Our objective was to establish a SNPs panel for pedigree reconstruction using chips of different densities and evaluate the genomic relationship coefficient of the inferred pedigree, in addition to analyzing the population structure based on genomic analyses in Gir cattle. For parentage analysis and genomic relationship, 16,205 genotyped Gir animals were used being 14,458 females and 1,747 males, and 1,810 common markers to the four SNP chips. For population structure analyses, which include linkage disequilibrium, effective population size, and runs of homozygosity (ROH), the genotypes of 21,656 animals were imputed. The likelihood ratio (LR) approach was used to reconstruct the pedigree. The LR approach deepened the pedigree and showed that it is well established in terms of recent information for this breed. The coefficients for each 2 relationship category of the inferred pedigree were adequate. Linkage disequilibrium showed rapid decay. We detected a decrease in the effective population size over the last 50 generations, with the average generation interval estimated at 9.08 years. A higher ROH-based inbreeding coefficient in a class of short segments of ROH, with moderate to high values was also detected, suggesting the presence of bottlenecks in the Gir cattle genome. Breeding strategies to minimize inbreeding and avoid massive use of a few proven sires with high genetic value are suggested to maintain genetic variability in future generations. In addition, we recommend reducing the generation interval to maximize genetic progress and increase effective population size.

No abstract