Genotyping of prolactin, kappa casein, and pituitary transcription factor 1 genes of the Anatolian water buffalo population in the Kızılırmak Delta

Abstract

Thirty-five Anatolian water buffalo were selected from among a total of almost 7000 animals from 11 herds in the KızılırmakDelta, which is known to be one of the most important areas for water buffalo farming in Turkey. The cleaved amplified polymorphicsequences (CAPS) method was used to identify single-nucleotide polymorphisms at 3 loci that are associated with milk production,namely PRL, CSN3, and PIT-1, which are associated with milk processing and milk yields, respectively. Sequence-tagged sites of PRL,CSN3, and PIT-1 were digested by restriction endonucleases RsaI, HindIII, and HinfI, respectively. Capillary electrophoretic analysisidentified all samples as belonging to the GG and BB genotypes, which are undesirable genotypes for PRL and PIT-1 gene loci, but idealfor the CSN3 locus. Then the samples were sequenced by an ABI 3730 DNA Analyzer (Applied Biosystems). DNA sequencing of theamplified CSN3 fragment revealed one polymorphism at codon 135 (ThrACC > IleATC) in some samples. A homozygous structure wasfound for all three loci and the huge population loss between 1991 and 2008 suggests that a genetic bottleneck may have occurred in thepopulation of Anatolian water buffalo in the Kızılırmak Delta.