Genome-Wide SNP Analyses Disclose Genetic Diversity and Structure of Wild and Domestic Cattle in Bangladesh

In spite of variation in coat color, size, as well as production traits among the indigenous Bangladeshi cattle populations, yet the real genetic difference among most of the populations is not well investigated and exploited. In this study we employed high density Bovine SNP 80 K Bead Chip derived from Bos indicus breeds to assess genetic diversity and population structure of 2 Bangladeshi zebu cattle populations (Red Chittangong, n = 28 and non-descript Deshi, n = 28) along with the semi-domesticated gayal (n= 17). Overall, 95% and 58% of the total SNPs (69,903) displayed polymorphism in the sampled cattle and gayal population, respectively. Similarly, the average minor allele frequency value was as high 0.29 in cattle and as low as 0.09 in gayal. The mean expected heterozygosity varied from 0.42 ± 0.14 in cattle to 0.148 ± 0.14 in gayal with significant of heterozgygosity deficiency of 0.06 (F_IS) observed in the later species. Coancestry estimations revealed that the two zebu populations are weakly differentiated with over 99% of the total genetic variation was retained within populations and only less than 1% accounted for between populations. Conversely, strong genetic differentiation (F_ST = 0.33) was observed between zebu and gayal. Results of population structure, PCA and phylogenetic tree showed that gayal is very distinct from Bos indicus while the two zebu populations were weakly structured. This study provides basic information regarding the genetic diversity and structure of Bangladeshi cattle and semi-domesticated gayals for future appraisal of proper breed utilization and management strategy.