Fine-scale estimation of inbreeding rates, runs of homozygosity and genome-wide heterozygosity levels in the Mangalarga Marchador horse breed

Detalhes bibliográficos
Autor(a) principal: Bizarria dos Santos, Wellington [UNESP]
Data de Publicação: 2020
Outros Autores: Pimenta Schettini, Gustavo [UNESP], Fonseca, Mayara Gonçalves, Pereira, Guilherme Luis [UNESP], Loyola Chardulo, Luis Artur [UNESP], Rodrigues Machado Neto, Otávio [UNESP], Baldassini, Welder Angelo [UNESP], Nunes de Oliveira, Henrique [UNESP], Abdallah Curi, Rogério [UNESP]
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://dx.doi.org/10.1111/jbg.12508
http://hdl.handle.net/11449/199402
Resumo: With the availability of high-density SNP panels and the establishment of approaches for characterizing homozygosity and heterozygosity sites, it is possible to access fine-scale information regarding genomes, providing more than just comparisons of different inbreeding coefficients. This is the first study that seeks to access such information for the Mangalarga Marchador (MM) horse breed on a genomic scale. To this end, we aimed to assess inbreeding levels using different coefficients, as well as to characterize homozygous and heterozygous runs in the population. Using Axiom ® Equine Genotyping Array—670k SNP (Thermo Fisher), 192 horses were genotyped. Our results showed different estimates: inbreeding from genomic coefficients (FROH) = 0.16; pedigree-based (FPED) = 0.008; and a method based on excess homozygosity (FHOM) = 0.010. The correlations between the inbreeding coefficients were low to moderate, and some comparisons showed negative correlations, being practically null. In total, 85,295 runs of homozygosity (ROH) and 10,016 runs of heterozygosity (ROHet) were characterized for the 31 horse autosomal chromosomes. The class with the highest percentage of ROH was 0–2 Mbps, with 92.78% of the observations. In the ROHet results, only the 0–2 class presented observations, with chromosome 11 highlighted in a region with high genetic variability. Three regions from the ROHet analyses showed genes with known functions: tripartite motif-containing 37 (TRIM37), protein phosphatase, Mg2+/Mn2+ dependent 1E (PPM1E) and carbonic anhydrase 10 (CA10). Therefore, our findings suggest moderate inbreeding, possibly attributed to breed formation, annulling possible recent inbreeding. Furthermore, regions with high variability in the MM genome were identified (ROHet), associated with the recent selection and important events in the development and performance of MM horses over generations.
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spelling Fine-scale estimation of inbreeding rates, runs of homozygosity and genome-wide heterozygosity levels in the Mangalarga Marchador horse breedEquus caballusFHOMFPEDFROHROHROHetWith the availability of high-density SNP panels and the establishment of approaches for characterizing homozygosity and heterozygosity sites, it is possible to access fine-scale information regarding genomes, providing more than just comparisons of different inbreeding coefficients. This is the first study that seeks to access such information for the Mangalarga Marchador (MM) horse breed on a genomic scale. To this end, we aimed to assess inbreeding levels using different coefficients, as well as to characterize homozygous and heterozygous runs in the population. Using Axiom ® Equine Genotyping Array—670k SNP (Thermo Fisher), 192 horses were genotyped. Our results showed different estimates: inbreeding from genomic coefficients (FROH) = 0.16; pedigree-based (FPED) = 0.008; and a method based on excess homozygosity (FHOM) = 0.010. The correlations between the inbreeding coefficients were low to moderate, and some comparisons showed negative correlations, being practically null. In total, 85,295 runs of homozygosity (ROH) and 10,016 runs of heterozygosity (ROHet) were characterized for the 31 horse autosomal chromosomes. The class with the highest percentage of ROH was 0–2 Mbps, with 92.78% of the observations. In the ROHet results, only the 0–2 class presented observations, with chromosome 11 highlighted in a region with high genetic variability. Three regions from the ROHet analyses showed genes with known functions: tripartite motif-containing 37 (TRIM37), protein phosphatase, Mg2+/Mn2+ dependent 1E (PPM1E) and carbonic anhydrase 10 (CA10). Therefore, our findings suggest moderate inbreeding, possibly attributed to breed formation, annulling possible recent inbreeding. Furthermore, regions with high variability in the MM genome were identified (ROHet), associated with the recent selection and important events in the development and performance of MM horses over generations.School of Agricultural and Veterinary Sciences (FCAV) São Paulo State University (Unesp)Federal University of Minas Gerais (UFMG)School of Veterinary Medicine and Animal Science (FMVZ) São Paulo State University (Unesp)School of Agricultural and Veterinary Sciences (FCAV) São Paulo State University (Unesp)School of Veterinary Medicine and Animal Science (FMVZ) São Paulo State University (Unesp)Universidade Estadual Paulista (Unesp)Universidade Federal de Minas Gerais (UFMG)Bizarria dos Santos, Wellington [UNESP]Pimenta Schettini, Gustavo [UNESP]Fonseca, Mayara GonçalvesPereira, Guilherme Luis [UNESP]Loyola Chardulo, Luis Artur [UNESP]Rodrigues Machado Neto, Otávio [UNESP]Baldassini, Welder Angelo [UNESP]Nunes de Oliveira, Henrique [UNESP]Abdallah Curi, Rogério [UNESP]2020-12-12T01:38:48Z2020-12-12T01:38:48Z2020-01-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1111/jbg.12508Journal of Animal Breeding and Genetics.1439-03880931-2668http://hdl.handle.net/11449/19940210.1111/jbg.125082-s2.0-85091019409Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengJournal of Animal Breeding and Geneticsinfo:eu-repo/semantics/openAccess2021-10-22T20:42:45Zoai:repositorio.unesp.br:11449/199402Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T17:28:03.955522Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Fine-scale estimation of inbreeding rates, runs of homozygosity and genome-wide heterozygosity levels in the Mangalarga Marchador horse breed
title Fine-scale estimation of inbreeding rates, runs of homozygosity and genome-wide heterozygosity levels in the Mangalarga Marchador horse breed
spellingShingle Fine-scale estimation of inbreeding rates, runs of homozygosity and genome-wide heterozygosity levels in the Mangalarga Marchador horse breed
Bizarria dos Santos, Wellington [UNESP]
Equus caballus
FHOM
FPED
FROH
ROH
ROHet
title_short Fine-scale estimation of inbreeding rates, runs of homozygosity and genome-wide heterozygosity levels in the Mangalarga Marchador horse breed
title_full Fine-scale estimation of inbreeding rates, runs of homozygosity and genome-wide heterozygosity levels in the Mangalarga Marchador horse breed
title_fullStr Fine-scale estimation of inbreeding rates, runs of homozygosity and genome-wide heterozygosity levels in the Mangalarga Marchador horse breed
title_full_unstemmed Fine-scale estimation of inbreeding rates, runs of homozygosity and genome-wide heterozygosity levels in the Mangalarga Marchador horse breed
title_sort Fine-scale estimation of inbreeding rates, runs of homozygosity and genome-wide heterozygosity levels in the Mangalarga Marchador horse breed
author Bizarria dos Santos, Wellington [UNESP]
author_facet Bizarria dos Santos, Wellington [UNESP]
Pimenta Schettini, Gustavo [UNESP]
Fonseca, Mayara Gonçalves
Pereira, Guilherme Luis [UNESP]
Loyola Chardulo, Luis Artur [UNESP]
Rodrigues Machado Neto, Otávio [UNESP]
Baldassini, Welder Angelo [UNESP]
Nunes de Oliveira, Henrique [UNESP]
Abdallah Curi, Rogério [UNESP]
author_role author
author2 Pimenta Schettini, Gustavo [UNESP]
