Dna Barcoding of Livestock and Poultry Breeds/strains in the Philippines

We have sequenced the DNA barcodes (i.e. cytochrome c oxidase subunit I or COI gene of the mitochondrial genome) of common breeds/strains of farm animals (mammals – buffalo, cattle, goat, sheep, pigs, dogs, and cat; poultry – chickens, quail, turkey, guinea fowl, ducks, geese, pigeons, and ostrich) in the Philippines. DNA was extracted from blood samples. The DNA barcode of the livestock and poultry breed/strain was amplified by polymerase chain reaction (PCR) method. Sequence divergences (“Kimura 2 parameter” or K2P differences) of the DNA barcode between the groups or taxa and a library of common livestock and poultry breeds/strains were analyzed. A neighbour-joining (NJ) tree based on COI barcodes was also created to provide graphic representation of sequence divergences among the breed/strain specimens to confirm identification. Our analyses indicate that DNA barcodes can be an effective tool for both differentiating and identifying most breeds/strains of livestock and poultry animals (except cattle and commercial hybrid chickens) in the Philippines. Hybrid or crossbred animals will be difficult to distinguish from their dam breed/strain because mitochondrial DNA is maternally inherited. We demonstrated that DNA barcodes can be used to quantify intra-specific diversity and recognize sibling species among common livestock and poultry breeds/strains. We also developed a local online database called the “UPLB-DA DNA Barcoding Project: a library information system for the Philippine livestock and poultry sector” and runs in parallel with the Barcode of Life Data systems. DNA barcoding has vast potential applications in the areas of animal production and health such as genetic improvement and conservation, tracking of invasive species, and labeling of breeding animals and traditional animal products. The library of a standardized gene region, i.e. mitochondrial COI sequences or DNA barcodes could also provide insight into evolutionary processes in the development of popular breeds/strains of farm animals and their wild types (e.g., Philippine red jungle fowls). Through DNA barcoding, livestock and poultry breeds/strains could be identified to quickly assess biodiversity and help speed up cataloguing of biodiversity. Conservationists/taxonomists as well as farmers could spot genetically distinct specimens, speeding up cataloguing of new breeds/strains before they become extinct.