Whole-genome resequencing revealed the genetic diversity and body weight-related genes of Gannan yak
Body weight (BW) is a crucial indicator of animal growth and development, significantly influencing animal husbandry practices. Previous research has identified several genes associated with BW in certain yak breeds. However, the genetic basis of BW in Gannan yaks has not been reported. In this stud...
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Frontiers Media S.A.
2025-06-01
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| Series: | Frontiers in Veterinary Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fvets.2025.1540523/full |
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| author | Minghao Zhang Minghao Zhang Chun Huang Chun Huang Qi Bao Tong Wang Tong Wang Xiaoming Ma Xiaoming Ma Guangyao Meng Guangyao Meng Xuelan Zhou Xuelan Zhou Qingbo Zheng Qingbo Zheng Min Chu Min Chu Chunnian Liang Chunnian Liang Xian Guo Xian Guo Pengjia Bao Pengjia Bao Ping Yan Ping Yan |
| author_facet | Minghao Zhang Minghao Zhang Chun Huang Chun Huang Qi Bao Tong Wang Tong Wang Xiaoming Ma Xiaoming Ma Guangyao Meng Guangyao Meng Xuelan Zhou Xuelan Zhou Qingbo Zheng Qingbo Zheng Min Chu Min Chu Chunnian Liang Chunnian Liang Xian Guo Xian Guo Pengjia Bao Pengjia Bao Ping Yan Ping Yan |
| author_sort | Minghao Zhang |
| collection | DOAJ |
| description | Body weight (BW) is a crucial indicator of animal growth and development, significantly influencing animal husbandry practices. Previous research has identified several genes associated with BW in certain yak breeds. However, the genetic basis of BW in Gannan yaks has not been reported. In this study, 309 yaks from six breeds across five provinces in China were sampled. This collection included 247 54-month-old female Gannan yaks, along with 20 Xizang yaks, 15 Muli yaks, 10 Pamir yaks, 9 Bazhou yaks, and 8 Zhongdian yaks. Body weight measurements were recorded for the Gannan yaks. Initial analyses of runs of homozygosity (ROH), nucleotide diversity, and linkage disequilibrium (LD) decay among the six yak breeds revealed that Gannan yaks exhibited the lowest ROH, the highest nucleotide diversity, and the fastest LD decay, indicating rich genetic diversity. Subsequently, a genome-wide association study (GWAS) identified 19 BW-related genes in the Gannan yaks, with PMAIP1, GABBR1, LRPPRC, and PPP1R11 identified as key genes. Genome-wide scanning of Group 1 and Group 2 (detailed in section 2.4) identified 90 genes, and Gene Ontology (GO) analysis highlighted FGF2, SHH, and WNT11 as significantly associated with growth, development, and metabolism. Three overlapping genes were identified between GWAS and genome-wide scans. Further analyses, including nucleotide diversity, LD analysis of significant GWAS sites, allele frequency analysis, and SNP association studies, suggested that DRC1 and SELENOI are novel candidate genes for BW in Gannan yaks. These findings provide a molecular foundation for the genetic improvement of Gannan yaks. |
| format | Article |
| id | doaj-art-239eade7927a403b89b05f6b0aa622c4 |
| institution | Kabale University |
| issn | 2297-1769 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Veterinary Science |
| spelling | doaj-art-239eade7927a403b89b05f6b0aa622c42025-08-20T03:30:15ZengFrontiers Media S.A.Frontiers in Veterinary Science2297-17692025-06-011210.3389/fvets.2025.15405231540523Whole-genome resequencing revealed the genetic diversity and body weight-related genes of Gannan yakMinghao Zhang0Minghao Zhang1Chun Huang2Chun Huang3Qi Bao4Tong Wang5Tong Wang6Xiaoming Ma7Xiaoming Ma8Guangyao Meng9Guangyao Meng10Xuelan Zhou11Xuelan Zhou12Qingbo Zheng13Qingbo Zheng14Min Chu15Min Chu16Chunnian Liang17Chunnian Liang18Xian Guo19Xian Guo20Pengjia Bao21Pengjia Bao22Ping Yan23Ping Yan24Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaKey Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaKey Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaKey Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, ChinaKey Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaKey Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaKey Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaKey Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaKey Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaKey Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaKey Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaKey Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaKey Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaKey Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaKey Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaKey Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaKey Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaKey Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaKey Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaKey Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaKey Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaKey Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaKey Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaKey Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaBody weight (BW) is a crucial indicator of animal growth and development, significantly influencing animal husbandry practices. Previous research has identified several genes associated with BW in certain yak breeds. However, the genetic basis of BW in Gannan yaks has not been reported. In this study, 309 yaks from six breeds across five provinces in China were sampled. This collection included 247 54-month-old female Gannan yaks, along with 20 Xizang yaks, 15 Muli yaks, 10 Pamir yaks, 9 Bazhou yaks, and 8 Zhongdian yaks. Body weight measurements were recorded for the Gannan yaks. Initial analyses of runs of homozygosity (ROH), nucleotide diversity, and linkage disequilibrium (LD) decay among the six yak breeds revealed that Gannan yaks exhibited the lowest ROH, the highest nucleotide diversity, and the fastest LD decay, indicating rich genetic diversity. Subsequently, a genome-wide association study (GWAS) identified 19 BW-related genes in the Gannan yaks, with PMAIP1, GABBR1, LRPPRC, and PPP1R11 identified as key genes. Genome-wide scanning of Group 1 and Group 2 (detailed in section 2.4) identified 90 genes, and Gene Ontology (GO) analysis highlighted FGF2, SHH, and WNT11 as significantly associated with growth, development, and metabolism. Three overlapping genes were identified between GWAS and genome-wide scans. Further analyses, including nucleotide diversity, LD analysis of significant GWAS sites, allele frequency analysis, and SNP association studies, suggested that DRC1 and SELENOI are novel candidate genes for BW in Gannan yaks. These findings provide a molecular foundation for the genetic improvement of Gannan yaks.https://www.frontiersin.org/articles/10.3389/fvets.2025.1540523/fullGannan yakbody weightgenetic diversitygenome-wide association studygenome-wide scanning |
| spellingShingle | Minghao Zhang Minghao Zhang Chun Huang Chun Huang Qi Bao Tong Wang Tong Wang Xiaoming Ma Xiaoming Ma Guangyao Meng Guangyao Meng Xuelan Zhou Xuelan Zhou Qingbo Zheng Qingbo Zheng Min Chu Min Chu Chunnian Liang Chunnian Liang Xian Guo Xian Guo Pengjia Bao Pengjia Bao Ping Yan Ping Yan Whole-genome resequencing revealed the genetic diversity and body weight-related genes of Gannan yak Frontiers in Veterinary Science Gannan yak body weight genetic diversity genome-wide association study genome-wide scanning |
| title | Whole-genome resequencing revealed the genetic diversity and body weight-related genes of Gannan yak |
| title_full | Whole-genome resequencing revealed the genetic diversity and body weight-related genes of Gannan yak |
| title_fullStr | Whole-genome resequencing revealed the genetic diversity and body weight-related genes of Gannan yak |
| title_full_unstemmed | Whole-genome resequencing revealed the genetic diversity and body weight-related genes of Gannan yak |
| title_short | Whole-genome resequencing revealed the genetic diversity and body weight-related genes of Gannan yak |
| title_sort | whole genome resequencing revealed the genetic diversity and body weight related genes of gannan yak |
| topic | Gannan yak body weight genetic diversity genome-wide association study genome-wide scanning |
| url | https://www.frontiersin.org/articles/10.3389/fvets.2025.1540523/full |
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