Assessing genomic diversity and signatures of selection in Pinan cattle using whole-genome sequencing data
Abstract Background Crossbreeding is an important way to improve production beef cattle performance. Pinan cattle is a new hybrid cattle obtained from crossing Piedmontese bulls with Nanyang cows. After more than 30 years of cross-breeding, Pinan cattle show a variety of excellent characteristics, i...
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| Format: | Article |
| Language: | English |
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BMC
2022-06-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-022-08645-y |
| _version_ | 1818547173892030464 |
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| author | Shunjin Zhang Zhi Yao Xinmiao Li Zijing Zhang Xian Liu Peng Yang Ningbo Chen Xiaoting Xia Shijie Lyu Qiaoting Shi Eryao Wang Baorui Ru Yu Jiang Chuzhao Lei Hong Chen Yongzhen Huang |
| author_facet | Shunjin Zhang Zhi Yao Xinmiao Li Zijing Zhang Xian Liu Peng Yang Ningbo Chen Xiaoting Xia Shijie Lyu Qiaoting Shi Eryao Wang Baorui Ru Yu Jiang Chuzhao Lei Hong Chen Yongzhen Huang |
| author_sort | Shunjin Zhang |
| collection | DOAJ |
| description | Abstract Background Crossbreeding is an important way to improve production beef cattle performance. Pinan cattle is a new hybrid cattle obtained from crossing Piedmontese bulls with Nanyang cows. After more than 30 years of cross-breeding, Pinan cattle show a variety of excellent characteristics, including fast growth, early onset of puberty, and good meat quality. In this study, we analyzed the genetic diversity, population structure, and genomic region under the selection of Pinan cattle based on whole-genome sequencing data of 30 Pinan cattle and 169 published cattle genomic data worldwide. Results Estimating ancestry composition analysis showed that the composition proportions for our Pinan cattle were mainly Piedmontese and a small amount of Nanyang cattle. The analyses of nucleotide diversity and linkage disequilibrium decay indicated that the genomic diversity of Pinan cattle was higher than that of European cattle and lower than that of Chinese indigenous cattle. De-correlated composite of multiple selection signals, which combines four different statistics including θπ, CLR, FST, and XP-EHH, was computed to detect the signatures of selection in the Pinan cattle genome. A total of 83 genes were identified, affecting many economically important traits. Functional annotation revealed that these selected genes were related to immune (BOLA-DQA2, BOLA-DQB, LSM14A, SEC13, and NAALADL2), growth traits (CYP4A11, RPL26, and MYH10), embryo development (REV3L, NT5E, CDX2, KDM6B, and ADAMTS9), hornless traits (C1H21orf62), and climate adaptation (ANTXR2). Conclusion In this paper, we elucidated the genomic characteristics, ancestry composition, and selective signals related to important economic traits in Pinan cattle. These results will provide the basis for further genetic improvement of Pinan cattle and reference for other hybrid cattle related studies. |
| first_indexed | 2024-12-12T08:03:11Z |
| format | Article |
| id | doaj.art-76f7f7f9b0cd4f93bc0697816c170414 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-12T08:03:11Z |
| publishDate | 2022-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-76f7f7f9b0cd4f93bc0697816c1704142022-12-22T00:32:04ZengBMCBMC Genomics1471-21642022-06-0123111010.1186/s12864-022-08645-yAssessing genomic diversity and signatures of selection in Pinan cattle using whole-genome sequencing dataShunjin Zhang0Zhi Yao1Xinmiao Li2Zijing Zhang3Xian Liu4Peng Yang5Ningbo Chen6Xiaoting Xia7Shijie Lyu8Qiaoting Shi9Eryao Wang10Baorui Ru11Yu Jiang12Chuzhao Lei13Hong Chen14Yongzhen Huang15Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F UniversityKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F UniversityKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F UniversityInstitute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural SciencesHenan Provincial Animal Husbandry General StationKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F UniversityKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F UniversityKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F UniversityInstitute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural SciencesInstitute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural SciencesInstitute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural SciencesHenan Provincial Animal Husbandry General StationKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F UniversityKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F UniversityKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F UniversityKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F UniversityAbstract Background Crossbreeding is an important way to improve production beef cattle performance. Pinan cattle is a new hybrid cattle obtained from crossing Piedmontese bulls with Nanyang cows. After more than 30 years of cross-breeding, Pinan cattle show a variety of excellent characteristics, including fast growth, early onset of puberty, and good meat quality. In this study, we analyzed the genetic diversity, population structure, and genomic region under the selection of Pinan cattle based on whole-genome sequencing data of 30 Pinan cattle and 169 published cattle genomic data worldwide. Results Estimating ancestry composition analysis showed that the composition proportions for our Pinan cattle were mainly Piedmontese and a small amount of Nanyang cattle. The analyses of nucleotide diversity and linkage disequilibrium decay indicated that the genomic diversity of Pinan cattle was higher than that of European cattle and lower than that of Chinese indigenous cattle. De-correlated composite of multiple selection signals, which combines four different statistics including θπ, CLR, FST, and XP-EHH, was computed to detect the signatures of selection in the Pinan cattle genome. A total of 83 genes were identified, affecting many economically important traits. Functional annotation revealed that these selected genes were related to immune (BOLA-DQA2, BOLA-DQB, LSM14A, SEC13, and NAALADL2), growth traits (CYP4A11, RPL26, and MYH10), embryo development (REV3L, NT5E, CDX2, KDM6B, and ADAMTS9), hornless traits (C1H21orf62), and climate adaptation (ANTXR2). Conclusion In this paper, we elucidated the genomic characteristics, ancestry composition, and selective signals related to important economic traits in Pinan cattle. These results will provide the basis for further genetic improvement of Pinan cattle and reference for other hybrid cattle related studies.https://doi.org/10.1186/s12864-022-08645-yPinan cattleWGSGenetic diversityPopulation StructureDCMS |
| spellingShingle | Shunjin Zhang Zhi Yao Xinmiao Li Zijing Zhang Xian Liu Peng Yang Ningbo Chen Xiaoting Xia Shijie Lyu Qiaoting Shi Eryao Wang Baorui Ru Yu Jiang Chuzhao Lei Hong Chen Yongzhen Huang Assessing genomic diversity and signatures of selection in Pinan cattle using whole-genome sequencing data BMC Genomics Pinan cattle WGS Genetic diversity Population Structure DCMS |
| title | Assessing genomic diversity and signatures of selection in Pinan cattle using whole-genome sequencing data |
| title_full | Assessing genomic diversity and signatures of selection in Pinan cattle using whole-genome sequencing data |
| title_fullStr | Assessing genomic diversity and signatures of selection in Pinan cattle using whole-genome sequencing data |
| title_full_unstemmed | Assessing genomic diversity and signatures of selection in Pinan cattle using whole-genome sequencing data |
| title_short | Assessing genomic diversity and signatures of selection in Pinan cattle using whole-genome sequencing data |
| title_sort | assessing genomic diversity and signatures of selection in pinan cattle using whole genome sequencing data |
| topic | Pinan cattle WGS Genetic diversity Population Structure DCMS |
| url | https://doi.org/10.1186/s12864-022-08645-y |
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