Whole-genome resequencing reveals the population structure and domestication processes of endemic endangered goose breeds (Anser cygnoides)
In recent years, the dwindling population of these endangered geese has hindered our understanding of their phenotypic variations and the genes associated with important traits. To investigate the population structure and genetic diversity of this breed, the whole-genome data of 90 individuals from...
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Elsevier
2025-05-01
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| Series: | Poultry Science |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0032579125002433 |
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| author | Shangzong Qi Teng Wu Hao Wu Yu Liang Wenming Zhao Yang Zhang Qi Xu Guohong Chen |
| author_facet | Shangzong Qi Teng Wu Hao Wu Yu Liang Wenming Zhao Yang Zhang Qi Xu Guohong Chen |
| author_sort | Shangzong Qi |
| collection | DOAJ |
| description | In recent years, the dwindling population of these endangered geese has hindered our understanding of their phenotypic variations and the genes associated with important traits. To investigate the population structure and genetic diversity of this breed, the whole-genome data of 90 individuals from a conservation farm were obtained using the Illumina 6000 paired-end platform. The research results indicate that each locally endangered goose variety has formed a monophyletic population. The Baizi (BZ), Lingxian White (LX), and Xupu (XP) geese exhibiting higher genetic diversity than the other goose breeds. Tree-Mix analysis revealed the presence of five gene flows events between goose populations, with Yangjiang (YJ) geese consistently exhibiting significant genetic distance from the other breeds. Under strong pressures from the natural environment and artificial selection, whole-genome selective scanning revealed 394 overlapping genes. Gene Ontology (GO) enrichment analysis of the putative candidate genes (PCGs) revealed significant enrichment of 20 terms (P < 0.05). Similarly, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed significant enrichment of PCGs in 23 terms (P < 0.05). Examination of overlapping genes identified through at least two selection methods revealed a set of genes associated with key traits, including growth and development (CCND1, DES, CCNO, SMC5, and NUBP1), immunity (ABCA2, ABCC8, UHRF2, and ABCA1), and body aging (KAT6B). Our findings provide insights into the genetic basis of endangered geese at the whole-genome level, laying the foundation for future molecular research on genetic variation and phenotypic changes. In summary, our results provide invaluable resources for delineating the uniqueness of endangered goose breeds. |
| format | Article |
| id | doaj-art-170cc033d8984a04b403eccd664f31b0 |
| institution | DOAJ |
| issn | 0032-5791 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Poultry Science |
| spelling | doaj-art-170cc033d8984a04b403eccd664f31b02025-08-20T03:09:44ZengElsevierPoultry Science0032-57912025-05-01104510500410.1016/j.psj.2025.105004Whole-genome resequencing reveals the population structure and domestication processes of endemic endangered goose breeds (Anser cygnoides)Shangzong Qi0Teng Wu1Hao Wu2Yu Liang3Wenming Zhao4Yang Zhang5Qi Xu6Guohong Chen7College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, PR ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, PR ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, PR ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, PR ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, PR ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, PR China; Key Laboratory for Evaluation and Utilization of Livestock and Poultry Resources (Poultry), Ministry of Agriculture and Rural Affairs, PR China; Corresponding authors at: No. 48 Wenhui East Road, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, PR China.College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu Province, 225009, PR China; Key Laboratory for Evaluation and Utilization of Livestock and Poultry Resources (Poultry), Ministry of Agriculture and Rural Affairs, PR ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu Province, 225009, PR China; Key Laboratory for Evaluation and Utilization of Livestock and Poultry Resources (Poultry), Ministry of Agriculture and Rural Affairs, PR ChinaIn recent years, the dwindling population of these endangered geese has hindered our understanding of their phenotypic variations and the genes associated with important traits. To investigate the population structure and genetic diversity of this breed, the whole-genome data of 90 individuals from a conservation farm were obtained using the Illumina 6000 paired-end platform. The research results indicate that each locally endangered goose variety has formed a monophyletic population. The Baizi (BZ), Lingxian White (LX), and Xupu (XP) geese exhibiting higher genetic diversity than the other goose breeds. Tree-Mix analysis revealed the presence of five gene flows events between goose populations, with Yangjiang (YJ) geese consistently exhibiting significant genetic distance from the other breeds. Under strong pressures from the natural environment and artificial selection, whole-genome selective scanning revealed 394 overlapping genes. Gene Ontology (GO) enrichment analysis of the putative candidate genes (PCGs) revealed significant enrichment of 20 terms (P < 0.05). Similarly, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed significant enrichment of PCGs in 23 terms (P < 0.05). Examination of overlapping genes identified through at least two selection methods revealed a set of genes associated with key traits, including growth and development (CCND1, DES, CCNO, SMC5, and NUBP1), immunity (ABCA2, ABCC8, UHRF2, and ABCA1), and body aging (KAT6B). Our findings provide insights into the genetic basis of endangered geese at the whole-genome level, laying the foundation for future molecular research on genetic variation and phenotypic changes. In summary, our results provide invaluable resources for delineating the uniqueness of endangered goose breeds.http://www.sciencedirect.com/science/article/pii/S0032579125002433Endemic endangered geeseWhole-genome resequencingPopulation genetic structureSelective sweep |
| spellingShingle | Shangzong Qi Teng Wu Hao Wu Yu Liang Wenming Zhao Yang Zhang Qi Xu Guohong Chen Whole-genome resequencing reveals the population structure and domestication processes of endemic endangered goose breeds (Anser cygnoides) Poultry Science Endemic endangered geese Whole-genome resequencing Population genetic structure Selective sweep |
| title | Whole-genome resequencing reveals the population structure and domestication processes of endemic endangered goose breeds (Anser cygnoides) |
| title_full | Whole-genome resequencing reveals the population structure and domestication processes of endemic endangered goose breeds (Anser cygnoides) |
| title_fullStr | Whole-genome resequencing reveals the population structure and domestication processes of endemic endangered goose breeds (Anser cygnoides) |
| title_full_unstemmed | Whole-genome resequencing reveals the population structure and domestication processes of endemic endangered goose breeds (Anser cygnoides) |
| title_short | Whole-genome resequencing reveals the population structure and domestication processes of endemic endangered goose breeds (Anser cygnoides) |
| title_sort | whole genome resequencing reveals the population structure and domestication processes of endemic endangered goose breeds anser cygnoides |
| topic | Endemic endangered geese Whole-genome resequencing Population genetic structure Selective sweep |
| url | http://www.sciencedirect.com/science/article/pii/S0032579125002433 |
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