Carrot alternative oxidase gene AOX2a demonstrates allelic and genotypic polymorphisms in intron 3
Autor(a) principal: | |
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Data de Publicação: | 2009 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | por |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10174/2729 |
Resumo: | Single nucleotide polymorphisms (SNPs) and insertion–deletions (InDels) are becoming important genetic markers for major crop species. In this study, we focus on variations at genomic level of the Daucus carota L. AOX2a gene. The use of gene- specific primers designed in exon regions on the boundaries of introns permitted to recognize intron length polymorphism (ILP) in intron 3 AOX2a by simple polymerase chain reaction (PCR) assays. The length of intron 3 can vary in individual carrot plants. Thus, allelic variation can be used as a tool to discriminate between single plant genotypes. Using this approach, individual plants from cv. Rotin and from diverse breeding lines and cultivars were identified that showed genetic variability by AOX2a ILPs. Repetitive patterns of intron length variation have been observed which allows grouping of genotypes. Polymorphic and identical PCR fragments revealed underlying high levels of sequence polymorphism. Variability was due to InDel events and intron single nucleotide polymorphisms (ISNPs), with a repetitive deletion in intron 3 affecting a putative pre-miRNA site. The results suggest that high AOX2a gene diversity in D. carota can be explored for the development of functional markers related to agronomic traits. |
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Carrot alternative oxidase gene AOX2a demonstrates allelic and genotypic polymorphisms in intron 3--Single nucleotide polymorphisms (SNPs) and insertion–deletions (InDels) are becoming important genetic markers for major crop species. In this study, we focus on variations at genomic level of the Daucus carota L. AOX2a gene. The use of gene- specific primers designed in exon regions on the boundaries of introns permitted to recognize intron length polymorphism (ILP) in intron 3 AOX2a by simple polymerase chain reaction (PCR) assays. The length of intron 3 can vary in individual carrot plants. Thus, allelic variation can be used as a tool to discriminate between single plant genotypes. Using this approach, individual plants from cv. Rotin and from diverse breeding lines and cultivars were identified that showed genetic variability by AOX2a ILPs. Repetitive patterns of intron length variation have been observed which allows grouping of genotypes. Polymorphic and identical PCR fragments revealed underlying high levels of sequence polymorphism. Variability was due to InDel events and intron single nucleotide polymorphisms (ISNPs), with a repetitive deletion in intron 3 affecting a putative pre-miRNA site. The results suggest that high AOX2a gene diversity in D. carota can be explored for the development of functional markers related to agronomic traits.Wiley2011-08-17T14:07:13Z2011-08-172009-10-06T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article8074 bytesapplication/pdfhttp://hdl.handle.net/10174/2729http://hdl.handle.net/10174/2729por592-6080031-9317 (print) 1399-3054 (online137Physiologia Plantarum4restrito_uehcardoso@uevora.ptndndndndeu_chair@uevora.pt577Cardoso, HéliaCampos, Maria DoroteiaCosta, Ana RitaCampos, CatarinaNothnagel, ThomasArnholdt-Schmitt, Birgitinfo:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-01-03T18:38:04Zoai:dspace.uevora.pt:10174/2729Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T00:57:47.229489Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Carrot alternative oxidase gene AOX2a demonstrates allelic and genotypic polymorphisms in intron 3 |
title |
Carrot alternative oxidase gene AOX2a demonstrates allelic and genotypic polymorphisms in intron 3 |
spellingShingle |
Carrot alternative oxidase gene AOX2a demonstrates allelic and genotypic polymorphisms in intron 3 Cardoso, Hélia - - |
title_short |
Carrot alternative oxidase gene AOX2a demonstrates allelic and genotypic polymorphisms in intron 3 |
title_full |
Carrot alternative oxidase gene AOX2a demonstrates allelic and genotypic polymorphisms in intron 3 |
title_fullStr |
Carrot alternative oxidase gene AOX2a demonstrates allelic and genotypic polymorphisms in intron 3 |
title_full_unstemmed |
Carrot alternative oxidase gene AOX2a demonstrates allelic and genotypic polymorphisms in intron 3 |
title_sort |
Carrot alternative oxidase gene AOX2a demonstrates allelic and genotypic polymorphisms in intron 3 |
author |
Cardoso, Hélia |
author_facet |
Cardoso, Hélia Campos, Maria Doroteia Costa, Ana Rita Campos, Catarina Nothnagel, Thomas Arnholdt-Schmitt, Birgit |
author_role |
author |
author2 |
Campos, Maria Doroteia Costa, Ana Rita Campos, Catarina Nothnagel, Thomas Arnholdt-Schmitt, Birgit |
author2_role |
author author author author author |
dc.contributor.author.fl_str_mv |
Cardoso, Hélia Campos, Maria Doroteia Costa, Ana Rita Campos, Catarina Nothnagel, Thomas Arnholdt-Schmitt, Birgit |
dc.subject.por.fl_str_mv |
- - |
topic |
- - |
description |
Single nucleotide polymorphisms (SNPs) and insertion–deletions (InDels) are becoming important genetic markers for major crop species. In this study, we focus on variations at genomic level of the Daucus carota L. AOX2a gene. The use of gene- specific primers designed in exon regions on the boundaries of introns permitted to recognize intron length polymorphism (ILP) in intron 3 AOX2a by simple polymerase chain reaction (PCR) assays. The length of intron 3 can vary in individual carrot plants. Thus, allelic variation can be used as a tool to discriminate between single plant genotypes. Using this approach, individual plants from cv. Rotin and from diverse breeding lines and cultivars were identified that showed genetic variability by AOX2a ILPs. Repetitive patterns of intron length variation have been observed which allows grouping of genotypes. Polymorphic and identical PCR fragments revealed underlying high levels of sequence polymorphism. Variability was due to InDel events and intron single nucleotide polymorphisms (ISNPs), with a repetitive deletion in intron 3 affecting a putative pre-miRNA site. The results suggest that high AOX2a gene diversity in D. carota can be explored for the development of functional markers related to agronomic traits. |
publishDate |
2009 |
dc.date.none.fl_str_mv |
2009-10-06T00:00:00Z 2011-08-17T14:07:13Z 2011-08-17 |
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://hdl.handle.net/10174/2729 http://hdl.handle.net/10174/2729 |
url |
http://hdl.handle.net/10174/2729 |
dc.language.iso.fl_str_mv |
por |
language |
por |
dc.relation.none.fl_str_mv |
592-608 0031-9317 (print) 1399-3054 (online 137 Physiologia Plantarum 4 restrito_ue hcardoso@uevora.pt nd nd nd nd eu_chair@uevora.pt 577 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
8074 bytes application/pdf |
dc.publisher.none.fl_str_mv |
Wiley |
publisher.none.fl_str_mv |
Wiley |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
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RCAAP |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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1799136461644103680 |