Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array
Chinese Red Steppe Cattle (CRS), a composite cattle breed, is well known for its milk production, high slaughter rate, carcass traits, and meat quality. Nowadays, it is widely bred in Jilin and Hebei Province and the Inner Mongolia Autonomous region. However, the population structure and the genetic...
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MDPI AG
2023-05-01
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| Series: | Animals |
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| Online Access: | https://www.mdpi.com/2076-2615/13/10/1717 |
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| author | Mingyue Hu Hao Jiang Weining Lai Lulu Shi Wenfeng Yi Hao Sun Chengzhen Chen Bao Yuan Shouqing Yan Jiabao Zhang |
| author_facet | Mingyue Hu Hao Jiang Weining Lai Lulu Shi Wenfeng Yi Hao Sun Chengzhen Chen Bao Yuan Shouqing Yan Jiabao Zhang |
| author_sort | Mingyue Hu |
| collection | DOAJ |
| description | Chinese Red Steppe Cattle (CRS), a composite cattle breed, is well known for its milk production, high slaughter rate, carcass traits, and meat quality. Nowadays, it is widely bred in Jilin and Hebei Province and the Inner Mongolia Autonomous region. However, the population structure and the genetic basis of prominent characteristics of CRS are still unknown. In this study, we systematically describe their population structure, genetic diversity, and selection signature based on genotyping data from 61 CRS individuals with GGP Bovine 100 K chip. The results showed that CRS cattle had low inbreeding levels and had formed a unique genetic structure feature. Using two complementary methods (including comprehensive haplotype score and complex likelihood ratio), we identified 1291 and 1285 potentially selected genes, respectively. There were 141 genes annotated in common 106 overlapping genomic regions covered 5.62 Mb, including <i>PLAG1</i>, <i>PRKG2</i>, <i>DGAT1</i>, <i>PARP10</i>, <i>TONSL</i>, <i>ADCK5</i>, and <i>BMP3</i>, most of which were enriched in pathways related to muscle growth and differentiation, milk production, and lipid metabolism. This study will contribute to understanding the genetic mechanism behind artificial selection and give an extensive reference for subsequent breeding. |
| first_indexed | 2024-03-11T04:00:19Z |
| format | Article |
| id | doaj.art-1c3ae6e209f445c7adc4f776587d7a2d |
| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-11T04:00:19Z |
| publishDate | 2023-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Animals |
| spelling | doaj.art-1c3ae6e209f445c7adc4f776587d7a2d2023-11-18T00:11:16ZengMDPI AGAnimals2076-26152023-05-011310171710.3390/ani13101717Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP ArrayMingyue Hu0Hao Jiang1Weining Lai2Lulu Shi3Wenfeng Yi4Hao Sun5Chengzhen Chen6Bao Yuan7Shouqing Yan8Jiabao Zhang9College of Animal Science, Jilin University, Changchun 130062, ChinaCollege of Animal Science, Jilin University, Changchun 130062, ChinaCollege of Animal Science, Jilin University, Changchun 130062, ChinaCollege of Animal Science, Jilin University, Changchun 130062, ChinaCollege of Animal Science, Jilin University, Changchun 130062, ChinaCollege of Animal Science, Jilin University, Changchun 130062, ChinaCollege of Animal Science, Jilin University, Changchun 130062, ChinaCollege of Animal Science, Jilin University, Changchun 130062, ChinaCollege of Animal Science, Jilin University, Changchun 130062, ChinaCollege of Animal Science, Jilin University, Changchun 130062, ChinaChinese Red Steppe Cattle (CRS), a composite cattle breed, is well known for its milk production, high slaughter rate, carcass traits, and meat quality. Nowadays, it is widely bred in Jilin and Hebei Province and the Inner Mongolia Autonomous region. However, the population structure and the genetic basis of prominent characteristics of CRS are still unknown. In this study, we systematically describe their population structure, genetic diversity, and selection signature based on genotyping data from 61 CRS individuals with GGP Bovine 100 K chip. The results showed that CRS cattle had low inbreeding levels and had formed a unique genetic structure feature. Using two complementary methods (including comprehensive haplotype score and complex likelihood ratio), we identified 1291 and 1285 potentially selected genes, respectively. There were 141 genes annotated in common 106 overlapping genomic regions covered 5.62 Mb, including <i>PLAG1</i>, <i>PRKG2</i>, <i>DGAT1</i>, <i>PARP10</i>, <i>TONSL</i>, <i>ADCK5</i>, and <i>BMP3</i>, most of which were enriched in pathways related to muscle growth and differentiation, milk production, and lipid metabolism. This study will contribute to understanding the genetic mechanism behind artificial selection and give an extensive reference for subsequent breeding.https://www.mdpi.com/2076-2615/13/10/1717Chinese Red Steppe Cattlegenetic diversitypopulation structureselection signaturesSNP chip |
| spellingShingle | Mingyue Hu Hao Jiang Weining Lai Lulu Shi Wenfeng Yi Hao Sun Chengzhen Chen Bao Yuan Shouqing Yan Jiabao Zhang Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array Animals Chinese Red Steppe Cattle genetic diversity population structure selection signatures SNP chip |
| title | Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array |
| title_full | Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array |
| title_fullStr | Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array |
| title_full_unstemmed | Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array |
| title_short | Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array |
| title_sort | assessing genomic diversity and signatures of selection in chinese red steppe cattle using high density snp array |
| topic | Chinese Red Steppe Cattle genetic diversity population structure selection signatures SNP chip |
| url | https://www.mdpi.com/2076-2615/13/10/1717 |
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