Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds.
Autor(a) principal: | |
---|---|
Data de Publicação: | 2017 |
Outros Autores: | , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
Texto Completo: | http://www.alice.cnptia.embrapa.br/alice/handle/doc/1086824 https://doi.org/10.1371/journal.pone.0173954 |
Resumo: | Whole-genome re-sequencing, alignment and annotation analyses were undertaken for 12 sires representing four important cattle breeds in Brazil: Guzerat (multi-purpose), Gyr, Girolando and Holstein (dairy production). A total of approximately 4.3 billion reads from an Illumina HiSeq 2000 sequencer generated for each animal 10.7 to 16.4-fold genome coverage. A total of 27,441,279 single nucleotide variations (SNVs) and 3,828,041 insertions/deletions (InDels) were detected in the samples, of which 2,557,670 SNVs and 883,219 InDels were novel. The submission of these genetic variants to the dbSNP database significantly increased the number of known variants, particularly for the indicine genome. The concordance rate between genotypes obtained using the Bovine HD BeadChip array and the same variants identified by sequencing was about 99.05%. The annotation of variants identified numerous non-synonymous SNVs and frameshift InDels which could affect phenotypic variation. Functional enrichment analysis was performed and revealed that variants in the olfactory transduction pathway was over represented in all four cattle breeds, while the ECM-receptor interaction pathway was over represented in Girolando and Guzerat breeds, the ABC transporters pathway was over represented only in Holstein breed, and the metabolic pathways was over represented only in Gyr breed. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Gyr, Girolando, Guzerat and Holstein breeding programs. |
id |
EMBR_5c40eb5254896c1c5db92c9e49c7260b |
---|---|
oai_identifier_str |
oai:www.alice.cnptia.embrapa.br:doc/1086824 |
network_acronym_str |
EMBR |
network_name_str |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
repository_id_str |
2154 |
spelling |
Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds.Polimorfismo de nucleotídeo únicoSingle nucleotide variationsImportant traitsGenetic variantsGadoVariação genéticaGenomeSingle nucleotide polymorphismCattle breedsWhole-genome re-sequencing, alignment and annotation analyses were undertaken for 12 sires representing four important cattle breeds in Brazil: Guzerat (multi-purpose), Gyr, Girolando and Holstein (dairy production). A total of approximately 4.3 billion reads from an Illumina HiSeq 2000 sequencer generated for each animal 10.7 to 16.4-fold genome coverage. A total of 27,441,279 single nucleotide variations (SNVs) and 3,828,041 insertions/deletions (InDels) were detected in the samples, of which 2,557,670 SNVs and 883,219 InDels were novel. The submission of these genetic variants to the dbSNP database significantly increased the number of known variants, particularly for the indicine genome. The concordance rate between genotypes obtained using the Bovine HD BeadChip array and the same variants identified by sequencing was about 99.05%. The annotation of variants identified numerous non-synonymous SNVs and frameshift InDels which could affect phenotypic variation. Functional enrichment analysis was performed and revealed that variants in the olfactory transduction pathway was over represented in all four cattle breeds, while the ECM-receptor interaction pathway was over represented in Girolando and Guzerat breeds, the ABC transporters pathway was over represented only in Holstein breed, and the metabolic pathways was over represented only in Gyr breed. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Gyr, Girolando, Guzerat and Holstein breeding programs.Artigo e0173954. Na publicação: Adhemar Zerlotini, Marcos Vinicius Gualberto Barbosa da Silva.NEDENIA BONVINO STAFUZZA, FCAV/Unesp; ADHEMAR ZERLOTINI NETO, CNPTIA; FRANCISCO PEREIRA LOBO, CNPTIA; MICHEL EDUARDO BELEZA YAMAGISHI, CNPTIA; TATIANE CRISTINA SELEGUIM CHUD, FCAV/Unesp; ALEXANDRE RODRIGUES CAETANO, Cenargen; DANÍSIO PRADO MUNARI, FCAV/Unesp; DORIAN J. GARRICK, Iowa State University; MARCO ANTONIO MACHADO, CNPGL; MARTA FONSECA MARTINS, CNPGL; MARIA RAQUEL CARVALHO, UFMG; JOHN BRUCE COLE, Agricultural Research Service; MARCOS VINICIUS GUALBERTO B SILVA, CNPGL.STAFUZZA, N. B.ZERLOTINI NETO, A.LOBO, F. P.YAMAGISHI, M. E. B.CHUD, T. C. S.CAETANO, A. R.MUNARI, D. P.GARRICK, D. J.MACHADO, M. A.MARTINS, M. F.CARVALHO, M. R.COLE, J. B.SILVA, M. V. G. B.2018-02-01T00:00:15Z2018-02-01T00:00:15Z2018-01-3120172018-02-01T11:11:11Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlePlos One, v. 12, n. 3, p. 1-15, 2017.http://www.alice.cnptia.embrapa.br/alice/handle/doc/1086824https://doi.org/10.1371/journal.pone.0173954enginfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)instacron:EMBRAPA2018-02-01T00:00:24Zoai:www.alice.cnptia.embrapa.br:doc/1086824Repositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestopendoar:21542018-02-01T00:00:24falseRepositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestcg-riaa@embrapa.bropendoar:21542018-02-01T00:00:24Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)false |
