Retrotransposon Insertion Polymorphisms (RIPs) in Pig Coat Color Candidate Genes
The diversity of livestock coat color results from human positive selection and represents an indispensable part of breed identity. As an important biodiversity resource, pigs have many special characteristics, including the most visualized feature, coat color, and excellent adaptation, and the coat...
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| Format: | Article |
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MDPI AG
2022-04-01
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| Series: | Animals |
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| Online Access: | https://www.mdpi.com/2076-2615/12/8/969 |
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| author | Zhanyu Du Enrico D’Alessandro Yao Zheng Mengli Wang Cai Chen Xiaoyan Wang Chengyi Song |
| author_facet | Zhanyu Du Enrico D’Alessandro Yao Zheng Mengli Wang Cai Chen Xiaoyan Wang Chengyi Song |
| author_sort | Zhanyu Du |
| collection | DOAJ |
| description | The diversity of livestock coat color results from human positive selection and represents an indispensable part of breed identity. As an important biodiversity resource, pigs have many special characteristics, including the most visualized feature, coat color, and excellent adaptation, and the coat color represents an important phenotypic characteristic of the pig breed. Exploring the genetic mechanisms of phenotypic characteristics and the melanocortin system is of considerable interest in domestic animals because their energy metabolism and pigmentation have been under strong selection. In this study, 20 genes related to coat color in mammals were selected, and the structural variations (SVs) in these genic regions were identified by sequence alignment across 17 assembled pig genomes, from representing different types of pigs (miniature, lean, and fat type). A total of 167 large structural variations (>50 bp) of coat-color genes, which overlap with retrotransposon insertions (>50 bp), were obtained and designated as putative RIPs. Finally, 42 RIPs were confirmed by PCR detection. Additionally, eleven RIP sites were further evaluated for their genotypic distributions by PCR in more individuals of eleven domesticated breeds representing different coat color groups. Differential distributions of these RIPs were observed across populations, and some RIPs may be associated with breed differences. |
| first_indexed | 2024-03-09T11:15:56Z |
| format | Article |
| id | doaj.art-6d1a52bfda8941da8730ef9f85a5c761 |
| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-09T11:15:56Z |
| publishDate | 2022-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Animals |
| spelling | doaj.art-6d1a52bfda8941da8730ef9f85a5c7612023-12-01T00:30:16ZengMDPI AGAnimals2076-26152022-04-0112896910.3390/ani12080969Retrotransposon Insertion Polymorphisms (RIPs) in Pig Coat Color Candidate GenesZhanyu Du0Enrico D’Alessandro1Yao Zheng2Mengli Wang3Cai Chen4Xiaoyan Wang5Chengyi Song6College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaDepartment of Veterinary Sciences, University of Messina, Via Palatucci, 98168 Messina, ItalyCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaThe diversity of livestock coat color results from human positive selection and represents an indispensable part of breed identity. As an important biodiversity resource, pigs have many special characteristics, including the most visualized feature, coat color, and excellent adaptation, and the coat color represents an important phenotypic characteristic of the pig breed. Exploring the genetic mechanisms of phenotypic characteristics and the melanocortin system is of considerable interest in domestic animals because their energy metabolism and pigmentation have been under strong selection. In this study, 20 genes related to coat color in mammals were selected, and the structural variations (SVs) in these genic regions were identified by sequence alignment across 17 assembled pig genomes, from representing different types of pigs (miniature, lean, and fat type). A total of 167 large structural variations (>50 bp) of coat-color genes, which overlap with retrotransposon insertions (>50 bp), were obtained and designated as putative RIPs. Finally, 42 RIPs were confirmed by PCR detection. Additionally, eleven RIP sites were further evaluated for their genotypic distributions by PCR in more individuals of eleven domesticated breeds representing different coat color groups. Differential distributions of these RIPs were observed across populations, and some RIPs may be associated with breed differences.https://www.mdpi.com/2076-2615/12/8/969coat colorphenotypic traitpig breedsSINERIPsmolecular marker |
| spellingShingle | Zhanyu Du Enrico D’Alessandro Yao Zheng Mengli Wang Cai Chen Xiaoyan Wang Chengyi Song Retrotransposon Insertion Polymorphisms (RIPs) in Pig Coat Color Candidate Genes Animals coat color phenotypic trait pig breeds SINE RIPs molecular marker |
| title | Retrotransposon Insertion Polymorphisms (RIPs) in Pig Coat Color Candidate Genes |
| title_full | Retrotransposon Insertion Polymorphisms (RIPs) in Pig Coat Color Candidate Genes |
| title_fullStr | Retrotransposon Insertion Polymorphisms (RIPs) in Pig Coat Color Candidate Genes |
| title_full_unstemmed | Retrotransposon Insertion Polymorphisms (RIPs) in Pig Coat Color Candidate Genes |
| title_short | Retrotransposon Insertion Polymorphisms (RIPs) in Pig Coat Color Candidate Genes |
| title_sort | retrotransposon insertion polymorphisms rips in pig coat color candidate genes |
| topic | coat color phenotypic trait pig breeds SINE RIPs molecular marker |
| url | https://www.mdpi.com/2076-2615/12/8/969 |
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