Philippine J. Vet Anim. Sci. 2006. 32(1):1-9 GENETIC STRUCTURE OF SELECTED CA TILE POPULATIONS IN THE PHILIPPINES USING MICROSATELLITES G.M.B. Aquino!, R.P. Laude 2 , H. Jianlin 3 , C.S. Sevilla l and O. Hanotte 3 ABSTRACT The genetic structure and relationships among four populations of the Philippine native cattle, namely: Ilocos, Batangas, Siquijor, and Philippine-Bali, were inferred from 16 DNA microsatellite loci by using F-statistics, for poten- tial purposes. Multilocus' FST values indicated that around 15.6% of the total genetic variation could be explained by differences between popula- tions and the remaining 84.4% by differences among individuals. Interpopula- tion genetic diversity was evident in the phylogenetic tree constructed from the weighted Reynolds' distance (DR) matrix, and supported by results of corre- spondence analysis. Analysis of population admixture suggested that. the indi- viduals from these populations descended from three parental populatIulls, pre- sumably the zebu (Bos indicus), taurine (Bos taurus), and banteng (Bos hanJeng) cattle. This serves as a preliminary study to provide basic information for possi- ble development of conservation programs for cattle in smallholder farms in the Philippines. Keywords: cattle, genetic diversity, microsatellite; Philippines, phylogeny INTRODUCTION The success of the smallholder beef industry in the Philippines has been lim- ited by a lack of knowledge on the true nature of the genetic composition of the beef cattle stocks. The native cattle in smallholder farms of'the Philippines were classified into different types based on their geographic location and phenotype by Villegas (1965). In the Global Information System of Domestic Animal Diversity (DAD-IS, http://dad.fao.org), these so-called indigenous cattle of the Philippines have been grouped into the Philippine native cattle. This breed is traditionally classified as zebu cattle (Bos indicus) based on morphology, though it has bee.n observed to be ad- mixed with taurine cattle (Bos taurus) (Arboleda 1986). These cattle have domesti- I Animal and Dairy Sciences Cluster, College of Agriculture, University of the Philippines Los Banos, Laguna (e-mail: gm.aguino@gmail.com;tel.no. 63-49-536-3450). 2Institute of Biological Sciences, College of Arts and Science, University of the Philippines Los Banos, Laguna. 3Intemational Livestock Research Institute, Nairobi, Kenya