Abstract
Detecting signatures of selection can provide a new insight into the mechanism of contemporary breeding and artificial selection and further reveal the causal genes associated to the phenotypic variation. However, the signatures of selection on genes entailing for profitable traits between Chinese commercial and indigenous goats have been poorly interpreted. We noticed footprints of positive selection at MC1R gene containing SNPs genotyped in five Chinese native goat breeds. An experimental distribution of F ST was built based on approximations of F ST for each SNP across five breeds. We identified selection using the high F ST outlier method and found that MC1R candidate gene show evidence of positive selection. Furthermore, adaptive selection pressure on specific codons was determined using different codon based on maximum‐likelihood methods; signature of positive selection in mammalian MC1R was explored in individual codons. Evolutionary analyses were inferred under maximum likelihood models, the HyPhy package implemented in the DATAMONKEY Web Server. The results of codon selection displayed positive diversifying selection at the sites were mainly involved in development of genetic variations in coat color in various mammalian species. Positive diversifying selection inferred with recent evolutionary changes in domesticated goat MC1R provides new insights that the gene evolution may have been modulated by domestication events in goats.
Highlights
Coat color variation in mammals is one of the most distinctive phenotypic traits, which put a significant biological and economic impact, and it can be enlightened by various selective pressures including communication, concealment, and regulation of physiological processes (Andersson, 2001; Chen et al, 2009)
The persistence of dominant black allele and a recessive red allele has been documented in few breeds (Sponenberg, 1990), and on the other hand, wild-type allele of agouti made different phenotypic effects in other species, as in Boer goat the missense mutation (p.k226E) in MC1R gene was associated with red color phenotype (Wu et al, 2006)
We identified MC1R1 loci in five goat populations as potential target of selection according to their genetic variation distribution by estimating the FST and mean heterozygosity as a measure of genetic differentiation at each locus, as six loci at five genes in goat populations were detected under positive selection by estimating their FST and heterozygosity (Pariset, Joost, Marsan, & Valentini, 2009)
Summary
Coat color variation in mammals is one of the most distinctive phenotypic traits, which put a significant biological and economic impact, and it can be enlightened by various selective pressures including communication, concealment, and regulation of physiological processes (Andersson, 2001; Chen et al, 2009). MC1R gene mutations associated with color phenotype have extensively been studied in different livestock species including goat (Fontanesi et al, 2009), sheep (Våge et al, 2003), and cattle (Klungland, Vage, Gomez-Raya, Adalsteinsson, & Lien, 1995). The adaptive evolution was measured by synonymous and nonsynonymous substitution (dN/dS) ratio, as in lion tamarin and mouse, the MC1R sequences have evolved with amino acid changes, which have higher ratio of dN/dS reflecting specific evolutionary episode related coat color (Mundy & Kelly, 2003). Understanding the evolutionary footprint of MC1R gene will provide valuable information for reconstructing evolutionary history of species and other functional genes, and may provide useful insights into the design of marker-assisted selection and breeding for genetic improvement in goats. We investigated the molecular evolutionary signatures that may exert selection processes in the MC1R gene in goats and identified evolution footprints that may influence adaptation to different environments
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