Timing and extent of inbreeding in African goats
Autor(a) principal: | |
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Data de Publicação: | 2019 |
Outros Autores: | , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.3389/fgene.2019.00537 http://hdl.handle.net/11449/187871 |
Resumo: | Genetic characterization of African goats is one of the current priorities in the improvement of goats in the continent. This study contributes to the characterization effort by determining the levels and number of generations to common ancestors (age) associated with inbreeding in African goat breeds and identifies regions that contain copy number variation mistyped as being homozygous. Illumina 50k single nucleotide polymorphism genotype data for 608 goats from 31 breeds were used to compute the level and age of inbreeding at both local (marker) and global levels (FG) using a model-based approach based on a hidden Markov model. Runs of homozygosity (ROH) segments detected using the Viterbi algorithm led to ROH-based inbreeding coefficients for all ROH (FROH) and for ROH longer than 2 Mb (FROH > 2Mb). Some of the genomic regions identified as having ROH are likely to be hemizygous regions (copy number deletions) mistyped as homozygous regions. Although the proportion of these miscalled ROH is small and does not substantially affect estimates of levels of inbreeding for individual animals, the inbreeding metrics were adjusted by removing these regions from the ROH. All the inbreeding metrics varied widely across breeds, with overall means of 0.0408, 0.0370, and 0.0691 and medians of 0.0125, 0.0098, and 0.0366 for FROH, FROH > 2Mb, and FG, respectively. Several breeds (including Menabe and Sofia from Madagascar) had high proportions of recent inbreeding, while Small East African, Ethiopian, and most of the West African breeds (including West African Dwarf) had more ancient inbreeding. |
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Timing and extent of inbreeding in African goatsAfricaAge-based inbreedingCopy number variationGoatsInbreedingLocal inbreedingRuns of homozygosityGenetic characterization of African goats is one of the current priorities in the improvement of goats in the continent. This study contributes to the characterization effort by determining the levels and number of generations to common ancestors (age) associated with inbreeding in African goat breeds and identifies regions that contain copy number variation mistyped as being homozygous. Illumina 50k single nucleotide polymorphism genotype data for 608 goats from 31 breeds were used to compute the level and age of inbreeding at both local (marker) and global levels (FG) using a model-based approach based on a hidden Markov model. Runs of homozygosity (ROH) segments detected using the Viterbi algorithm led to ROH-based inbreeding coefficients for all ROH (FROH) and for ROH longer than 2 Mb (FROH > 2Mb). Some of the genomic regions identified as having ROH are likely to be hemizygous regions (copy number deletions) mistyped as homozygous regions. Although the proportion of these miscalled ROH is small and does not substantially affect estimates of levels of inbreeding for individual animals, the inbreeding metrics were adjusted by removing these regions from the ROH. All the inbreeding metrics varied widely across breeds, with overall means of 0.0408, 0.0370, and 0.0691 and medians of 0.0125, 0.0098, and 0.0366 for FROH, FROH > 2Mb, and FG, respectively. Several breeds (including Menabe and Sofia from Madagascar) had high proportions of recent inbreeding, while Small East African, Ethiopian, and most of the West African breeds (including West African Dwarf) had more ancient inbreeding.Division of Livestock Sciences Department of Sustainable Agricultural Systems University of Natural Resources and Life SciencesDepartment of Animal Science Faculty of Agriculture Lilongwe University of Agriculture and Natural ResourcesAnimal Genomics and Improvement Laboratory United States Department of Agriculture Agriculture Research ServiceNational Livestock Resources Research InstituteDepartment of Agriculture Kyambogo UniversitySchool of Agricultural and Veterinarian Sciences Jaboticabal São Paulo State University (UNESP)Department of Animal Science Faculty of Agriculture University of ZagrebSchool of Agricultural and Veterinarian Sciences Jaboticabal São Paulo State University (UNESP)University of Natural Resources and Life SciencesLilongwe University of Agriculture and Natural ResourcesAgriculture Research ServiceNational Livestock Resources Research InstituteKyambogo UniversityUniversidade Estadual Paulista (Unesp)University of ZagrebNandolo, WilsonMészáros, GáborBanda, Liveness JessicaGondwe, Timothy N.Lamuno, DoreenMulindwa, Henry AaronNakimbugwe, Helen N.Wurzinger, MariaUtsunomiya, Yuri T. [UNESP]Woodward-Greene, M. JenniferLiu, MeiLiu, GeorgeVan Tassell, Curtis P.Curik, InoRosen, Benjamin D.Sölkner, Johann2019-10-06T15:49:50Z2019-10-06T15:49:50Z2019-01-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.3389/fgene.2019.00537Frontiers in Genetics, v. 10, n. JUN, 2019.1664-8021http://hdl.handle.net/11449/18787110.3389/fgene.2019.005372-s2.0-85068996563Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengFrontiers in Geneticsinfo:eu-repo/semantics/openAccess2021-10-22T18:33:44Zoai:repositorio.unesp.br:11449/187871Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T21:59:58.429096Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Timing and extent of inbreeding in African goats |
