Genetic Diversity of Bangladeshi Cattle and Their Wild Relative Using High-density Chip

A recently developed high-density bovine SNP 80K Bead Chip derived from Bos indicus breeds was applied onto two Bangladeshi zebu breeds (RC, red Chittagong; ND, non-descript deshi) and a semi-domesticated population of gayal (Bos frontlis). The average minor allele frequency value was as high 0.29 in zebu and as low as 0.09 in gayal with the total 69,804 genome-wide polymorphic SNPs . The mean expected heterozygosity varied from 0.42±0.14 in zebu to 0.148±0.14 in gayal with significant heterozygosity deficiency of 0.06 (FIS) in the latter. Coancestry estimations revealed that the two zebu populations are weakly differentiated, with over 99% of the total genetic variation retained within populations and less than 1% accounted for between populations. Conversely, strong genetic differentiation (FST = 0.33) was observed between zebu and gayal populations. Apart from the large within breeds genomic diversity has been found, the variation in size and production & reproduction traits are also large between the zebu breeds. As far as the body size is concerned a potential candidate PLAG1 sequence analyzed between the breeds didn’t establish the gene attributable important for their size differences. On the other hand, the genome-wide comparison of allelic frequencies has identified differences in the markers spanning an important QTL region of 39.8 to 61 Mb on BTA16 and some other chromosomal regions between two zebu breeds. So, our study provides basic information about the genetic diversity of Bangladeshi cattle and the semi-domesticated gayal population which can be used for the purposeful utilization of these local breeds.