当地的乡村鸡,或马来西亚著名的“Ayamkampung”,被认为是价格比其他鸡品种更高的优质鸡品种。由于它们的外观和尺寸相当,彩色肉鸡通常作为乡村鸡出售,这是一种食品欺诈形式,可能导致利润上升3到4倍。因此,开发特定品种的认证方法对于防止家禽业中的食品欺诈至关重要。本研究旨在调查市场上其他商业鸡品种种群(肉鸡[Cobb],彩色肉鸡[哈伯德],和层[DeKalb])以鉴定品种特异性DNA片段作为乡村鸡认证的生物标志物。12只鸡(3只鸡/品种)的全基因组测序和突变识别导致总共鉴定了73,454,654个单核苷酸多态性(SNP)和8,762,338个插入和缺失(InDel)变体,与商业品种相比,在乡村鸡种群中检测到更多的变异(6,346,704SNP;752,408InDel)。因此,这项研究表明,与马来西亚其他品种相比,乡村鸡的遗传变异更大。此外,发现并验证了位于1号染色体(1:84,405,652)上的具有高辨别能力的SNP(C-T)的特定品种基因组区域,该区域可被视为一种新型的特定品种生物标志物,以开发一种准确认证方法马来西亚的乡村鸡。这种身份验证方法在鸡肉行业和食品安全中提供了潜在的应用。
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.