Whole-Genome Sequencing Reveals the Genomic Characteristics and Selection Signatures of Hainan Black Goat

Qiaoling Chen; Yuan Chai; Wencan Zhang; Yiwen Cheng; Zhenxing Zhang; Qi An; Si Chen; Churiga Man; Li Du; Wenguang Zhang; Fengyang Wang

doi:10.3390/genes13091539

Whole-Genome Sequencing Reveals the Genomic Characteristics and Selection Signatures of Hainan Black Goat

Genes (Basel). 2022 Aug 26;13(9):1539. doi: 10.3390/genes13091539.

Authors

Affiliations

¹ Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, College of Animal Science and Technology, Hainan University, Haikou 570228, China.
² College of Agronomy, Animal Husbandry and Bioengineering, Xing'an Vocational and Technical College, Ulanhot 137400, China.
³ College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010010, China.

Abstract

Goats have become one of the most adaptive and important livestock species distributed in developing countries in recent years. The Hainan Black goat is a native goat breed of the Hainan region that is generally well-liked by the local population and is thus raised in large numbers. However, the genomic diversity and selective signals of the Hainan Black goat have not been clearly elucidated yet. Therefore, in this study, we performed whole-genome resequencing of 16 Hainan Black goats and compared the results with those of 71 goats of 6 other breeds from different geographic regions. Principal component analysis (PCA) and phylogenetic analysis identified seven lineages for all goats. Hainan Black goats showed the most similarity with Leizhou goats and the least similarity with Boer goats. Selective sweep analysis identified candidate genes associated with various functions, including immune resistance to disease (TNFAIP2 (TNF alpha induced protein 2) and EXOC3L4 (exocyst complex component 3 like 4)), melanin biosynthetic process (CDH15 (cadherin 15), ASIP (agouti signaling protein), and PARD3 (par-3 family cell polarity regulator)), and light sensitivity (CNGB3 (cyclic nucleotide gated channel subunit beta 3) and CNBD1 (cyclic nucleotide binding domain containing 1)), underlying strong selection signatures in Hainan Black goats. The melanin biosynthetic process, circadian entrainment, regulation of cyclic adenosine 3,5-monophosphate (cAMP)-mediated signaling, and the Rap-1 signaling pathway were significantly enriched in Hainan Black and Alashan Cashmere goats. This result may be important for understanding each trait. Selection signature analysis revealed candidate single nucleotide polymorphisms (SNPs) and genes correlated with the traits of Hainan Black goats. Collectively, our results provide valuable insights into the genetic basis of specific traits correlated with the Hainan island climate, artificial selection in certain local goat breeds, and the importance of protecting breed resources.

Keywords: Hainan Black goat; genetic diversity; selective signal; whole-genome resequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adenosine
Agouti Signaling Protein / genetics
Animals
Cyclic Nucleotide-Gated Cation Channels / genetics
Genomics
Goats* / genetics
Melanins / genetics
Nucleotides, Cyclic
Phylogeny
Selection, Genetic*
Tumor Necrosis Factor-alpha / genetics

Substances

Agouti Signaling Protein
Cyclic Nucleotide-Gated Cation Channels
Melanins
Nucleotides, Cyclic
Tumor Necrosis Factor-alpha
Adenosine

Grants and funding

This work was financially supported by the Academician Innovation Platform Project of Hainan Province (No. YSPTZX202153), the Hainan Innovation Center for Academicians of Zhang Yong; the China Agriculture Research System of MOF and MARA (CARS-38), and Special Funding Projects for Local Science and Technology Development Guided by the Central Committee (ZY2022HN09).