Genetic Origin and Introgression Pattern of Pingliang Red Cattle Revealed Using Genome-Wide SNP Analyses
The Pingliang red cattle, an outstanding indigenous resource in China, possesses an exceptional breeding value attributed to its tender meat and superior marbling quality. Currently, research efforts have predominantly concentrated on exploring its maternal origin and conducting conventional phenoty...
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| Format: | Article |
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MDPI AG
2023-12-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/12/2198 |
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| author | Yuanqing Wang Jun Ma Jing Wang Lupei Zhang Junwei Hu Minghao Ma Lingyang Xu Yan Chen Bo Zhu Zezhao Wang Huijiang Gao Junya Li Xue Gao |
| author_facet | Yuanqing Wang Jun Ma Jing Wang Lupei Zhang Junwei Hu Minghao Ma Lingyang Xu Yan Chen Bo Zhu Zezhao Wang Huijiang Gao Junya Li Xue Gao |
| author_sort | Yuanqing Wang |
| collection | DOAJ |
| description | The Pingliang red cattle, an outstanding indigenous resource in China, possesses an exceptional breeding value attributed to its tender meat and superior marbling quality. Currently, research efforts have predominantly concentrated on exploring its maternal origin and conducting conventional phenotypic studies. However, there remains a lack of comprehensive understanding regarding its genetic basis. To address this gap, we conducted a thorough whole-genome analysis to investigate the population structure, phylogenetic relationships, and gene flows of this breed using genomic SNP chip data from 17 bovine breeds. The results demonstrate that Pingliang red cattle have evolved distinct genetic characteristics unique to this breed, clearly distinguishing it from other breeds. Based on the analysis of the population structure and phylogenetic tree, it can be classified as a hybrid lineage between <i>Bos taurus</i> and <i>Bos indicus</i>. Furthermore, Pingliang red cattle display a more prominent <i>B. taurus</i> pedigree in comparison with Jinnan, Qinchuan, Zaosheng, Nanyang, and Luxi cattle. Moreover, this study also revealed closer genetic proximity within the Chinese indigenous cattle breed, particularly Qinchuan cattle, which shares the longest identical by descent (IBD) fragment with Pingliang red cattle. Gene introgression analysis shows that Pingliang red cattle have undergone gene exchange with South Devon and Red Angus cattle from Europe. Admixture analysis revealed that the proportions of East Asian taurine and Chinese indicine in the ancestry of Pingliang red cattle are approximately 52.44% and 21.00%, respectively, while Eurasian taurine, European taurine, and Indian indicine account for approximately 17.55%, 7.27%, and 1.74%. Our findings unveil distinct genetic characteristics in Pingliang red cattle and attribute their origin to <i>B. taurus</i> and <i>B. indicus</i> ancestry, as well as contributions from Qinchuan cattle, South Devon, and Red Angus. |
| first_indexed | 2024-03-08T20:43:29Z |
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| id | doaj.art-18cdd2909bc34319aaa918d2b0159224 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-08T20:43:29Z |
| publishDate | 2023-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-18cdd2909bc34319aaa918d2b01592242023-12-22T14:11:17ZengMDPI AGGenes2073-44252023-12-011412219810.3390/genes14122198Genetic Origin and Introgression Pattern of Pingliang Red Cattle Revealed Using Genome-Wide SNP AnalysesYuanqing Wang0Jun Ma1Jing Wang2Lupei Zhang3Junwei Hu4Minghao Ma5Lingyang Xu6Yan Chen7Bo Zhu8Zezhao Wang9Huijiang Gao10Junya Li11Xue Gao12Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaAcademy of Pingliang Red Cattle, 492 South Ring Road, Kongtong District, Pingliang 744000, ChinaAcademy of Pingliang Red Cattle, 492 South Ring Road, Kongtong District, Pingliang 744000, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaThe Pingliang red cattle, an outstanding indigenous resource in China, possesses an exceptional breeding value attributed to its tender meat and superior marbling quality. Currently, research efforts have predominantly concentrated on exploring its maternal origin and conducting conventional phenotypic studies. However, there remains a lack of comprehensive understanding regarding its genetic basis. To address this gap, we conducted a thorough whole-genome analysis to investigate the population structure, phylogenetic relationships, and gene flows of this breed using genomic SNP chip data from 17 bovine breeds. The results demonstrate that Pingliang red cattle have evolved distinct genetic characteristics unique to this breed, clearly distinguishing it from other breeds. Based on the analysis of the population structure and phylogenetic tree, it can be classified as a hybrid lineage between <i>Bos taurus</i> and <i>Bos indicus</i>. Furthermore, Pingliang red cattle display a more prominent <i>B. taurus</i> pedigree in comparison with Jinnan, Qinchuan, Zaosheng, Nanyang, and Luxi cattle. Moreover, this study also revealed closer genetic proximity within the Chinese indigenous cattle breed, particularly Qinchuan cattle, which shares the longest identical by descent (IBD) fragment with Pingliang red cattle. Gene introgression analysis shows that Pingliang red cattle have undergone gene exchange with South Devon and Red Angus cattle from Europe. Admixture analysis revealed that the proportions of East Asian taurine and Chinese indicine in the ancestry of Pingliang red cattle are approximately 52.44% and 21.00%, respectively, while Eurasian taurine, European taurine, and Indian indicine account for approximately 17.55%, 7.27%, and 1.74%. Our findings unveil distinct genetic characteristics in Pingliang red cattle and attribute their origin to <i>B. taurus</i> and <i>B. indicus</i> ancestry, as well as contributions from Qinchuan cattle, South Devon, and Red Angus.https://www.mdpi.com/2073-4425/14/12/2198Pingliang red cattlepopulation geneticsgenetic originintrogression pattern |
| spellingShingle | Yuanqing Wang Jun Ma Jing Wang Lupei Zhang Junwei Hu Minghao Ma Lingyang Xu Yan Chen Bo Zhu Zezhao Wang Huijiang Gao Junya Li Xue Gao Genetic Origin and Introgression Pattern of Pingliang Red Cattle Revealed Using Genome-Wide SNP Analyses Genes Pingliang red cattle population genetics genetic origin introgression pattern |
| title | Genetic Origin and Introgression Pattern of Pingliang Red Cattle Revealed Using Genome-Wide SNP Analyses |
| title_full | Genetic Origin and Introgression Pattern of Pingliang Red Cattle Revealed Using Genome-Wide SNP Analyses |
| title_fullStr | Genetic Origin and Introgression Pattern of Pingliang Red Cattle Revealed Using Genome-Wide SNP Analyses |
| title_full_unstemmed | Genetic Origin and Introgression Pattern of Pingliang Red Cattle Revealed Using Genome-Wide SNP Analyses |
| title_short | Genetic Origin and Introgression Pattern of Pingliang Red Cattle Revealed Using Genome-Wide SNP Analyses |
| title_sort | genetic origin and introgression pattern of pingliang red cattle revealed using genome wide snp analyses |
| topic | Pingliang red cattle population genetics genetic origin introgression pattern |
| url | https://www.mdpi.com/2073-4425/14/12/2198 |
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