Rapid array mapping of circadian clock and developmental mutations in Arabidopsis

Autores
Hazen, Samuel P.; Borevitz, Justin O.; Harmon, Frank G.; Pruneda Paz, Jose Luis Pablo; Schultz, Thomas F.; Yanovsky, Marcelo Javier; Liljegren, Sarah J.; Ecker, Joseph R.; Kay, Steve A.
Año de publicación
2005
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Classical forward genetics, the identification of genes responsible for mutant phenotypes, remains an important part of functional characterization of the genome. With the advent of extensive genome sequence, phenotyping and genotyping remain the critical limiting variables in the process of map-based cloning. Here, we reduce the genotyping problem by hybridizing labeled genomic DNA to the Affymetrix Arabidopsis (Arabidopsis thaliana) ATH1 GeneChip. Genotyping was carried out on the scale of detecting greater than 8,000 single feature polymorphisms from over 200,000 loci in a single assay. By combining this technique with bulk segregant analysis, several high heritability development and circadian clock traits were mapped. The mapping accuracy using bulk pools of 26 to 100 F2 individuals ranged from 0.22 to 1.96 Mb of the mutations revealing mutant alleles of EARLY FLOWERING 3, EARLY FLOWERING 4, TIMING OF CAB EXPRESSION 1, and ASYMMETRIC LEAVES 1. While direct detection of small mutations, such as an ethyl-methane sulfonate derived single base substitutions, is limited by array coverage and sensitivity, large deletions such as those that can be caused by fast neutrons are easily detected. We demonstrate this by resolving two deletions, the 77-kb flavin-binding, kelch repeat, f-box 1 and the 7-kb cryptochrome2-1 deletions, via direct hybridization of mutant DNA to ATH1 expression arrays.
Fil: Hazen, Samuel P.. The Scripps Research Institute; Estados Unidos
Fil: Borevitz, Justin O.. University of Chicago; Estados Unidos. Salk Institute for Biological Studies; Estados Unidos
Fil: Harmon, Frank G.. The Scripps Research Institute; Estados Unidos
Fil: Pruneda Paz, Jose Luis Pablo. The Scripps Research Institute; Estados Unidos
Fil: Schultz, Thomas F.. The Scripps Research Institute; Estados Unidos
Fil: Yanovsky, Marcelo Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; Argentina
Fil: Liljegren, Sarah J.. The Scripps Research Institute; Estados Unidos
Fil: Ecker, Joseph R.. Salk Institute for Biological Studies; Estados Unidos
Fil: Kay, Steve A.. The Scripps Research Institute; Estados Unidos
Materia
Plant Biology
Arabidopsis
Circadian Clock
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/39079
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/39079
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Rapid array mapping of circadian clock and developmental mutations in ArabidopsisHazen, Samuel P.Borevitz, Justin O.Harmon, Frank G.Pruneda Paz, Jose Luis PabloSchultz, Thomas F.Yanovsky, Marcelo JavierLiljegren, Sarah J.Ecker, Joseph R.Kay, Steve A.Plant BiologyArabidopsisCircadian Clockhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Classical forward genetics, the identification of genes responsible for mutant phenotypes, remains an important part of functional characterization of the genome. With the advent of extensive genome sequence, phenotyping and genotyping remain the critical limiting variables in the process of map-based cloning. Here, we reduce the genotyping problem by hybridizing labeled genomic DNA to the Affymetrix Arabidopsis (Arabidopsis thaliana) ATH1 GeneChip. Genotyping was carried out on the scale of detecting greater than 8,000 single feature polymorphisms from over 200,000 loci in a single assay. By combining this technique with bulk