Genetic diversity of microsatellite and cytochrome oxidase subunit I (COI) gene in Indonesian Buffalo

Abstract

This study aims to determine genetic diversity in Indonesian buffaloes using microsatellite markers and cytochrome oxidase subunit I gene. The sample used in this study were 211 samples of buffaloes (30 samples of swamp buffaloes from Aceh, North Sumatra, Banten, Central Java, West Nusa Tenggara, South Sulawesi, and 19 samples from Riau) and 12 samples of river buffaloes from North Sumatra. Microsatellite markers used were CSSM66, ILSTS61, and ILSTS17 loci. Microsatellite data in term of observed number of alleles (na); effective number of alleles (ne); Observed heterozygosity (Ho); Expected heterozygosity (He); and polymorphism information content (PIC) were analyzed by GenAlEx 6.41 and Cervus 3.1. COI gene sequences were analyzed using MEGA 5.1 software with the Neighbor-joining method and kimura 2 parameter substitution models. This study showed that CSSM66 loci had two alleles and two genotypes. ILSTS61 loci had five alleles and 14 genotypes. ILSTS17 loci had two alleles and three genotypes. Microsatellite genetic distance between populations could separate Indonesian swamp buffalo. The reconstructed phylogeny tree based on COI gene sequences were able to distinguish Subspecies of swamp buffalo and river buffalo. COI gene sequences showed four haplotypes for Indonesian swamp buffalo, namely H1, H2, H3 and H4.