Identification and validation of novel breed-specific biomarker for the purpose of village chicken authentication using genomics approaches
Local village chicken, or "Ayam kampung" as it's known in Malaysia, is considered a premium chicken breed with a higher price than other chicken breeds. As a result of their comparable appearances and sizes, colored broiler chickens are often sold as village chickens, which is a form...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2024
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| Online Access: | http://psasir.upm.edu.my/id/eprint/113734/ http://psasir.upm.edu.my/id/eprint/113734/1/113734.pdf |
| _version_ | 1848866306986606592 |
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| author | Nematbakhsh, Sara Pei, Chong Pei Nordin, Noordiana Selamat, Jinap Idris, Lokman Hakim Abdull Razis, Ahmad Faizal |
| author_facet | Nematbakhsh, Sara Pei, Chong Pei Nordin, Noordiana Selamat, Jinap Idris, Lokman Hakim Abdull Razis, Ahmad Faizal |
| author_sort | Nematbakhsh, Sara |
| building | UPM Institutional Repository |
| collection | Online Access |
| description | Local village chicken, or "Ayam kampung" as it's known in Malaysia, is considered a premium chicken breed with a higher price than other chicken breeds. As a result of their comparable appearances and sizes, colored broiler chickens are often sold as village chickens, which is a form of food fraud that can result in a 3- to 4-fold rise in profit. Therefore, developing a breed-specific authentication method is crucial for preventing food fraud in the poultry industry. This study aims to investigate the genetic diversity of village chickens from other commercial chicken breed populations available in the market (broiler [Cobb], colored broiler [Hubbard], and layer [DeKalb]) to identify breed-specific DNA fragments as biomarkers for village chicken authentication. The Whole-genome sequencing and mutation calling of 12 chickens (3 chickens/breed) led to the identification of a total of 73,454,654 single nucleotide polymorphisms (SNP) and 8,762,338 insertion and deletions (InDel) variants, with more variants detected in the village chicken population (6,346,704 SNPs; 752,408 InDels) compared to commercial breeds. Therefore, this study revealed that village chickens were more genetically variable compared to other breeds in Malaysia. Furthermore, the breed-specific genomic region located on chromosome 1 (1:84,405,652) harboring SNP (C–T) with high discrimination power was discovered and validated which can be considered as a novel breed-specific biomarker to develop a method for accurate authentication of village chickens in Malaysia. This authentication method offers potentialw applications in the chicken industry and food safety. © 2024 The Authors |
| first_indexed | 2025-11-15T14:18:31Z |
| format | Article |
| id | upm-113734 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T14:18:31Z |
| publishDate | 2024 |
| publisher | Elsevier |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-1137342025-01-15T06:32:47Z http://psasir.upm.edu.my/id/eprint/113734/ Identification and validation of novel breed-specific biomarker for the purpose of village chicken authentication using genomics approaches Nematbakhsh, Sara Pei, Chong Pei Nordin, Noordiana Selamat, Jinap Idris, Lokman Hakim Abdull Razis, Ahmad Faizal Local village chicken, or "Ayam kampung" as it's known in Malaysia, is considered a premium chicken breed with a higher price than other chicken breeds. As a result of their comparable appearances and sizes, colored broiler chickens are often sold as village chickens, which is a form of food fraud that can result in a 3- to 4-fold rise in profit. Therefore, developing a breed-specific authentication method is crucial for preventing food fraud in the poultry industry. This study aims to investigate the genetic diversity of village chickens from other commercial chicken breed populations available in the market (broiler [Cobb], colored broiler [Hubbard], and layer [DeKalb]) to identify breed-specific DNA fragments as biomarkers for village chicken authentication. The Whole-genome sequencing and mutation calling of 12 chickens (3 chickens/breed) led to the identification of a total of 73,454,654 single nucleotide polymorphisms (SNP) and 8,762,338 insertion and deletions (InDel) variants, with more variants detected in the village chicken population (6,346,704 SNPs; 752,408 InDels) compared to commercial breeds. Therefore, this study revealed that village chickens were more genetically variable compared to other breeds in Malaysia. Furthermore, the breed-specific genomic region located on chromosome 1 (1:84,405,652) harboring SNP (C–T) with high discrimination power was discovered and validated which can be considered as a novel breed-specific biomarker to develop a method for accurate authentication of village chickens in Malaysia. This authentication method offers potentialw applications in the chicken industry and food safety. © 2024 The Authors Elsevier 2024 Article PeerReviewed text en cc_by_nc_nd_4 http://psasir.upm.edu.my/id/eprint/113734/1/113734.pdf Nematbakhsh, Sara and Pei, Chong Pei and Nordin, Noordiana and Selamat, Jinap and Idris, Lokman Hakim and Abdull Razis, Ahmad Faizal (2024) Identification and validation of novel breed-specific biomarker for the purpose of village chicken authentication using genomics approaches. Poultry Science, 103 (11). art. no. 104128. pp. 1-14. ISSN 0032-5791; eISSN: 1525-3171 https://linkinghub.elsevier.com/retrieve/pii/S0032579124007077 10.1016/j.psj.2024.104128 |
| spellingShingle | Nematbakhsh, Sara Pei, Chong Pei Nordin, Noordiana Selamat, Jinap Idris, Lokman Hakim Abdull Razis, Ahmad Faizal Identification and validation of novel breed-specific biomarker for the purpose of village chicken authentication using genomics approaches |
| title | Identification and validation of novel breed-specific biomarker for the purpose of village chicken authentication using genomics approaches |
| title_full | Identification and validation of novel breed-specific biomarker for the purpose of village chicken authentication using genomics approaches |
| title_fullStr | Identification and validation of novel breed-specific biomarker for the purpose of village chicken authentication using genomics approaches |
| title_full_unstemmed | Identification and validation of novel breed-specific biomarker for the purpose of village chicken authentication using genomics approaches |
| title_short | Identification and validation of novel breed-specific biomarker for the purpose of village chicken authentication using genomics approaches |
| title_sort | identification and validation of novel breed-specific biomarker for the purpose of village chicken authentication using genomics approaches |
| url | http://psasir.upm.edu.my/id/eprint/113734/ http://psasir.upm.edu.my/id/eprint/113734/ http://psasir.upm.edu.my/id/eprint/113734/ http://psasir.upm.edu.my/id/eprint/113734/1/113734.pdf |