segregant analysis, several high heritability development and circadian clock traits were mapped. The mapping accuracy using bulk pools of 26 to 100 F2 individuals ranged from 0.22 to 1.96 Mb of the mutations revealing mutant alleles of EARLY FLOWERING 3, EARLY FLOWERING 4, TIMING OF CAB EXPRESSION 1, and ASYMMETRIC LEAVES 1. While direct detection of small mutations, such as an ethyl-methane sulfonate derived single base substitutions, is limited by array coverage and sensitivity, large deletions such as those that can be caused by fast neutrons are easily detected. We demonstrate this by resolving two deletions, the 77-kb flavin-binding, kelch repeat, f-box 1 and the 7-kb cryptochrome2-1 deletions, via direct hybridization of mutant DNA to ATH1 expression arrays.Fil: Hazen, Samuel P.. The Scripps Research Institute; Estados UnidosFil: Borevitz, Justin O.. University of Chicago; Estados Unidos. Salk Institute for Biological Studies; Estados UnidosFil: Harmon, Frank G.. The Scripps Research Institute; Estados UnidosFil: Pruneda Paz, Jose Luis Pablo. The Scripps Research Institute; Estados UnidosFil: Schultz, Thomas F.. The Scripps Research Institute; Estados UnidosFil: Yanovsky, Marcelo Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; ArgentinaFil: Liljegren, Sarah J.. The Scripps Research Institute; Estados UnidosFil: Ecker, Joseph R.. Salk Institute for Biological Studies; Estados UnidosFil: Kay, Steve A.. The Scripps Research Institute; Estados UnidosAmerican Society of Plant Biologist2005-12info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/39079Hazen, Samuel P.; Borevitz, Justin O.; Harmon, Frank G.; Pruneda Paz, Jose Luis Pablo; Schultz, Thomas F.; et al.; Rapid array mapping of circadian clock and developmental mutations in Arabidopsis; American Society of Plant Biologist; Plant Physiology; 138; 2; 12-2005; 990-9970032-08891532-2548CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/http://www.plantphysiol.org/content/138/2/990.longinfo:eu-repo/semantics/altIdentifier/doi/10.1104/pp.105.061408info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T10:08:10Zoai:ri.conicet.gov.ar:11336/39079instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 10:08:10.484CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Rapid array mapping of circadian clock and developmental mutations in Arabidopsis
title Rapid array mapping of circadian clock and developmental mutations in Arabidopsis
spellingShingle Rapid array mapping of circadian clock and developmental mutations in Arabidopsis
Hazen, Samuel P.
Plant Biology
Arabidopsis
Circadian Clock
title_short Rapid array mapping of circadian clock and developmental mutations in Arabidopsis
title_full Rapid array mapping of circadian clock and developmental mutations in Arabidopsis
title_fullStr Rapid array mapping of circadian clock and developmental mutations in Arabidopsis
title_full_unstemmed Rapid array mapping of circadian clock and developmental mutations in Arabidopsis
title_sort Rapid array mapping of circadian clock and developmental mutations in Arabidopsis
dc.creator.none.fl_str_mv Hazen, Samuel P.
Borevitz, Justin O.
Harmon, Frank G.
Pruneda Paz, Jose Luis Pablo
Schultz, Thomas F.
Yanovsky, Marcelo Javier
Liljegren, Sarah J.
Ecker, Joseph R.
Kay, Steve A.
author Hazen, Samuel P.
author_facet Hazen, Samuel P.
Borevitz, Justin O.
Harmon, Frank G.
Pruneda Paz, Jose Luis Pablo
Schultz, Thomas F.
Yanovsky, Marcelo Javier
Liljegren, Sarah J.
Ecker, Joseph R.
Kay, Steve A.
author_role author
author2 Borevitz, Justin O.
Harmon, Frank G.
Pruneda Paz, Jose Luis Pablo
Schultz, Thomas F.
Yanovsky, Marcelo Javier
Liljegren, Sarah J.
Ecker, Joseph R.
Kay, Steve A.
