The Chongming white goat (CM) is an indigenous goat breed exhibits unique traits that are adapted to the local environment and artificial selection. By performing whole-genome re-sequencing, we generated 14–20× coverage sequences from 10 domestic goat breeds to explore the genomic characteristics and selection signatures of the CM breed. We identified a total of 23,508,551 single-nucleotide polymorphisms (SNPs) and 2,830,800 insertion–deletion mutations (indels) after read mapping and variant calling. We further specifically identified 1.2% SNPs (271,713) and 0.9% indels (24,843) unique to the CM breed in comparison with the other nine goat breeds. Missense (SIFT < 0.05), frameshift, splice-site, start-loss, stop-loss, and stop-gain variants were identified in 183 protein-coding genes of the CM breed. Of the 183, 36 genes, including AP4E1, FSHR, COL11A2, and DYSF, are involved in phenotype ontology terms related to the nervous system, short stature, and skeletal muscle morphology. Moreover, based on genome-wide FST and pooled heterozygosity (Hp) calculation, we further identified selection signature genes between the CM and the other nine goat breeds. These genes are significantly associated with the nervous system (C2CD3, DNAJB13, UCP2, ZMYND11, CEP126, SCAPER, and TSHR), growth (UCP2, UCP3, TSHR, FGFR1, ERLIN2, and ZNF703), and coat color (KITLG, ASIP, AHCY, RALY, and MC1R). Our results suggest that the CM breed may be differentiated from other goat breeds in terms of nervous system owing to natural or artificial selection. The whole-genome analysis provides an improved understanding of genetic diversity and trait exploration for this indigenous goat breed.
Global livestock genetic diversity encompasses species, breeds, strains, and their variations. The diversity between and within breeds rather than species is always considered to be essential for the purposes of conservation biology (Yaro et al., 2017). Goats are important husbandry animals with an ancient domestication history and economic value. It has been reported that their domestication occurred approximately 10,000 years ago and spread worldwide following human migrations and trade routes (Benjelloun et al., 2015; Kim et al., 2019). China is the global leader in terms of goat production (Skapetas and Bampidis, 2016), including many commercial, indigenous, and composite breeds. Owing to the weaker production potential compared with that of some global commercial breeds, indigenous goat breeds are facing the problem of genetic invasion and resource degradation in recent years (Kim et al., 2019; Monau et al., 2020).
Indigenous goats are unique groups that have developed under the forces of natural selection, domestication, and local environmental conditions. Their genetic background, unique traits, and biodiversity, as well as their environmental adaptability, serve as a kind of biological heritage that can be used for the genetic improvement of animal husbandry (Kim et al., 2019). The Chongming white goat (CM) is an indigenous island-type goat breed distributed and bred on Shanghai Chongming Island. Although there have not been sufficient systematic studies on the selection signal genes for island climate adaptation, this may be a direction of research. The CM goats were also marked as special agricultural products with geographical indications registered by the State Administration for Industry and Commerce of China. Moreover, the relatively small size and ease of husbandry make it a suitable animal model for some specific human diseases such as acute spinal cord compression injuries (Huang et al., 2013). However, even with rich domestication history, studies on the genome-wide characteristics of this indigenous goat have not been reported yet to the best of our knowledge.
Whole-genome sequencing (WGS) information bypasses the study limitations of maternal mitochondrial DNA and paternal Y chromosome inheritance in species evolution and population history dynamics. Moreover, WGS can also ameliorate the current problems of breed bias and insufficient markers in genotyping chips, and the new genetic variation information also provides research materials for the further production of high-density chips. The use of WGS and reference genome alignment can identify more comprehensive, genome-wide variation, such as the presence of single-nucleotide polymorphisms (SNPs), insertion–deletion mutations (indels), and structural variants (SVs). Although high-throughput sequencing technology enables the comparison of patterns of polymorphisms at whole-genome levels, characterizing genetic structure from individual sequencing data still remains expensive for non-model species. The DNA pooling strategy (Pool-seq) represents an attractive and cost-effective alternative for SNP discovery (Futschik and Schlötterer, 2010; Hivert et al., 2018) and have been successfully applied to many domestic animal studies such as chicken (Rubin et al., 2010), pig (Rubin et al., 2012), goat (Wang et al., 2016; Guo et al., 2018), and sheep (Liu et al., 2016).
Molecular genetic markers, such as high-density SNPs, are often used to analyze genetic variation at the genome-wide level caused by natural and artificial selection of species. For example, the Chinese Tibetan cashmere goat adapted to a high-altitude area and hypoxic environment. In which, 339 genes were identified through exome sequencing, which are potentially under high-altitude selection (Song et al., 2016). Another study (Kim et al., 2019) analyzed the genome of the Korean indigenous goat (KNG) in comparison with that of nine other goat breeds and revealed that the KNG has selection signatures for Salmonella infection and cardiomyopathy pathways. Wang et al. (2016) generated 9–13× coverage sequences from eight domesticated goat breeds and identified 22 genomic regions that may be associated with specific phenotypic traits, including coat color, body size, cashmere traits, and high-altitude adaptation.
In this study, we aimed to explore the genomic characteristics in the CM goat. Utilizing WGS and genomic approaches, we conducted the first comparative genomic study to reveal the genome-wide variation and selection signatures in the CM breed.