Runs of homozygosity and signatures of selection for number of oocytes and embryos in the Gir Indicine cattle

Abstract

Abstract Runs of homozygosity (ROH) and signatures of selection are results of selection processes in livestock species that has been shown to affect several traits in cattle. The aim of the current work was to verify the profile of ROH and inbreeding depression in the number of total (TO) and viable oocytes (VO), and number of embryos (EMBR) in Gir Indicine cattle. In addition, we aimed to identify signatures of selection, genes and enriched regions between Gir subpopulations sorted by breeding value for these traits. The genotype file contained 2,093 animals and 420,718 SNP markers. Breeding values used to sort Gir animals were previously obtained. ROH and signature of selection analyses were performed using PLINK software, followed by ROH- and pedigree-based inbreeding (FROH) and search for genes and their functions. A total of 105,327 ROHs were found in Gir cattle. ROHs were separated in classes according to the size, ranging from 1 to 2 Mb (ROH1–2 Mb: 58.17%), representing ancient inbreeding, ROH2–4 Mb (22.74%), ROH4 − 8 Mb (11.34%), ROH8 − 16 Mb (5.51%) and ROH> 16 Mb (2.24%). Putting together our results, we conclude that the increase in general ROH-based and pedigree-based inbreeding significantly decreases TO and VO; however, the way ROH affects the traits vary among chromosomes. In the analysis for signatures of selection, we identified 15 genes from 47 significant genomic regions, indicating differences in populations with high and low breeding value for the three traits.