dc.title.none.fl_str_mv |
Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds. |
title |
Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds. |
spellingShingle |
Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds. STAFUZZA, N. B. Polimorfismo de nucleotídeo único Single nucleotide variations Important traits Genetic variants Gado Variação genética Genome Single nucleotide polymorphism Cattle breeds |
title_short |
Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds. |
title_full |
Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds. |
title_fullStr |
Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds. |
title_full_unstemmed |
Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds. |
title_sort |
Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds. |
author |
STAFUZZA, N. B. |
author_facet |
STAFUZZA, N. B. ZERLOTINI NETO, A. LOBO, F. P. YAMAGISHI, M. E. B. CHUD, T. C. S. CAETANO, A. R. MUNARI, D. P. GARRICK, D. J. MACHADO, M. A. MARTINS, M. F. CARVALHO, M. R. COLE, J. B. SILVA, M. V. G. B. |
author_role |
author |
author2 |
ZERLOTINI NETO, A. LOBO, F. P. YAMAGISHI, M. E. B. CHUD, T. C. S. CAETANO, A. R. MUNARI, D. P. GARRICK, D. J. MACHADO, M. A. MARTINS, M. F. CARVALHO, M. R. COLE, J. B. SILVA, M. V. G. B. |
author2_role |
author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
NEDENIA BONVINO STAFUZZA, FCAV/Unesp; ADHEMAR ZERLOTINI NETO, CNPTIA; FRANCISCO PEREIRA LOBO, CNPTIA; MICHEL EDUARDO BELEZA YAMAGISHI, CNPTIA; TATIANE CRISTINA SELEGUIM CHUD, FCAV/Unesp; ALEXANDRE RODRIGUES CAETANO, Cenargen; DANÍSIO PRADO MUNARI, FCAV/Unesp; DORIAN J. GARRICK, Iowa State University; MARCO ANTONIO MACHADO, CNPGL; MARTA FONSECA MARTINS, CNPGL; MARIA RAQUEL CARVALHO, UFMG; JOHN BRUCE COLE, Agricultural Research Service; MARCOS VINICIUS GUALBERTO B SILVA, CNPGL. |
dc.contributor.author.fl_str_mv |
STAFUZZA, N. B. ZERLOTINI NETO, A. LOBO, F. P. YAMAGISHI, M. E. B. CHUD, T. C. S. CAETANO, A. R. MUNARI, D. P. GARRICK, D. J. MACHADO, M. A. MARTINS, M. F. CARVALHO, M. R. COLE, J. B. SILVA, M. V. G. B. |
dc.subject.por.fl_str_mv |
Polimorfismo de nucleotídeo único Single nucleotide variations Important traits Genetic variants Gado Variação genética Genome Single nucleotide polymorphism Cattle breeds |
topic |
Polimorfismo de nucleotídeo único Single nucleotide variations Important traits Genetic variants Gado Variação genética Genome Single nucleotide polymorphism Cattle breeds |
description |
Whole-genome re-sequencing, alignment and annotation analyses were undertaken for 12 sires representing four important cattle breeds in Brazil: Guzerat (multi-purpose), Gyr, Girolando and Holstein (dairy production). A total of approximately 4.3 billion reads from an Illumina HiSeq 2000 sequencer generated for each animal 10.7 to 16.4-fold genome coverage. A total of 27,441,279 single nucleotide variations (SNVs) and 3,828,041 insertions/deletions (InDels) were detected in the samples, of which 2,557,670 SNVs and 883,219 InDels were novel. The submission of these genetic variants to the dbSNP database significantly increased the number of known variants, particularly for the indicine genome. The concordance rate between genotypes obtained using the Bovine HD BeadChip array and the same variants identified by sequencing was about 99.05%. The annotation of variants identified numerous non-synonymous SNVs and frameshift InDels which could affect phenotypic variation. Functional enrichment analysis was performed and revealed that variants in the olfactory transduction pathway was over represented in all four cattle breeds, while the ECM-receptor interaction pathway was over represented in Girolando and Guzerat breeds, the ABC transporters pathway was over represented only in Holstein breed, and the metabolic pathways was over represented only in Gyr breed. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Gyr, Girolando, Guzerat and Holstein breeding programs. |
publishDate |
2017 |
dc.date.none.fl_str_mv |
2017 2018-02-01T00:00:15Z 2018-02-01T00:00:15Z 2018-01-31 2018-02-01T11:11:11Z |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/publishedVersion info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
Plos One, v. 12, n. 3, p. 1-15, 2017. http://www.alice.cnptia.embrapa.br/alice/handle/doc/1086824 https://doi.org/10.1371/journal.pone.0173954 |
identifier_str_mv |
Plos One, v. 12, n. 3, p. 1-15, 2017. |
url |
http://www.alice.cnptia.embrapa.br/alice/handle/doc/1086824 https://doi.org/10.1371/journal.pone.0173954 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
reponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa) instacron:EMBRAPA |
instname_str |
Empresa Brasileira de Pesquisa Agropecuária (Embrapa) |
instacron_str |
EMBRAPA |
institution |
EMBRAPA |
reponame_str |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
collection |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
repository.name.fl_str_mv |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa) |
repository.mail.fl_str_mv |
cg-riaa@embrapa.br |
_version_ |
1794503449241452544 |