author2_role author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Plant Biology
Arabidopsis
Circadian Clock
topic Plant Biology
Arabidopsis
Circadian Clock
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Classical forward genetics, the identification of genes responsible for mutant phenotypes, remains an important part of functional characterization of the genome. With the advent of extensive genome sequence, phenotyping and genotyping remain the critical limiting variables in the process of map-based cloning. Here, we reduce the genotyping problem by hybridizing labeled genomic DNA to the Affymetrix Arabidopsis (Arabidopsis thaliana) ATH1 GeneChip. Genotyping was carried out on the scale of detecting greater than 8,000 single feature polymorphisms from over 200,000 loci in a single assay. By combining this technique with bulk segregant analysis, several high heritability development and circadian clock traits were mapped. The mapping accuracy using bulk pools of 26 to 100 F2 individuals ranged from 0.22 to 1.96 Mb of the mutations revealing mutant alleles of EARLY FLOWERING 3, EARLY FLOWERING 4, TIMING OF CAB EXPRESSION 1, and ASYMMETRIC LEAVES 1. While direct detection of small mutations, such as an ethyl-methane sulfonate derived single base substitutions, is limited by array coverage and sensitivity, large deletions such as those that can be caused by fast neutrons are easily detected. We demonstrate this by resolving two deletions, the 77-kb flavin-binding, kelch repeat, f-box 1 and the 7-kb cryptochrome2-1 deletions, via direct hybridization of mutant DNA to ATH1 expression arrays.
Fil: Hazen, Samuel P.. The Scripps Research Institute; Estados Unidos
Fil: Borevitz, Justin O.. University of Chicago; Estados Unidos. Salk Institute for Biological Studies; Estados Unidos
Fil: Harmon, Frank G.. The Scripps Research Institute; Estados Unidos
Fil: Pruneda Paz, Jose Luis Pablo. The Scripps Research Institute; Estados Unidos
Fil: Schultz, Thomas F.. The Scripps Research Institute; Estados Unidos
Fil: Yanovsky, Marcelo Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; Argentina
Fil: Liljegren, Sarah J.. The Scripps Research Institute; Estados Unidos
Fil: Ecker, Joseph R.. Salk Institute for Biological Studies; Estados Unidos
Fil: Kay, Steve A.. The Scripps Research Institute; Estados Unidos
description Classical forward genetics, the identification of genes responsible for mutant phenotypes, remains an important part of functional characterization of the genome. With the advent of extensive genome sequence, phenotyping and genotyping remain the critical limiting variables in the process of map-based cloning. Here, we reduce the genotyping problem by hybridizing labeled genomic DNA to the Affymetrix Arabidopsis (Arabidopsis thaliana) ATH1 GeneChip. Genotyping was carried out on the scale of detecting greater than 8,000 single feature polymorphisms from over 200,000 loci in a single assay. By combining this technique with bulk segregant analysis, several high heritability development and circadian clock traits were mapped. The mapping accuracy using bulk pools of 26 to 100 F2 individuals ranged from 0.22 to 1.96 Mb of the mutations revealing mutant alleles of EARLY FLOWERING 3, EARLY FLOWERING 4, TIMING OF CAB EXPRESSION 1, and ASYMMETRIC LEAVES 1. While direct detection of small mutations, such as an ethyl-methane sulfonate derived single base substitutions, is limited by array coverage and sensitivity, large deletions such as those that can be caused by fast neutrons are easily detected. We demonstrate this by resolving two deletions, the 77-kb flavin-binding, kelch repeat, f-box 1 and the 7-kb cryptochrome2-1 deletions, via direct hybridization of mutant DNA to ATH1 expression arrays.
publishDate 2005
dc.date.none.fl_str_mv 2005-12
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/39079
Hazen, Samuel P.; Borevitz, Justin O.; Harmon, Frank G.; Pruneda Paz, Jose Luis Pablo; Schultz, Thomas F.; et al.; Rapid array mapping of circadian clock and developmental mutations in Arabidopsis; American Society of Plant Biologist; Plant Physiology; 138; 2; 12-2005; 990-997
0032-0889
1532-2548
CONICET Digital
CONICET
url http://hdl.handle.net/11336/39079
identifier_str_mv Hazen, Samuel P.; Borevitz, Justin O.; Harmon, Frank G.; Pruneda Paz, Jose Luis Pablo; Schultz, Thomas F.; et al.; Rapid array mapping of circadian clock and developmental mutations in Arabidopsis; American Society of Plant Biologist; Plant Physiology; 138; 2; 12-2005; 990-997
0032-0889
1532-2548
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/http://www.plantphysiol.org/content/138/2/990.long
info:eu-repo/semantics/altIdentifier/doi/10.1104/pp.105.061408
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv American Society of Plant Biologist
publisher.none.fl_str_mv American Society of Plant Biologist
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.13397

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