as separate, intermediate traits
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