Y-chromosome variation in Indian native cattle breeds and crossbred population

The paternally inherited Y chromosome markers have been used widely in population genetic studies to trace paternal lineages, to understand differences in migration pattern and populations admixture in animals. In the absence of crossing over, Y-chromosomal markers in the non-recombining male-specific region (MSY) are mostly transmitted as a haplotype. Recent studies of five polymorphic sites on DDX3Y, UTY and ZFY genes of bull MSY assisted in the identification of three haplogroups (Y1, Y2 and Y3) in contemporary cattle. Here we report the screening of five SNPs (ZFY9–120> C/T; ZFY10–655> C/T; DDX3Y1–425>C/T; DDX3Y7–123>C/T and UTY19–423>C/A) of bull MSY employing optimized and validated allele-specific PCR (AS-PCR) protocols that are useful in effective differentiation of bull/semen samples of Bos indicus and Bos taurus origin. Three haplogroups (Y1, Y2 and Y3) were identified in the present study by the screening of 181 bulls from 10 native cattle breeds and 50 HF crossbred. Y1 and Y2 haplogroups were restricted to HF crossbred with a frequency of 0.98 and 0.02, respectively. The high frequency of Y1 haplogroups is possibly due to the occurrence of Y1 lineage predominantly in HF bulls. All the native cattle breeds were observed to have pure indicine lineage (Y3). These cost effective AS-PCR protocols may be useful for reliable and accurate genotyping of Y-SNPs in diverse native cattle breeds, exotic and crossbred cattle populations.