Abstract
Runs of homozygosity (ROH) and signatures of selection are the results of selection processes in livestock species that have 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 the number of embryos (EMBR) in Gir Indicine cattle. In addition, we aim to identify signatures of selection, genes, and enriched regions between Gir subpopulations sorted by breeding value for these traits. The genotype file contained 2093 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-based (FROH) and pedigree-based inbreeding (Fped) and a search for genes and their functions. An average of 50 ± 8.59 ROHs were found per animal. ROHs were separated into classes according to size, ranging from 1 to 2 Mb (ROH1–2Mb: 58.17%), representing ancient inbreeding, ROH2–4Mb (22.74%), ROH4-8Mb (11.34%), ROH8-16Mb (5.51%), and ROH>16Mb (2.24%). Combining our results, we conclude that the increase in general FROH and Fped significantly decreases TO and VO; however, in different chromosomes traits can increase or decrease with FROH. 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.
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Data availability
The datasets generated and analyzed during this study are available from the corresponding author on reasonable request.
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We thank the farmers who provided data for this study.
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Coordination and Improvement of Higher Level Personnel (CAPES), National Council for Scientific and Technological Development (CNPq), Ministério da Ciência Tecnologia e Inovação (MCTI), and Brazilian National Institute of Science and Technology in Animal Science (INCT-CA) provided financial support towards this study.
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JCdCP, MAM, MVBdS, and SEFG: conceptualization of the study. RFBR and SEFG: drafted the manuscript. RFBR: performed the experiments and analysis. AOG and PIO: statistical analyses support. MVGBdS, MFM, MAM, and JCdCP: bioinformatics technical support. All authors read and approved the final manuscript.
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Rocha, R.d.B., Garcia, A.O., Otto, P.I. et al. Runs of homozygosity and signatures of selection for number of oocytes and embryos in the Gir Indicine cattle. Mamm Genome 34, 482–496 (2023). https://doi.org/10.1007/s00335-023-09989-w
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DOI: https://doi.org/10.1007/s00335-023-09989-w