DNA BARCODING OF DOMESTIC SWINE BREEDS AND CROSSBREEDS (Sus scrofa) IN THE PHILIPPINES

Abstract

Philipp J Vet Anim Sci 2013, 39 (1): 31-42

DNA barcodes (i.e. cytochrome c oxidase subunit I or COI in the mitochondrial genome) obtained from eight domestic pig breeds and crossbreeds (Sus scrofa) in the Philippines and five swine breeds retrieved from GenBank were analyzed using Neighbour-Joining method based on Kimura 2-parameter model in MEGA5. Based on 617 COI positions, overall
genetic diversity of domestic swine breeds and crossbreeds was 36.3%. Average genetic distance was highest among commercial purebred pigs (d=0.291), followed by crossbred pigs (d=0.289), native pigs (d=0.202) and smallest among GenBank-accessed breeds (d=0.008). The results indicate that DNA barcodes can be effective in differentiating between breeds sampled in the Philippines, but not among swine breeds whose COI sequences were
derived from GenBank. DNA barcodes can distinguish purebred pigs sampled in the Philippines from their counterpart breed listed in GenBank. Wide genetic distances of COI sequences imply greater diversity of native genetic resources that are distinctly different from pig breeds raised locally and abroad. Genetic distances between a crossbred pig and its dam’s breed are
not small. However, more COI sequences should be determined from distinct crossbred populations to improve reliability of DNA barcoding to discriminate them from their dam’s breed and to confirm breed origin of pigs.