Inbreeding coefficients and runs of homozygosity islands in Brazilian water buffalo

Nascimento, André Vieira do; Cardoso, Diércles Francisco; Santos, D. R. dos; Romero, Andrea; Scalez, Daiane Cristina Becker; Aspilcueta-Borquis, Rusbel Raúl; Neto, Francisco Ribeiro de Araujo; Gondro, Cedric; Tonhati, Humberto

doi:10.3168/jds.2020-18397

Cited by 10 publications

(2 citation statements)

References 56 publications

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“…ROH are used to explore genetic diversity and demography, identi cation of candidate genes and/or to estimate inbreeding in many species such as chicken (Talebi et al 2020), pigs (Shi et al 2020), small ruminants (Bertolini et al 2018;Nosrati et al 2021) and large ruminants (Nascimento et al 2021;Neves et al 2015;Šidlová et al 2015). ROHs have been also used as a potential inbreeding measure in livestock (Bosse et al 2012; Marras et al 2015), including the Gir breed (Peripolli et al 2018; Toro Ospina et al…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2023

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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 pro le 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 le 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 (F ROH ) 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 (ROH 1-2 Mb : 58.17%), representing ancient inbreeding, ROH 2-4 Mb (22.74%), ROH 4 − 8 Mb (11.34%), ROH 8 − 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 signi cantly decreases TO and VO; however, the way ROH affects the traits vary among chromosomes. In the analysis for signatures of selection, we identi ed 15 genes from 47 signi cant genomic regions, indicating differences in populations with high and low breeding value for the three traits.

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Section: Introductionmentioning

confidence: 99%

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

et al. 2023

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show abstract

Section: Introductionmentioning

confidence: 99%

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

Rocha

Garcia

Otto

et al. 2022

Preprint

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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.

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Water Buffalo Genomic Diversity

Colli

Williams

Ajmone‐Marsan

2022

Biotechnological Applications in Buffalo Research

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Inbreeding coefficients and runs of homozygosity islands in Brazilian water buffalo

Cited by 10 publications

References 56 publications

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

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

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

Water Buffalo Genomic Diversity

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