Genome-Wide Characterization and Comparative Analyses of Simple Sequence Repeats among Four Miniature Pig Breeds
Simple sequence repeats (SSRs) are commonly used as molecular markers in research on genetic diversity and discrimination among taxa or breeds because polymorphisms in these regions contribute to gene function and phenotypically important traits. In this study, we investigated genome-wide characteri...
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MDPI AG
2020-10-01
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| Online Access: | https://www.mdpi.com/2076-2615/10/10/1792 |
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| author | Hongyang Wang Yang Fu Peng Gu Yingying Zhang Weilong Tu Zhe Chao Huali Wu Jianguo Cao Xiang Zhou Bang Liu Jennifer J. Michal Chun Fan Yongsong Tan |
| author_facet | Hongyang Wang Yang Fu Peng Gu Yingying Zhang Weilong Tu Zhe Chao Huali Wu Jianguo Cao Xiang Zhou Bang Liu Jennifer J. Michal Chun Fan Yongsong Tan |
| author_sort | Hongyang Wang |
| collection | DOAJ |
| description | Simple sequence repeats (SSRs) are commonly used as molecular markers in research on genetic diversity and discrimination among taxa or breeds because polymorphisms in these regions contribute to gene function and phenotypically important traits. In this study, we investigated genome-wide characteristics, repeat units, and polymorphisms of SSRs using sequencing data from SSR-enriched libraries created from Wuzhishan (WZS), Bama (BM), inbred Luchuan (LC) and Zangxiang (ZX) miniature pig breeds. The numbers and types of SSRs, distributions of repeat units and polymorphic SSRs varied among the four breeds. Compared to the Duroc pig reference genome, 2518 polymorphic SSRs were unique and common to all four breeds and functional annotation revealed that they may affect the coding and regulatory regions of genes. Several examples, such as <i>FGF23</i>, <i>MYF6</i>, <i>IGF1R</i>, and <i>LEPROT</i>, are associated with growth and development in pigs. Three of the polymorphic SSRs were selected to confirm the polymorphism and the corresponding alleles through fluorescence polymerase chain reaction (PCR) and capillary electrophoresis. Together, this study provides useful insights into the discovery, characteristics and distribution of SSRs in four pig breeds. The polymorphic SSRs, especially those common and unique to all four pig breeds, might affect associated genes and play important roles in growth and development. |
| first_indexed | 2024-03-10T15:52:59Z |
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| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-10T15:52:59Z |
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| spelling | doaj.art-7df978fc88e9471a9c7d7c52430216632023-11-20T15:52:51ZengMDPI AGAnimals2076-26152020-10-011010179210.3390/ani10101792Genome-Wide Characterization and Comparative Analyses of Simple Sequence Repeats among Four Miniature Pig BreedsHongyang Wang0Yang Fu1Peng Gu2Yingying Zhang3Weilong Tu4Zhe Chao5Huali Wu6Jianguo Cao7Xiang Zhou8Bang Liu9Jennifer J. Michal10Chun Fan11Yongsong Tan12Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, ChinaResearch Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, ChinaInstitute of Comparative Medicine & Laboratory Animal Management Center, Southern Medical University, Guangzhou 510515, ChinaInstitute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, ChinaInstitute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, ChinaInstitute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, ChinaInstitute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, ChinaInstitute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, ChinaKey Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, ChinaKey Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, ChinaDepartment of Animal Sciences, Washington State University, Pullman, WA 99164, USAShanghai Laboratory Animal Research Center, Shanghai 201203, ChinaInstitute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, ChinaSimple sequence repeats (SSRs) are commonly used as molecular markers in research on genetic diversity and discrimination among taxa or breeds because polymorphisms in these regions contribute to gene function and phenotypically important traits. In this study, we investigated genome-wide characteristics, repeat units, and polymorphisms of SSRs using sequencing data from SSR-enriched libraries created from Wuzhishan (WZS), Bama (BM), inbred Luchuan (LC) and Zangxiang (ZX) miniature pig breeds. The numbers and types of SSRs, distributions of repeat units and polymorphic SSRs varied among the four breeds. Compared to the Duroc pig reference genome, 2518 polymorphic SSRs were unique and common to all four breeds and functional annotation revealed that they may affect the coding and regulatory regions of genes. Several examples, such as <i>FGF23</i>, <i>MYF6</i>, <i>IGF1R</i>, and <i>LEPROT</i>, are associated with growth and development in pigs. Three of the polymorphic SSRs were selected to confirm the polymorphism and the corresponding alleles through fluorescence polymerase chain reaction (PCR) and capillary electrophoresis. Together, this study provides useful insights into the discovery, characteristics and distribution of SSRs in four pig breeds. The polymorphic SSRs, especially those common and unique to all four pig breeds, might affect associated genes and play important roles in growth and development.https://www.mdpi.com/2076-2615/10/10/1792SSRrepeat unitlength polymorphismminiature pigmolecular marker |
| spellingShingle | Hongyang Wang Yang Fu Peng Gu Yingying Zhang Weilong Tu Zhe Chao Huali Wu Jianguo Cao Xiang Zhou Bang Liu Jennifer J. Michal Chun Fan Yongsong Tan Genome-Wide Characterization and Comparative Analyses of Simple Sequence Repeats among Four Miniature Pig Breeds Animals SSR repeat unit length polymorphism miniature pig molecular marker |
| title | Genome-Wide Characterization and Comparative Analyses of Simple Sequence Repeats among Four Miniature Pig Breeds |
| title_full | Genome-Wide Characterization and Comparative Analyses of Simple Sequence Repeats among Four Miniature Pig Breeds |
| title_fullStr | Genome-Wide Characterization and Comparative Analyses of Simple Sequence Repeats among Four Miniature Pig Breeds |
| title_full_unstemmed | Genome-Wide Characterization and Comparative Analyses of Simple Sequence Repeats among Four Miniature Pig Breeds |
| title_short | Genome-Wide Characterization and Comparative Analyses of Simple Sequence Repeats among Four Miniature Pig Breeds |
| title_sort | genome wide characterization and comparative analyses of simple sequence repeats among four miniature pig breeds |
| topic | SSR repeat unit length polymorphism miniature pig molecular marker |
| url | https://www.mdpi.com/2076-2615/10/10/1792 |
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