Abstract
BackgroundAs one of the important livestock species around the world, goats provide abundant meat, milk, and fiber to fulfill basic human needs. However, the genetic loci that underlie phenotypic variations in domestic goats are largely unknown, particularly for economically important traits. In this study, we sequenced the whole genome of 38 goats from three Chinese breeds (Chengdu Brown, Jintang Black, and Tibetan Cashmere) and downloaded the genome sequence data of 30 goats from five other breeds (four non-Chinese and one Chinese breed) and 21 Bezoar ibexes to investigate the genetic composition and selection signatures of the Chinese goat breeds after domestication.ResultsBased on population structure analysis and FST values (average FST = 0.22), the genetic composition of Chengdu Brown goats differs considerably from that of Bezoar ibexes as a result of geographic isolation. Strikingly, the genes under selection that we identified in Tibetan Cashmere goats were significantly enriched in the categories hair growth and bone and nervous system development, possibly because they are involved in adaptation to high-altitude. In particular, we found a large difference in allele frequency of one novel SNP (c.-253G>A) in the 5′-UTR of FGF5 between Cashmere goats and goat breeds with short hair. The mutation at this site introduces a start codon that results in the occurrence of a premature FGF5 protein and is likely a natural causal variant that is involved in the long hair phenotype of cashmere goats. The haplotype tagged with the AGG-allele in exon 12 of DSG3, which encodes a cell adhesion molecule that is expressed mainly in the skin, was almost fixed in Tibetan Cashmere goats, whereas this locus still segregates in the lowland goat breeds. The pigmentation gene KITLG showed a strong signature of selection in Tibetan Cashmere goats. The genes ASIP and LCORL were identified as being under positive selection in Jintang Black goats.ConclusionsAfter domestication, geographic isolation of some goat breeds has resulted in distinct genetic structures. Furthermore, our work highlights several positively selected genes that likely contributed to breed-related traits in domestic goats.
Highlights
As one of the important livestock species around the world, goats provide abundant meat, milk, and fiber to fulfill basic human needs
We showed that three loci involved in pigmentation (i.e., RALY-EIF2S2, IRF4EXOC2, and KITLG) were under positive selection in domestic goats [22] but the evidence was weak mainly because individual genotypes were unavailable from our pooled sequence data
Abundant genomic variation and low genetic diversity in the goat genome Based on our genome sequence data for 38 goats from three Chinese goat breeds (Fig. 1) and and the whole-genome sequence data from 30 individuals of five other goat breeds and 21 Bezoar ibexes downloaded from NCBI, 19,791,420 single nucleotide variations (SNVs) (18,082,455 biallelic and 109,280 multiallelic single nucleotide polymorphism (SNP) and 1,599,685 indels) were identified across these 89 goat autosomal genomes
Summary
As one of the important livestock species around the world, goats provide abundant meat, milk, and fiber to fulfill basic human needs. The phenotypic variation of a Mendelian trait in livestock can be determined by a single genetic locus with large effect, e.g., plumage color in Pekin ducks [10]. In such cases, artificial selection or adaptation to local conditions usually leads to a rapid increase in the frequency of the desirable allele at the population level and leaves a classical selection signature that is referred to as a “hard sweep” [11]. Based on an analysis of eight domestic cattle breeds with an ~ 800 K single nucleotide polymorphism (SNP) chip, Kemper et al [15] reported that strong artificial selection for quantitative traits (e.g., milk yield) left little or no classic signatures of selection, whereas recent studies have revealed selection signatures for some complex traits, such as fiber and meat production traits in goats [7, 16], immune traits in sheep [16], and milk-related traits in cattle [17]
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