Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array
Huaxi cattle, a specialized beef cattle breed in China, has the characteristics of fast growth, high slaughter rate, and net meat rate, good reproductive performance, strong stress resistance, and wide adaptability. In this study, we evaluated the genetic diversity, population structure, and genetic...
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MDPI AG
2021-12-01
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| Online Access: | https://www.mdpi.com/2076-2615/11/12/3469 |
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| author | Jun Ma Xue Gao Junya Li Huijiang Gao Zezhao Wang Lupei Zhang Lingyang Xu Han Gao Hongwei Li Yahui Wang Bo Zhu Wentao Cai Congyong Wang Yan Chen |
| author_facet | Jun Ma Xue Gao Junya Li Huijiang Gao Zezhao Wang Lupei Zhang Lingyang Xu Han Gao Hongwei Li Yahui Wang Bo Zhu Wentao Cai Congyong Wang Yan Chen |
| author_sort | Jun Ma |
| collection | DOAJ |
| description | Huaxi cattle, a specialized beef cattle breed in China, has the characteristics of fast growth, high slaughter rate, and net meat rate, good reproductive performance, strong stress resistance, and wide adaptability. In this study, we evaluated the genetic diversity, population structure, and genetic relationships of Huaxi cattle and its ancestor populations at the genome-wide level, as well as detecting the selection signatures of Huaxi cattle. Principal component analysis (PCA) and phylogenetic analysis revealed that Huaxi cattle were obviously separated from other cattle populations. The admixture analysis showed that Huaxi cattle has distinct genetic structures among all populations at K = 4. It can be concluded that Huaxi cattle has formed its own unique genetic features. Using integrated haplotype score (iHS) and composite likelihood ratio (CLR) methods, we identified 143 and 199 potentially selected genes in Huaxi cattle, respectively, among which nine selected genes (<i>KCNK1</i>, <i>PDLIM5</i>, <i>CPXM2</i>, <i>CAPN14</i>, <i>MIR2285D</i>, <i>MYOF</i>, <i>PKDCC</i>, <i>FOXN3</i>, and <i>EHD3</i>) related to ion binding, muscle growth and differentiation, and immunity were detected by both methods. Our study sheds light on the unique genetic feature and phylogenetic relationship of Huaxi cattle, provides a basis for the genetic mechanism analysis of important economic traits, and guides further intensive breeding improvement of Huaxi cattle. |
| first_indexed | 2024-03-10T04:39:31Z |
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| language | English |
| last_indexed | 2024-03-10T04:39:31Z |
| publishDate | 2021-12-01 |
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| record_format | Article |
| series | Animals |
| spelling | doaj.art-5b8d61c33d9e4e989eb1931161bb8a212023-11-23T03:27:27ZengMDPI AGAnimals2076-26152021-12-011112346910.3390/ani11123469Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP ArrayJun Ma0Xue Gao1Junya Li2Huijiang Gao3Zezhao Wang4Lupei Zhang5Lingyang Xu6Han Gao7Hongwei Li8Yahui Wang9Bo Zhu10Wentao Cai11Congyong Wang12Yan Chen13Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaBeijing Lianyu Beef Cattle Breeding Technology Limited Company, Beijing 100193, ChinaInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaHuaxi cattle, a specialized beef cattle breed in China, has the characteristics of fast growth, high slaughter rate, and net meat rate, good reproductive performance, strong stress resistance, and wide adaptability. In this study, we evaluated the genetic diversity, population structure, and genetic relationships of Huaxi cattle and its ancestor populations at the genome-wide level, as well as detecting the selection signatures of Huaxi cattle. Principal component analysis (PCA) and phylogenetic analysis revealed that Huaxi cattle were obviously separated from other cattle populations. The admixture analysis showed that Huaxi cattle has distinct genetic structures among all populations at K = 4. It can be concluded that Huaxi cattle has formed its own unique genetic features. Using integrated haplotype score (iHS) and composite likelihood ratio (CLR) methods, we identified 143 and 199 potentially selected genes in Huaxi cattle, respectively, among which nine selected genes (<i>KCNK1</i>, <i>PDLIM5</i>, <i>CPXM2</i>, <i>CAPN14</i>, <i>MIR2285D</i>, <i>MYOF</i>, <i>PKDCC</i>, <i>FOXN3</i>, and <i>EHD3</i>) related to ion binding, muscle growth and differentiation, and immunity were detected by both methods. Our study sheds light on the unique genetic feature and phylogenetic relationship of Huaxi cattle, provides a basis for the genetic mechanism analysis of important economic traits, and guides further intensive breeding improvement of Huaxi cattle.https://www.mdpi.com/2076-2615/11/12/3469Huaxi cattlegenetic diversitypopulation structuregenetic relationshipsselection signature |
| spellingShingle | Jun Ma Xue Gao Junya Li Huijiang Gao Zezhao Wang Lupei Zhang Lingyang Xu Han Gao Hongwei Li Yahui Wang Bo Zhu Wentao Cai Congyong Wang Yan Chen Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array Animals Huaxi cattle genetic diversity population structure genetic relationships selection signature |
| title | Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array |
| title_full | Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array |
| title_fullStr | Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array |
| title_full_unstemmed | Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array |
| title_short | Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array |
| title_sort | assessing the genetic background and selection signatures of huaxi cattle using high density snp array |
| topic | Huaxi cattle genetic diversity population structure genetic relationships selection signature |
| url | https://www.mdpi.com/2076-2615/11/12/3469 |
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