Comparative genome analyses reveal the unique genetic composition and selection signals underlying the phenotypic characteristics of three Chinese domestic goat breeds

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.

Identification of Genomic Characteristics and Selective Signals in a Du’an Goat Flock

“…Study of genetic diversity plays an important role in the conservation and utilization of germplasm resources, revelation of evolutionary history, and investigation of phylogenetic relationships. The number of the detected SNPs in the Du’an goat (~17M) was lower than that in the Moroccan (~33M) and Korean indigenous (~37M), and higher than that in the Tibetan Cashmere (~12M), Chengdu Brown (~10M), and Jintang Black goat (~12M) [ 8 ], which could be explained by the difference in the number of individuals, reference genome, detection method, filtering criteria, or breed. The average nucleotide diversity in the Du’an goat was lower than that in the Iranian indigenous goat, while it was found to be higher than that in the Nubian and Korean indigenous goat.…”

“…The average r 2 in 50 Kb in the Du’an goat was higher than that in the Iranian indigenous, Moroccan indigenous, and Boer goat, while it was lower than that in the Nubian goat ( Table 2 ). However, ROH-based inbreeding coefficient (0.0025) was lower in the Du’an goat than the Chengdu Brown (0.194), Tibetan Cashmere (0.068), Moroccan indigenous (0.085), and Jintang Black goat (0.119) [ 8 ]. The revelation of individual ROH may help the conservation of this breed, since animals with high levels of ROH could be excluded or assigned lower priority for mating to minimize the loss in genetic diversity.…”

“…More importantly, the study identified a strong signature of selection harboring MUC6 gene conferred enhanced immune resistance to gastrointestinal pathogens [ 7 ]. Furthermore, studies showed selective signals in other important traits, such as hair growth in the Cashmere goat [ 8 ], litter size traits in the Laoshan dairy goat [ 9 ], and high altitude adaptation in the Tibetan goat [ 3 ]. However, there have been scarce or no attempts to analyze the genomic characteristics and selective signals in the Du’an goat.…”

Deletion of an Enhancer in FGF5 is Associated With Ectopic Expression in Goat Hair Follicles and the Cashmere Growth Phenotype

“…Studies on the FGF5 gene demonstrated the relation to coat hair length in mice [50], dogs [51], cats [52], humans [53], donkeys [54] and alpacas [55]. The same selection target has been described in a number of cashmere goat investigations [10,56]. In addition, disruption of the FGF5 gene via the CRISPR/Cas9 system in cashmere goats increased the number of secondary hair follicles and enhanced the ber length [57].…”

“…Previous studies have found a few SNP variants of the FGF5 gene that may be associated with hair length, including a missense SNP (c.284G> T) in dogs, four SNPs (c.194C>A, c.182T>A, c.474delT and c.475A>C) in cats, two SNPs (c.433_434delAT and c.245G> A) in donkeys and a missense SNP (c.499C>T) in alpacas [51,52,54,55]. Recently, one SNP (c.253G>A) in the 5'-UTR of FGF5 resulted in a start codon that could lead to a premature/dysfunctional protein in Tibetan cashmere goats [56].…”