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 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.

Heavy Metal Contamination in Oryza sativa L. at the Eastern Region of Malaysia and Its Risk Assessment.

Paddy plants tend to accumulate heavy metals from both natural and anthropogenic sources, and this poses adverse risks to human health. The objective of this study was to investigate heavy metal contamination in paddy plants in Kelantan, Malaysia, and its health risk assessment. The bioaccumulation of heavy metals was studied by means of enrichment (EF) and translocation factors (TF). The health risk assessment was performed based on USEPA guidelines. The EF for heavy metals in the studied areas was in the descending order of Cu > As > Cr > Cd > Pb. Meanwhile, Cr and Pb exhibited higher TF values from stem to grain compared with the others. The combined hazard index (HI) resulting from five heavy metals exceeded the acceptable limit (HI >1). The lifetime cancer risk, in both adult and children, was beyond the acceptable limit (10-4) and mainly resulted from exposure. The total cancer risk (CRt) due to simultaneous exposures to multiple carcinogenic elements also exceeded 10-4. In conclusion, intake of heavy metal through rice ingestion is likely to cause both non-carcinogenic and carcinogenic health risks. Further research is required to investigate the extent of heavy metal contamination in agricultural soils and, moreover, to establish human exposure as a result of rice consumption.

Omics-Based Analytical Approaches for Assessing Chicken Species and Breeds in Food Authentication.

Chicken is known to be the most common meat type involved in food mislabeling and adulteration. Establishing a method to authenticate chicken content precisely and identifying chicken breeds as declared in processed food is crucial for protecting consumers' rights. Categorizing the authentication method into their respective omics disciplines, such as genomics, transcriptomics, proteomics, lipidomics, metabolomics, and glycomics, and the implementation of bioinformatics or chemometrics in data analysis can assist the researcher in improving the currently available techniques. Designing a vast range of instruments and analytical methods at the molecular level is vital for overcoming the technical drawback in discriminating chicken from other species and even within its breed. This review aims to provide insight and highlight previous and current approaches suitable for countering different circumstances in chicken authentication.

Chicken Authentication and Discrimination via Live Weight, Body Size, Carcass Traits, and Breast Muscle Fat Content Clustering as Affected by Breed and Sex Varieties in Malaysia.

Nowadays, the high demand for village chickens in Malaysia leads to the fraudulent substitution of indigenous chickens with other cheaper counterparts. Discriminating different chicken breeds based on their phenotypic characteristics is one strategy to avoid chicken adulteration. The main objective of this study was to authenticate and group dominant chicken breeds in Malaysia, including commercial chickens (Cobb, Hubbard, DeKalb) and cross-bred village chickens (Ayam Kampung, Akar Putra). The further discrimination of village chickens from underaged colored broilers (UCBs) (Hubbard, Sasso) was performed based on phenotype traits. The results showed that the breed had a significant effect (p < 0.05) on phenotypic characteristics, while the sex effect was not significant for some characteristics. In the first phase, the most remarkable discriminating factors were abdominal fat weight, breast muscle weight, chest circumference, shank length, and wingspan. However, in the second phase, notable variations in phenotypic characteristics between village chickens and UCBs were not detected. Principal component analysis (PCA) showed the successful separation of village chickens from high-performance breeds (broiler and colored broiler). Nevertheless, there was overlap among observations for Sasso and village chickens, which approved the possible similarities in their phenotypic characteristics. This study showed clear breed clustering, which leads to the chicken authentication based on their phenotypic characteristics.

Molecular Regulation of Lipogenesis, Adipogenesis and Fat Deposition in Chicken.

In the poultry industry, excessive fat deposition is considered an undesirable factor, affecting feed efficiency, meat production cost, meat quality, and consumer's health. Efforts to reduce fat deposition in economically important animals, such as chicken, can be made through different strategies; including genetic selection, feeding strategies, housing, and environmental strategies, as well as hormone supplementation. Recent investigations at the molecular level have revealed the significant role of the transcriptional and post-transcriptional regulatory networks and their interaction on modulating fat metabolism in chickens. At the transcriptional level, different transcription factors are known to regulate the expression of lipogenic and adipogenic genes through various signaling pathways, affecting chicken fat metabolism. Alternatively, at the post-transcriptional level, the regulatory mechanism of microRNAs (miRNAs) on lipid metabolism and deposition has added a promising dimension to understand the structural and functional regulatory mechanism of lipid metabolism in chicken. Therefore, this review focuses on the progress made in unraveling the molecular function of genes, transcription factors, and more notably significant miRNAs responsible for regulating adipogenesis, lipogenesis, and fat deposition in chicken. Moreover, a better understanding of the molecular regulation of lipid metabolism will give researchers novel insights to use functional molecular markers, such as miRNAs, for selection against excessive fat deposition to improve chicken production efficiency and meat quality.