Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Sep;34(3):482-496.
doi: 10.1007/s00335-023-09989-w. Epub 2023 Mar 31.

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

Renata de Fátima Bretanha Rocha  1 , Arielly Oliveira Garcia  1 , Pamela Itajara Otto  2 , Marcos Vinícius Barbosa da Silva  3 , Marta Fonseca Martins  3 , Marco Antônio Machado  3 , João Claudio do Carmo Panetto  3 , Simone Eliza Facioni Guimarães  4
Affiliations

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

Renata de Fátima Bretanha Rocha et al. Mamm Genome. 2023 Sep.

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.

PubMed Disclaimer

References

    1. Akey JM, Zhang G, Zhang K et al (2002) Interrogating a high-density SNP map for signatures of natural selection. Genome Res 12:1805–1814. https://doi.org/10.1101/gr.631202 - DOI - PubMed - PMC
    1. An Y, Yang S, Guo K et al (2015) Reduced USP39 expression inhibits malignant proliferation of medullary thyroid carcinoma in vitro. World J Surg Oncol. https://doi.org/10.1186/s12957-015-0669-4 - DOI - PubMed - PMC
    1. Ayasan T, Hizli H, Çamlidag A et al (2011) Determination of relationship between milk production and the quality of embryo of donor cows. Indian J Anim Sci 81:912–914
    1. Barranco I, Padilla L, Martinez CA et al (2020) Seminal plasma modulates mirna expression by sow genital tract lining explants. Biomolecules 10:933. https://doi.org/10.3390/biom10060933 - DOI - PubMed - PMC
    1. Bertolini F, Cardoso TF, Marras G et al (2018) Genome-wide patterns of homozygosity provide clues about the population history and adaptation of goats. Genet Sel Evol. https://doi.org/10.1186/s12711-018-0424-8 - DOI - PubMed - PMC

Publication types

LinkOut - more resources