Identification of Taihang-chicken-specific genetic markers using genome-wide SNPs and machine learning
Taihang is an indigenous breed in Hebei Province and has a long history of evolution. To uncover the genetic basis and protect the genetic resources, it is important to develop accurate markers to identify Taihang at the molecular level. In this study, a total of 137 individuals from Taihang and oth...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-01-01
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| Series: | Poultry Science |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0032579124011635 |
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| author | Fu Wei Zhang Ran Ding Hong Wang Wenjun Liu Huage Zang Sumin Zhou Rongyan |
| author_facet | Fu Wei Zhang Ran Ding Hong Wang Wenjun Liu Huage Zang Sumin Zhou Rongyan |
| author_sort | Fu Wei |
| collection | DOAJ |
| description | Taihang is an indigenous breed in Hebei Province and has a long history of evolution. To uncover the genetic basis and protect the genetic resources, it is important to develop accurate markers to identify Taihang at the molecular level. In this study, a total of 137 individuals from Taihang and other 4 breeds were selected to construct a genome-wide SNP map. The population genetic structure analysis revealed clear differentiation among the five breeds. A total of 47 SNPs were identified for differentiating Taihang from other breeds based on the fixation index (FST), linkage disequilibrium (LD) pruning, and machine learning, further validated using principal component analysis (PCA) and genetic relationship matrix (GRM). The 47 SNPs were annotated to genes associated with production, growth and development, immunity, adaptation, and appearance. Overall, the combination of 47 SNPs enables precise identification of Taihang, which significantly contributes to the preservation of native genetic resources. |
| format | Article |
| id | doaj-art-12e150e7e20f4b3a9c88cce62836b38c |
| institution | Kabale University |
| issn | 0032-5791 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Poultry Science |
| spelling | doaj-art-12e150e7e20f4b3a9c88cce62836b38c2025-01-22T05:40:35ZengElsevierPoultry Science0032-57912025-01-011041104585Identification of Taihang-chicken-specific genetic markers using genome-wide SNPs and machine learningFu Wei0Zhang Ran1Ding Hong2Wang Wenjun3Liu Huage4Zang Sumin5Zhou Rongyan6Hebei Agricultural University, Baoding, Hebei province 071001, ChinaHebei Agricultural University, Baoding, Hebei province 071001, ChinaInstitute of Animal Science and Veterinary Medicine, Baoding, Hebei province 071000, ChinaHebei Agricultural University, Baoding, Hebei province 071001, ChinaInstitute of Animal Science and Veterinary Medicine, Baoding, Hebei province 071000, ChinaHebei Agricultural University, Baoding, Hebei province 071001, ChinaHebei Agricultural University, Baoding, Hebei province 071001, China; Corresponding author.Taihang is an indigenous breed in Hebei Province and has a long history of evolution. To uncover the genetic basis and protect the genetic resources, it is important to develop accurate markers to identify Taihang at the molecular level. In this study, a total of 137 individuals from Taihang and other 4 breeds were selected to construct a genome-wide SNP map. The population genetic structure analysis revealed clear differentiation among the five breeds. A total of 47 SNPs were identified for differentiating Taihang from other breeds based on the fixation index (FST), linkage disequilibrium (LD) pruning, and machine learning, further validated using principal component analysis (PCA) and genetic relationship matrix (GRM). The 47 SNPs were annotated to genes associated with production, growth and development, immunity, adaptation, and appearance. Overall, the combination of 47 SNPs enables precise identification of Taihang, which significantly contributes to the preservation of native genetic resources.http://www.sciencedirect.com/science/article/pii/S0032579124011635Taihang chickenSpecific SNPsMachine learningBreed indentification |
| spellingShingle | Fu Wei Zhang Ran Ding Hong Wang Wenjun Liu Huage Zang Sumin Zhou Rongyan Identification of Taihang-chicken-specific genetic markers using genome-wide SNPs and machine learning Poultry Science Taihang chicken Specific SNPs Machine learning Breed indentification |
| title | Identification of Taihang-chicken-specific genetic markers using genome-wide SNPs and machine learning |
| title_full | Identification of Taihang-chicken-specific genetic markers using genome-wide SNPs and machine learning |
| title_fullStr | Identification of Taihang-chicken-specific genetic markers using genome-wide SNPs and machine learning |
| title_full_unstemmed | Identification of Taihang-chicken-specific genetic markers using genome-wide SNPs and machine learning |
| title_short | Identification of Taihang-chicken-specific genetic markers using genome-wide SNPs and machine learning |
| title_sort | identification of taihang chicken specific genetic markers using genome wide snps and machine learning |
| topic | Taihang chicken Specific SNPs Machine learning Breed indentification |
| url | http://www.sciencedirect.com/science/article/pii/S0032579124011635 |
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