In the present study, to analyze the genomic ROH fragments, haplotypes, inbreeding coefficient and effective population size (N_e), SNP50K data of 72 Vrindavani crossbred cattle strain were obtained. After a quality check, 24,449 biallelic SNPs were retained, which were in HWE, MAF > 0.01 and genotyping rate >95%. A total of 385 ROH were found, and chromosome 25 was mostly covered with 50.86%, while chromosome one was least with 12.42%. We classified ROH into 20Mb categories and observed a 3% inbreeding coefficient for the population in >20Mb category. Inbreeding from an excess of homozygosity was found to be 6% in the population. N_e was also estimated through N_e Estimator and SNeP and in the recent generation, it was found to be 40 for a census size of 464 cattle. The N_e/N_c ratio was found to be 0.086 and a decreasing trend of N_e was observed for over five generations. 45.95% of the autosomal genome was covered with haplotypic structure with highest total block length in chromosome one and lowest in 28. From all the observations made in this study, it can be concluded that Vrindavani is an admixed cattle strain but have an unstable population structure in the current period.

Background: Elucidating genome-wide structural variants including copy number variations (CNVs) have gained increased significance in recent times owing to their contribution to genetic diversity and association with important pathophysiological states. The present study aimed to elucidate the high-resolution CNV map of six different global buffalo breeds using whole genome resequencing data at two coverages (10X and 30X). Post-quality control, the sequence reads were aligned to the latest draft release of the Bubaline genome. The genome-wide CNVs were elucidated using a read-depth approach in CNVnator with different bin sizes. Adjacent CNVs were concatenated into copy number variation regions (CNVRs) in different breeds and their genomic coverage was elucidated. Results: Overall, the average size of CNVR was lower at 30X coverage, providing finer details. Most of the CNVRs were either deletion or duplication type while the occurrence of mixed events was lesser in number on a comparative basis in all breeds. The average CNVR size was lower at 30X coverage (0.201 Mb) as compared to 10X (0.013 Mb) with the finest variants in Banni buffaloes. The maximum number of CNVs was observed in Murrah (2627) and Pandharpuri (25,688) at 10X and 30X coverages, respectively. Whereas the minimum number of CNVs were scored in Surti at both coverages (2092 and 17,373). On the other hand, the highest and lowest number of CNVRs were scored in Jaffarabadi (833 and 10,179 events) and Surti (783 and 7553 events) at both coverages. Deletion events overnumbered duplications in all breeds at both coverages. Gene profiling of common overlapped genes and longest CNVRs provided important insights into the evolutionary history of these breeds and indicate the genomic regions under selection in respective breeds. Conclusion: The present study is the first of its kind to elucidate the high-resolution CNV map in major buffalo populations using a read-depth approach on whole genome resequencing data. The results revealed important insights into the divergence of major global buffalo breeds along the evolutionary timescale.