Whole-genome sequencing reveals genetic structure and adaptive genes in Nepalese buffalo breeds
Abstract Background Indigenous buffaloes, as the important livestock species contributing to economy of the country, are the lifeline of livelihood in Nepal. They are distributed across diverse geographical regions of the country and have adapted to various feeding, breeding, and management conditio...
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BMC
2024-11-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-024-10993-w |
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| author | Aashish Dhakal Jingfang Si Saroj Sapkota Alfredo Pauciullo Jianlin Han Neena Amatya Gorkhali Xingbo Zhao Yi Zhang |
| author_facet | Aashish Dhakal Jingfang Si Saroj Sapkota Alfredo Pauciullo Jianlin Han Neena Amatya Gorkhali Xingbo Zhao Yi Zhang |
| author_sort | Aashish Dhakal |
| collection | DOAJ |
| description | Abstract Background Indigenous buffaloes, as the important livestock species contributing to economy of the country, are the lifeline of livelihood in Nepal. They are distributed across diverse geographical regions of the country and have adapted to various feeding, breeding, and management conditions. The larger group of these native buffalo breeds are present in narrow and stiff hilly terrains. Their dispersal indicates a possible environmental adaptation mechanism, which is crucial for the conservation of these breeds. Results We utilized whole-genome sequencing (WGS) to investigate the genetic diversity, population structure, and selection signatures of Nepalese indigenous buffaloes. We compared 66 whole-genome sequences with 118 publicly available sequences from six river and five swamp buffalo breeds. Genomic diversity parameters indicated genetic variability level in the Nepalese buffaloes comparable to those of Indian breeds, and population genetic structure revealed distinct geography-mediated genetic differentiation among these breeds. We used locus-specific branch length analysis (LSBL) for genome-wide scan, which revealed a list of potentially selected genes in Lime and Parkote breeds that inhabit the hilly region. A gene ontology (GO) analysis discovered that many GO terms were associated with cardiac function regulation. Furthermore, complementary analyses of local selection signatures, tissue expression profiles, and haplotype differences identified candidate genes, including KCNE1, CSF1R, and PDGFRB, related to the regulation of cardiac and pulmonary functions. Conclusions This study is a comprehensive WGS-based genetic analysis of the native Nepalese buffalo breeds. Our study suggested that the Nepalese “hilly” buffaloes, especially the Lime and Parkote breeds, have undergone some characteristic genetic changes and evolved increased cardiac and pulmonary function for their adaptation to the steep hilly terrains of the country. |
| format | Article |
| id | doaj-art-4c30547b2ec647439c3bfcd35d838c19 |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-4c30547b2ec647439c3bfcd35d838c192024-11-17T12:11:27ZengBMCBMC Genomics1471-21642024-11-0125111110.1186/s12864-024-10993-wWhole-genome sequencing reveals genetic structure and adaptive genes in Nepalese buffalo breedsAashish Dhakal0Jingfang Si1Saroj Sapkota2Alfredo Pauciullo3Jianlin Han4Neena Amatya Gorkhali5Xingbo Zhao6Yi Zhang7State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural UniversityState Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural UniversityNational Animal Breeding and Genetics Research Centre, Nepal Agricultural Research CouncilDepartment of Agricultural, Forest and Food Sciences, University of TorinoYazhouwan National LaboratoryNational Animal Breeding and Genetics Research Centre, Nepal Agricultural Research CouncilState Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural UniversityState Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural UniversityAbstract Background Indigenous buffaloes, as the important livestock species contributing to economy of the country, are the lifeline of livelihood in Nepal. They are distributed across diverse geographical regions of the country and have adapted to various feeding, breeding, and management conditions. The larger group of these native buffalo breeds are present in narrow and stiff hilly terrains. Their dispersal indicates a possible environmental adaptation mechanism, which is crucial for the conservation of these breeds. Results We utilized whole-genome sequencing (WGS) to investigate the genetic diversity, population structure, and selection signatures of Nepalese indigenous buffaloes. We compared 66 whole-genome sequences with 118 publicly available sequences from six river and five swamp buffalo breeds. Genomic diversity parameters indicated genetic variability level in the Nepalese buffaloes comparable to those of Indian breeds, and population genetic structure revealed distinct geography-mediated genetic differentiation among these breeds. We used locus-specific branch length analysis (LSBL) for genome-wide scan, which revealed a list of potentially selected genes in Lime and Parkote breeds that inhabit the hilly region. A gene ontology (GO) analysis discovered that many GO terms were associated with cardiac function regulation. Furthermore, complementary analyses of local selection signatures, tissue expression profiles, and haplotype differences identified candidate genes, including KCNE1, CSF1R, and PDGFRB, related to the regulation of cardiac and pulmonary functions. Conclusions This study is a comprehensive WGS-based genetic analysis of the native Nepalese buffalo breeds. Our study suggested that the Nepalese “hilly” buffaloes, especially the Lime and Parkote breeds, have undergone some characteristic genetic changes and evolved increased cardiac and pulmonary function for their adaptation to the steep hilly terrains of the country.https://doi.org/10.1186/s12864-024-10993-wWhole-genome sequencingBuffaloGenetic diversityPopulation structureSelection signaturesNepal |
| spellingShingle | Aashish Dhakal Jingfang Si Saroj Sapkota Alfredo Pauciullo Jianlin Han Neena Amatya Gorkhali Xingbo Zhao Yi Zhang Whole-genome sequencing reveals genetic structure and adaptive genes in Nepalese buffalo breeds BMC Genomics Whole-genome sequencing Buffalo Genetic diversity Population structure Selection signatures Nepal |
| title | Whole-genome sequencing reveals genetic structure and adaptive genes in Nepalese buffalo breeds |
| title_full | Whole-genome sequencing reveals genetic structure and adaptive genes in Nepalese buffalo breeds |
| title_fullStr | Whole-genome sequencing reveals genetic structure and adaptive genes in Nepalese buffalo breeds |
| title_full_unstemmed | Whole-genome sequencing reveals genetic structure and adaptive genes in Nepalese buffalo breeds |
| title_short | Whole-genome sequencing reveals genetic structure and adaptive genes in Nepalese buffalo breeds |
| title_sort | whole genome sequencing reveals genetic structure and adaptive genes in nepalese buffalo breeds |
| topic | Whole-genome sequencing Buffalo Genetic diversity Population structure Selection signatures Nepal |
| url | https://doi.org/10.1186/s12864-024-10993-w |
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