title |
Timing and extent of inbreeding in African goats |
spellingShingle |
Timing and extent of inbreeding in African goats Nandolo, Wilson Africa Age-based inbreeding Copy number variation Goats Inbreeding Local inbreeding Runs of homozygosity |
title_short |
Timing and extent of inbreeding in African goats |
title_full |
Timing and extent of inbreeding in African goats |
title_fullStr |
Timing and extent of inbreeding in African goats |
title_full_unstemmed |
Timing and extent of inbreeding in African goats |
title_sort |
Timing and extent of inbreeding in African goats |
author |
Nandolo, Wilson |
author_facet |
Nandolo, Wilson Mészáros, Gábor Banda, Liveness Jessica Gondwe, Timothy N. Lamuno, Doreen Mulindwa, Henry Aaron Nakimbugwe, Helen N. Wurzinger, Maria Utsunomiya, Yuri T. [UNESP] Woodward-Greene, M. Jennifer Liu, Mei Liu, George Van Tassell, Curtis P. Curik, Ino Rosen, Benjamin D. Sölkner, Johann |
author_role |
author |
author2 |
Mészáros, Gábor Banda, Liveness Jessica Gondwe, Timothy N. Lamuno, Doreen Mulindwa, Henry Aaron Nakimbugwe, Helen N. Wurzinger, Maria Utsunomiya, Yuri T. [UNESP] Woodward-Greene, M. Jennifer Liu, Mei Liu, George Van Tassell, Curtis P. Curik, Ino Rosen, Benjamin D. Sölkner, Johann |
author2_role |
author author author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
University of Natural Resources and Life Sciences Lilongwe University of Agriculture and Natural Resources Agriculture Research Service National Livestock Resources Research Institute Kyambogo University Universidade Estadual Paulista (Unesp) University of Zagreb |
dc.contributor.author.fl_str_mv |
Nandolo, Wilson Mészáros, Gábor Banda, Liveness Jessica Gondwe, Timothy N. Lamuno, Doreen Mulindwa, Henry Aaron Nakimbugwe, Helen N. Wurzinger, Maria Utsunomiya, Yuri T. [UNESP] Woodward-Greene, M. Jennifer Liu, Mei Liu, George Van Tassell, Curtis P. Curik, Ino Rosen, Benjamin D. Sölkner, Johann |
dc.subject.por.fl_str_mv |
Africa Age-based inbreeding Copy number variation Goats Inbreeding Local inbreeding Runs of homozygosity |
topic |
Africa Age-based inbreeding Copy number variation Goats Inbreeding Local inbreeding Runs of homozygosity |
description |
Genetic characterization of African goats is one of the current priorities in the improvement of goats in the continent. This study contributes to the characterization effort by determining the levels and number of generations to common ancestors (age) associated with inbreeding in African goat breeds and identifies regions that contain copy number variation mistyped as being homozygous. Illumina 50k single nucleotide polymorphism genotype data for 608 goats from 31 breeds were used to compute the level and age of inbreeding at both local (marker) and global levels (FG) using a model-based approach based on a hidden Markov model. Runs of homozygosity (ROH) segments detected using the Viterbi algorithm led to ROH-based inbreeding coefficients for all ROH (FROH) and for ROH longer than 2 Mb (FROH > 2Mb). Some of the genomic regions identified as having ROH are likely to be hemizygous regions (copy number deletions) mistyped as homozygous regions. Although the proportion of these miscalled ROH is small and does not substantially affect estimates of levels of inbreeding for individual animals, the inbreeding metrics were adjusted by removing these regions from the ROH. All the inbreeding metrics varied widely across breeds, with overall means of 0.0408, 0.0370, and 0.0691 and medians of 0.0125, 0.0098, and 0.0366 for FROH, FROH > 2Mb, and FG, respectively. Several breeds (including Menabe and Sofia from Madagascar) had high proportions of recent inbreeding, while Small East African, Ethiopian, and most of the West African breeds (including West African Dwarf) had more ancient inbreeding. |
publishDate |
2019 |
dc.date.none.fl_str_mv |
2019-10-06T15:49:50Z 2019-10-06T15:49:50Z 2019-01-01 |
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/10.3389/fgene.2019.00537 Frontiers in Genetics, v. 10, n. JUN, 2019. 1664-8021 http://hdl.handle.net/11449/187871 10.3389/fgene.2019.00537 2-s2.0-85068996563 |
url |
http://dx.doi.org/10.3389/fgene.2019.00537 http://hdl.handle.net/11449/187871 |
identifier_str_mv |
Frontiers in Genetics, v. 10, n. JUN, 2019. 1664-8021 10.3389/fgene.2019.00537 2-s2.0-85068996563 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Frontiers in 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 |
|
_version_ |
1808129381910970368 |