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Wang H, Fu Y, Gu P, Zhang Y, Tu W, Chao Z, Wu H, Cao J, Zhou X, Liu B, Michal JJ, Fan C, Tan Y. Genome-Wide Characterization and Comparative Analyses of Simple Sequence Repeats among Four Miniature Pig Breeds. Animals (Basel) 2020; 10:ani10101792. [PMID: 33023098 PMCID: PMC7600727 DOI: 10.3390/ani10101792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/15/2020] [Accepted: 09/28/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Simple sequence repeats (SSRs) are present at high densities in regulatory elements, suggesting that they may affect gene function and phenotypic traits. Therefore, SSRs can be exploited in marker-assisted selection. In addition, they can be widely used as molecular markers to study genetic diversity, population structure, and evolution. While SSRs have been widely studied in many mammalian species, very little research has focused on genome-wide SSRs of miniature pigs, a small but special group of pigs that express the dwarf phenotype. Based on the SSR-enriched library building and sequencing, about 30,000 novel polymorphic SSRs for four miniature pig breeds were mapped to the Duroc pig reference genome. The four miniature pig breeds had different numbers and types of SSRs and distributions of repeat units. There were 2518 polymorphic SSRs in the intron or exon regions that were common to all four breeds and functional analyses revealed 17 genes that were associated with body size and other genes that were associated with growth and development. In conclusion, the SSRs detected in the miniature pigs in this study may provide useful genetic markers for the selection of farm animals and the polymorphic SSRs provide valuable insights into the determination of mature body size, as well as the immunity, growth and development of animals. Abstract 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 FGF23, MYF6, IGF1R, and LEPROT, 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.
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Affiliation(s)
- Hongyang Wang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (H.W.); (Y.Z.); (W.T.); (H.W.); (J.C.)
- Shanghai Engineering Research Center of Breeding Pig, Shanghai 201302, China
| | - Yang Fu
- Research Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China;
| | - Peng Gu
- Institute of Comparative Medicine & Laboratory Animal Management Center, Southern Medical University, Guangzhou 510515, China;
| | - Yingying Zhang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (H.W.); (Y.Z.); (W.T.); (H.W.); (J.C.)
- Shanghai Engineering Research Center of Breeding Pig, Shanghai 201302, China
| | - Weilong Tu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (H.W.); (Y.Z.); (W.T.); (H.W.); (J.C.)
- Shanghai Engineering Research Center of Breeding Pig, Shanghai 201302, China
| | - Zhe Chao
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China;
| | - Huali Wu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (H.W.); (Y.Z.); (W.T.); (H.W.); (J.C.)
- Shanghai Engineering Research Center of Breeding Pig, Shanghai 201302, China
| | - Jianguo Cao
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (H.W.); (Y.Z.); (W.T.); (H.W.); (J.C.)
- Shanghai Engineering Research Center of Breeding Pig, Shanghai 201302, China
| | - Xiang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (X.Z.); (B.L.)
| | - Bang Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (X.Z.); (B.L.)
| | - Jennifer J. Michal
- Department of Animal Sciences, Washington State University, Pullman, WA 99164, USA;
| | - Chun Fan
- Shanghai Laboratory Animal Research Center, Shanghai 201203, China;
| | - Yongsong Tan
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (H.W.); (Y.Z.); (W.T.); (H.W.); (J.C.)
- Shanghai Engineering Research Center of Breeding Pig, Shanghai 201302, China
- Correspondence: ; Tel.: +86-021-34505325
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