Fonseca, Mayara Gonçalves
Pereira, Guilherme Luis [UNESP]
Loyola Chardulo, Luis Artur [UNESP]
Rodrigues Machado Neto, Otávio [UNESP]
Baldassini, Welder Angelo [UNESP]
Nunes de Oliveira, Henrique [UNESP]
Abdallah Curi, Rogério [UNESP]
author2_role author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Universidade Estadual Paulista (Unesp)
Universidade Federal de Minas Gerais (UFMG)
dc.contributor.author.fl_str_mv Bizarria dos Santos, Wellington [UNESP]
Pimenta Schettini, Gustavo [UNESP]
Fonseca, Mayara Gonçalves
Pereira, Guilherme Luis [UNESP]
Loyola Chardulo, Luis Artur [UNESP]
Rodrigues Machado Neto, Otávio [UNESP]
Baldassini, Welder Angelo [UNESP]
Nunes de Oliveira, Henrique [UNESP]
Abdallah Curi, Rogério [UNESP]
dc.subject.por.fl_str_mv Equus caballus
FHOM
FPED
FROH
ROH
ROHet
topic Equus caballus
FHOM
FPED
FROH
ROH
ROHet
description With the availability of high-density SNP panels and the establishment of approaches for characterizing homozygosity and heterozygosity sites, it is possible to access fine-scale information regarding genomes, providing more than just comparisons of different inbreeding coefficients. This is the first study that seeks to access such information for the Mangalarga Marchador (MM) horse breed on a genomic scale. To this end, we aimed to assess inbreeding levels using different coefficients, as well as to characterize homozygous and heterozygous runs in the population. Using Axiom ® Equine Genotyping Array—670k SNP (Thermo Fisher), 192 horses were genotyped. Our results showed different estimates: inbreeding from genomic coefficients (FROH) = 0.16; pedigree-based (FPED) = 0.008; and a method based on excess homozygosity (FHOM) = 0.010. The correlations between the inbreeding coefficients were low to moderate, and some comparisons showed negative correlations, being practically null. In total, 85,295 runs of homozygosity (ROH) and 10,016 runs of heterozygosity (ROHet) were characterized for the 31 horse autosomal chromosomes. The class with the highest percentage of ROH was 0–2 Mbps, with 92.78% of the observations. In the ROHet results, only the 0–2 class presented observations, with chromosome 11 highlighted in a region with high genetic variability. Three regions from the ROHet analyses showed genes with known functions: tripartite motif-containing 37 (TRIM37), protein phosphatase, Mg2+/Mn2+ dependent 1E (PPM1E) and carbonic anhydrase 10 (CA10). Therefore, our findings suggest moderate inbreeding, possibly attributed to breed formation, annulling possible recent inbreeding. Furthermore, regions with high variability in the MM genome were identified (ROHet), associated with the recent selection and important events in the development and performance of MM horses over generations.
publishDate 2020
dc.date.none.fl_str_mv 2020-12-12T01:38:48Z
2020-12-12T01:38:48Z
2020-01-01
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://dx.doi.org/10.1111/jbg.12508
Journal of Animal Breeding and Genetics.
1439-0388
0931-2668
http://hdl.handle.net/11449/199402
10.1111/jbg.12508
2-s2.0-85091019409
url http://dx.doi.org/10.1111/jbg.12508
http://hdl.handle.net/11449/199402
identifier_str_mv Journal of Animal Breeding and Genetics.
1439-0388
0931-2668
10.1111/jbg.12508
2-s2.0-85091019409
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Journal of Animal Breeding and Genetics
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.source.none.fl_str_mv Scopus
reponame:Repositório Institucional da UNESP
instname:Universidade Estadual Paulista (UNESP)
instacron:UNESP
instname_str Universidade Estadual Paulista (UNESP)
instacron_str UNESP
institution UNESP
reponame_str Repositório Institucional da UNESP
collection Repositório Institucional da UNESP
repository.name.fl_str_mv Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)
repository.mail.fl_str_mv
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