Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale, Merino and Creole sheep
Autor(a) principal: | |
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Data de Publicação: | 2014 |
Outros Autores: | , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Genetics and Molecular Biology |
Texto Completo: | http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572014000300011 |
Resumo: | The aim of this study was to investigate the genetic diversity within and among three breeds of sheep: Corriedale, Merino and Creole. Sheep from the three breeds (Merino n = 110, Corriedale n = 108 and Creole n = 10) were genotyped using the Illumina Ovine SNP50 beadchip®. Genetic diversity was evaluated by comparing the minor allele frequency (MAF) among breeds. Population structure and genetic differentiation were assessed using STRUCTURE software, principal component analysis (PCA) and fixation index (F ST). Fixed markers (MAF = 0) that were different among breeds were identified as specific breed markers. Using a subset of 18,181 single nucleotide polymorphisms (SNPs), PCA and STUCTURE analysis were able to explain population stratification within breeds. Merino and Corriedale divergent lines showed high levels of polymorphism (89.4% and 86% of polymorphic SNPs, respectively) and moderate genetic differentiation (F ST = 0.08) between them. In contrast, Creole had only 69% polymorphic SNPs and showed greater genetic differentiation from the other two breeds (F ST = 0.17 for both breeds). Hence, a subset of molecular markers present in the OvineSNP50 is informative enough for breed assignment and population structure analysis of commercial and Creole breeds. |
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Genetics and Molecular Biology |
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Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale, Merino and Creole sheepallele frequencies breed compositionfixation indexOvine SNP50population stratificationprincipal component analysisThe aim of this study was to investigate the genetic diversity within and among three breeds of sheep: Corriedale, Merino and Creole. Sheep from the three breeds (Merino n = 110, Corriedale n = 108 and Creole n = 10) were genotyped using the Illumina Ovine SNP50 beadchip®. Genetic diversity was evaluated by comparing the minor allele frequency (MAF) among breeds. Population structure and genetic differentiation were assessed using STRUCTURE software, principal component analysis (PCA) and fixation index (F ST). Fixed markers (MAF = 0) that were different among breeds were identified as specific breed markers. Using a subset of 18,181 single nucleotide polymorphisms (SNPs), PCA and STUCTURE analysis were able to explain population stratification within breeds. Merino and Corriedale divergent lines showed high levels of polymorphism (89.4% and 86% of polymorphic SNPs, respectively) and moderate genetic differentiation (F ST = 0.08) between them. In contrast, Creole had only 69% polymorphic SNPs and showed greater genetic differentiation from the other two breeds (F ST = 0.17 for both breeds). Hence, a subset of molecular markers present in the OvineSNP50 is informative enough for breed assignment and population structure analysis of commercial and Creole breeds.Sociedade Brasileira de Genética2014-06-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersiontext/htmlhttp://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572014000300011Genetics and Molecular Biology v.37 n.2 2014reponame:Genetics and Molecular Biologyinstname:Sociedade Brasileira de Genética (SBG)instacron:SBG10.1590/S1415-47572014000300011info:eu-repo/semantics/openAccessGrasso,Andrés NGoldberg,VirginiaNavajas,Elly AIriarte,WandaGimeno,DiegoAguilar,IgnacioMedrano,Juan FRincón,GonzaloCiappesoni,Gabrieleng2014-09-17T00:00:00Zoai:scielo:S1415-47572014000300011Revistahttp://www.gmb.org.br/ONGhttps://old.scielo.br/oai/scielo-oai.php||editor@gmb.org.br1678-46851415-4757opendoar:2014-09-17T00:00Genetics and Molecular Biology - Sociedade Brasileira de Genética (SBG)false |
dc.title.none.fl_str_mv |
Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale, Merino and Creole sheep |
title |
Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale, Merino and Creole sheep |
spellingShingle |
Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale, Merino and Creole sheep Grasso,Andrés N allele frequencies breed composition fixation index Ovine SNP50 population stratification principal component analysis |
title_short |
Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale, Merino and Creole sheep |
title_full |
Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale, Merino and Creole sheep |
title_fullStr |
Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale, Merino and Creole sheep |
title_full_unstemmed |
Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale, Merino and Creole sheep |
title_sort |
Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale, Merino and Creole sheep |
author |
Grasso,Andrés N |
author_facet |
Grasso,Andrés N Goldberg,Virginia Navajas,Elly A Iriarte,Wanda Gimeno,Diego Aguilar,Ignacio Medrano,Juan F Rincón,Gonzalo Ciappesoni,Gabriel |
author_role |
author |
author2 |
Goldberg,Virginia Navajas,Elly A Iriarte,Wanda Gimeno,Diego Aguilar,Ignacio Medrano,Juan F Rincón,Gonzalo Ciappesoni,Gabriel |
author2_role |
author author author author author author author author |
dc.contributor.author.fl_str_mv |
Grasso,Andrés N Goldberg,Virginia Navajas,Elly A Iriarte,Wanda Gimeno,Diego Aguilar,Ignacio Medrano,Juan F Rincón,Gonzalo Ciappesoni,Gabriel |
dc.subject.por.fl_str_mv |
allele frequencies breed composition fixation index Ovine SNP50 population stratification principal component analysis |
topic |
allele frequencies breed composition fixation index Ovine SNP50 population stratification principal component analysis |
description |
The aim of this study was to investigate the genetic diversity within and among three breeds of sheep: Corriedale, Merino and Creole. Sheep from the three breeds (Merino n = 110, Corriedale n = 108 and Creole n = 10) were genotyped using the Illumina Ovine SNP50 beadchip®. Genetic diversity was evaluated by comparing the minor allele frequency (MAF) among breeds. Population structure and genetic differentiation were assessed using STRUCTURE software, principal component analysis (PCA) and fixation index (F ST). Fixed markers (MAF = 0) that were different among breeds were identified as specific breed markers. Using a subset of 18,181 single nucleotide polymorphisms (SNPs), PCA and STUCTURE analysis were able to explain population stratification within breeds. Merino and Corriedale divergent lines showed high levels of polymorphism (89.4% and 86% of polymorphic SNPs, respectively) and moderate genetic differentiation (F ST = 0.08) between them. In contrast, Creole had only 69% polymorphic SNPs and showed greater genetic differentiation from the other two breeds (F ST = 0.17 for both breeds). Hence, a subset of molecular markers present in the OvineSNP50 is informative enough for breed assignment and population structure analysis of commercial and Creole breeds. |
publishDate |
2014 |
dc.date.none.fl_str_mv |
2014-06-01 |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572014000300011 |
url |
http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572014000300011 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
10.1590/S1415-47572014000300011 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
text/html |
dc.publisher.none.fl_str_mv |
Sociedade Brasileira de Genética |
publisher.none.fl_str_mv |
Sociedade Brasileira de Genética |
dc.source.none.fl_str_mv |
Genetics and Molecular Biology v.37 n.2 2014 reponame:Genetics and Molecular Biology instname:Sociedade Brasileira de Genética (SBG) instacron:SBG |
instname_str |
Sociedade Brasileira de Genética (SBG) |
instacron_str |
SBG |
institution |
SBG |
reponame_str |
Genetics and Molecular Biology |
collection |
Genetics and Molecular Biology |
repository.name.fl_str_mv |
Genetics and Molecular Biology - Sociedade Brasileira de Genética (SBG) |
repository.mail.fl_str_mv |
||editor@gmb.org.br |
_version_ |
1752122385889230848 |