The Use of DNA Barcodes in the Evolutionary Analysis of Domestic Breeds and Strains of Chicken (Gallus gallus domesticus) in the Philippines

摘要

DNA barcodes (cytochrome c oxidase subunit I or COI in the mitochondrial genome) were used to differentiate 31 domestic chicken breeds and strains (Gallus gallus domesticus) and 25 red jungle fowls (Gallus gallus philipensis Hatchisuka) in the Philippines. Evolutionary analyses using Kimura 2-parameter model in MEGA5 and the Neighbour-Joining method that created a bootstrap consensus tree inferred from 1000 replicates indicated the existence of two evolutionary clades. Based on 610 COI sequences, overall genetic diversity among domestic chickens was 50.6%. Average evolutionary divergence over sequence pairs within chicken groups was highest among 11 standard breeds (71.4%), followed by 7 native chickens (51.0%), 10 fighting cocks (38.3%), and lowest among 3 commercial hybrid chickens (2.5%). Our analyses indicated that DNA barcodes can effectively identify and differentiate chicken breeds and strains, but not distinguish between commercial hybrid chickens. DNA barcoding is recommended to complement recently-developed molecular tools capable of calculating genetic distances between important chicken breeding populations and to determine those needing more detailed phylogenetic analysis. DNA barcoding, together with phenotypic performance data and history of populations, is recommended to describe the existent resources and should provide reliable guidelines for conservation decisions and for the design of local breeding programs for native chickens.