Molecular characterization and A1/A2 genotyping of casein beta gene in zebu and crossbred cattle of Bangladesh

Casein beta (CSN2) is the most explored gene in cattle due to its potential impact on human health. Here, we investigated the entire coding sequence of CSN2 gene except the last two codons for detection of polymorphisms in different cattle populations of Bangladesh as well as genotyping of A1 and A2 allelic variants using a newly developed allele specific polymerase chain reaction (AS-PCR) based the genotyping protocol. Five primer pairs were used to amplify the coding sequences of CSN2 gene. This study included a total of 258 DNA samples from six Bangladeshi zebu populations and one Holstein Friesian (HF) derived crossbred cattle population. Sequence analysis detected five nonsynonymous mutations in the coding sequence of CSN2 gene that defined five allelic variants as A1, A2, B, F and I. In addition, substitution of GTA (Val) by GCA (Ala) at position 197 resulted in an undefined allele in the zebu cattle population of Bangladesh that has not yet been reported elsewhere. Like other Bos indicus cattle populations, A2 allele is predominant in the studied zebu populations. The mean frequencies of A1A1, A1A2 and A2A2 genotypes were 0.02, 0.16 and 0.82, respectively, in zebu cattle populations while the corresponding allele frequencies were A1 (0.10) and A2 (0.90). In opposite, the aforesaid genotype frequencies were 0.14 (A1A1), 0.50 (A1A2) and 0.36 (A2A2) in the HF crossbred population with allele frequencies of 0.39 (A1) and 0.61 (A2). The adopted AS-PCR method was found cost-effective, rapid and had high specificity for genotyping of A1 and A2 allelic variants. Altogether, this study provides information for the selection of desired zebu and crossbred individuals in order to produce premium quality milk as well as to design a breeding plan in the crossbreeding program.