MATRILINEAL PHYLOGENY AND GENETIC DIVERSITY OF RED JUNGLE FOWL (Gallus gallus L.) AND NATIVE CHICKEN (Gallus gallus domesticus L.)IN ILOILO AND GUIMARAS, PHILIPPINES

Abstract

The origin and genetic diversity of chickens remain unclear, particularly concerning Philippine wild fowls and native chickens. This study aims to provide genetic insights into the matrilineal phylogeny and genetic diversity of these populations and to assess the genetic distance of Philippine wild fowls relative to Red Jungle Fowl (RJF) subspecies across Southeast Asia (SEA) using complete mitochondrial D-loop sequences. A total of 13 RJFs and 178 native chickens were analyzed. Results revealed that Guimaras RJFs exhibited a nucleotide diversity of 0.0020, which was lower than that observed in three RJF subspecies (Gallus gallus gallus, G. g. spadiceus, and G. g. jabouillei). Similarly, native chickens from Iloilo and Guimaras showed lower nucleotide diversity (0.0054) than domestic fowls from neighboring SEA countries but higher than African and European chicken populations. Phylogenetic analysis identified three haplotypes of Guimaras RJFs clustering within haplogroup D1, while 94.74% of Iloilo and Guimaras native chickens aligned with a haplogroup shared by domestic chickens and RJFs. Haplogroups A and B, along with subhaplogroups C1, D1, D2, D3, and E1, were widely distributed in Iloilo and Guimaras. The genetic distance analysis indicated a high degree of similarity between Guimaras RJFs and RJFs from Myanmar (99.59%), Thailand (99.38%), and Indonesia (99.27%). This study represents an initial effort to estimate the matrilineal phylogeny and genetic diversity of chicken populations in Iloilo and Guimaras, Philippines, providing a foundation for future conservation and genetic resource improvement strategies