Whole-Genome Sequencing Reveals the Genomic Characteristics and Selection Signatures of Hainan Black Goat
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 gen...
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| Format: | Article |
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MDPI AG
2022-08-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/13/9/1539 |
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| author | Qiaoling Chen Yuan Chai Wencan Zhang Yiwen Cheng Zhenxing Zhang Qi An Si Chen Churiga Man Li Du Wenguang Zhang Fengyang Wang |
| author_facet | Qiaoling Chen Yuan Chai Wencan Zhang Yiwen Cheng Zhenxing Zhang Qi An Si Chen Churiga Man Li Du Wenguang Zhang Fengyang Wang |
| author_sort | Qiaoling Chen |
| collection | DOAJ |
| description | 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 (<i>TNFAIP2</i> (TNF alpha induced protein 2) and <i>EXOC3L4</i> (exocyst complex component 3 like 4)), melanin biosynthetic process (<i>CDH15</i> (cadherin 15)<i>, ASIP</i> (agouti signaling protein)<i>,</i> and <i>PARD3</i> (par-3 family cell polarity regulator)), and light sensitivity (<i>CNGB3</i> (cyclic nucleotide gated channel subunit beta 3) and <i>CNBD1</i> (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. |
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| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T23:56:30Z |
| publishDate | 2022-08-01 |
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| series | Genes |
| spelling | doaj.art-7a1bf5c8860f408480f829857bd4abf62023-11-23T16:23:48ZengMDPI AGGenes2073-44252022-08-01139153910.3390/genes13091539Whole-Genome Sequencing Reveals the Genomic Characteristics and Selection Signatures of Hainan Black GoatQiaoling Chen0Yuan Chai1Wencan Zhang2Yiwen Cheng3Zhenxing Zhang4Qi An5Si Chen6Churiga Man7Li Du8Wenguang Zhang9Fengyang Wang10Hainan 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, ChinaCollege of Agronomy, Animal Husbandry and Bioengineering, Xing’an Vocational and Technical College, Ulanhot 137400, ChinaHainan 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, ChinaHainan 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, ChinaHainan 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, ChinaHainan 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, ChinaHainan 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, ChinaHainan 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, ChinaHainan 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, ChinaCollege of Animal Science, Inner Mongolia Agricultural University, Hohhot 010010, ChinaHainan 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, ChinaGoats 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 (<i>TNFAIP2</i> (TNF alpha induced protein 2) and <i>EXOC3L4</i> (exocyst complex component 3 like 4)), melanin biosynthetic process (<i>CDH15</i> (cadherin 15)<i>, ASIP</i> (agouti signaling protein)<i>,</i> and <i>PARD3</i> (par-3 family cell polarity regulator)), and light sensitivity (<i>CNGB3</i> (cyclic nucleotide gated channel subunit beta 3) and <i>CNBD1</i> (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.https://www.mdpi.com/2073-4425/13/9/1539Hainan Black goatwhole-genome resequencinggenetic diversityselective signal |
| spellingShingle | Qiaoling Chen Yuan Chai Wencan Zhang Yiwen Cheng Zhenxing Zhang Qi An Si Chen Churiga Man Li Du Wenguang Zhang Fengyang Wang Whole-Genome Sequencing Reveals the Genomic Characteristics and Selection Signatures of Hainan Black Goat Genes Hainan Black goat whole-genome resequencing genetic diversity selective signal |
| title | Whole-Genome Sequencing Reveals the Genomic Characteristics and Selection Signatures of Hainan Black Goat |
| title_full | Whole-Genome Sequencing Reveals the Genomic Characteristics and Selection Signatures of Hainan Black Goat |
| title_fullStr | Whole-Genome Sequencing Reveals the Genomic Characteristics and Selection Signatures of Hainan Black Goat |
| title_full_unstemmed | Whole-Genome Sequencing Reveals the Genomic Characteristics and Selection Signatures of Hainan Black Goat |
| title_short | Whole-Genome Sequencing Reveals the Genomic Characteristics and Selection Signatures of Hainan Black Goat |
| title_sort | whole genome sequencing reveals the genomic characteristics and selection signatures of hainan black goat |
| topic | Hainan Black goat whole-genome resequencing genetic diversity selective signal |
| url | https://www.mdpi.com/2073-4425/13/9/1539 |
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