JOURNAL of BIOTECHNOLOGY RESEARCH in TROPICAL REGION, Vol. 1, Oct. 2008 (Special Edition) ISSN: 1979-9756 Y Chromosomal Microsatellites Polymorphism in Madura Cattle (Bos javanicus) 1 Y Chromosomal Microsatellites Polymorphism in Madura Cattle (Bos javanicus) Aris Winaya 1 *, Herwintono 2 , Mohamad Amin 3 1 Research Center & Development for Biotechnology, University of Muhammadiyah Malang 2 Faculty of Animal Husbandry and Fisheries, University of Muhammadiyah Malang 3 Biotechnology Research Center, Faculty of Mathematics and Sciences, State University of Malang Abstract Five loci of Y chromosome specific microsatellites were genotyped and assessed for polymorphisms in 18 unrelated males of Madura cattle breed. PCR amplification was conducted by using 5 primer pairs that flanking microsatellites (INRA008, INRA057, INRA062, INRA124 and INRA126). PCR products were separated by 6% polyacrylamide gel electro- phoresis and silver staining method was used to detect allele polymorphism at each locus. A small number haplotypes were detected in this population. Locus INRA 008 and INRA 124 were more polymor- phic than others by 3 alleles where these alleles known as Indicine alleles. In our previous study which based on 16 microsatellite markers indicated that Madura cattle has genetic relationship to Indi- cine breed. So, Y chromosomal microsatellite may be important in domesticated animals because a limited number of males may have an enormous impact on highly selected animal populations. Keywords: Madura cattle, Indicine, Y chromosome, microsatellite, polymorphism. INTRODUCTION Madura cattle is one of the Indonesian cattle breed that has been popular in Madura island espe- cially in traditional activity, like “Karapan Sapi” (bull racing). Madura cattle is presumably one of offspring Indonesian wild bull ancestor, Banteng (Bos banteng). So, it will be important to protect this existence. Recently, all wild ancestors of lives- tock and native breed were extinct or limited in their populations. The conditions could be caused by many reasons, such as local stress and unpredictable environment, animal diseases, as well as selection processes to improve and specialized production ability. *Correspondence to: Aris Winaya e-mail: winaya@umm.ac.id But, in many countries especially in tropical re- gions, the genetic variability of cattle has been maintained by society related to agricultural back- grounds. Therefore, the effort to protect those breeds followed by well recording not only in phenotypic traits, but also in genetic levels will assist to docu- ment their production and genetic status. Measuring diverse aspects of a population, such as phenotypic traits, reproduction, geographic dis- tribution, origin and habitat is important for genetic characterization. The genetic characterization of populations, breeds and species allows evaluation of genetic variability is a fundamental element in plan- ning breeding strategies and genetic conservation, and the use of molecular marker to measure diverse aspects of a population will assist the plan (Pandey et al., 2006). Microsatellite as a genetic molecular marker is presently the most popular marker, especially in analysis using Polymerase Chain Reaction (PCR). Also, the polymorphic allele in microsatellites marker is more helpfull in enormous genetic diversi- ty and relationship among cattle (Nave et al., 1997; MacHugh et al., 1997; Kim et al., 2002; Maudet et al., 2002). The information about breed specific allele from molecular data of Indonesian native cattle is still limited. Muladno et al. (2000) found specific allele in Bali cattle at INRA023 microsatellite locus. Another study conducted by Noor et al. (2001) showed that Bali cattle has specific allele at locus HEL9 and INRA035 microsatellite compared to Bos taurus (Simmental, Limousin and Brangus), but this result is a primarily study related to specific allele phenomena in Indonesian native cattle. Based on 16 locus of microsatellites study (Winaya, 2000; Wi- naya et al., 2000), it was showed that microsatellites loci could illustrate the phylogenetic relationship between Bali, Madura, Ongole offspring and Bran- gus cattle. The aim of this study was to develop the set of Y chromosomal microsatellite DNA for the genetic variation of Madura cattle breed.