A candidate gene survey of quantitative trait loci affecting chemical composition in tomato fruit

Autores
Bermúdez, Luisa; Urias, Ursula; Milstein, D.; Kamenetzky, Laura; Asís, Ramón; Fernie, Alisdair R.; Van Sluys, M.A.; Carrari, Fernando; Rossi, Magdalena
Año de publicación
2008
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
In tomato, numerous wild-related species have been demonstrated to be untapped sources of valuable genetic variability, including pathogen-resistance genes, nutritional, and industrial quality traits. From a collection of S. pennellii introgressed lines, 889 fruit metabolic loci (QML) and 326 yield-associated loci (YAL), distributed across the tomato genome, had been identified previously. By using a combination of molecular marker sequence analysis, PCR amplification and sequencing, analysis of allelic variation, and evaluation of co-response between gene expression and metabolite composition traits, the present report, provides a comprehensive list of candidate genes co-localizing with a subset of 106 QML and 20 YAL associated either with important agronomic or nutritional characteristics. This combined strategy allowed the identification and analysis of 127 candidate genes located in 16 regions of the tomato genome. Eighty-five genes were cloned and partially sequenced, totalling 45 816 and 45 787 bases from S. lycopersicum and S. pennellii, respectively. Allelic variation at the amino acid level was confirmed for 37 of these candidates. Furthermore, out of the 127 gene-metabolite co-locations, some 56 were recovered following correlation of parallel transcript and metabolite profiling. Results obtained here represent the initial steps in the integration of genetic, genomic, and expressional patterns of genes co-localizing with chemical compositional traits of the tomato fruit.
Instituto de Biotecnología
Fil: Bermúdez, Luisa. Universidade de Sao Paulo. Instituto de Biociências. Departamento de Botânica; Brasil
Fil: Urias, Ursula. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Universidade de Sao Paulo. Instituto de Biociências. Departamento de Botânica; Brasil
Fil: Milstein, D. Universidade de Sao Paulo. Instituto de Biociências. Departamento de Botânica; Brasil
Fil: Kamenetzky, Laura. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.
Fil: Asis, Ramón. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas; Argentina
Fil: Fernie, Alisdair R. Max Planck Institute for Molecular Plant Physiology; Alemania
Fil: Van Sluys, M.A. Universidade de Sao Paulo. Instituto de Biociências. Departamento de Botânica; Brasil
Fil: Carrari, Fernando Oscar. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.
Fil: Rossi, Magdalena. Universidade de São Pablo. Instituto de Biociências. Departamento de Botânica; Brasil
Fuente
Journal of Experimental Botany 59 (10) : 2875–2890 (July 2008)
Materia
Tomate
Loci de Rasgos Cuantitativos
Variación Genética
Marcadores Genéticos
Tomatoes
Quantitative Trait Loci
Genetic Variation
Genetic Markers
QTL (quantitative trait loci)
Marcadores Moleculares
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/7493
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oai_identifier_str oai:localhost:20.500.12123/7493
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network_name_str INTA Digital (INTA)
spelling A candidate gene survey of quantitative trait loci affecting chemical composition in tomato fruitBermúdez, LuisaUrias, UrsulaMilstein, D.Kamenetzky, LauraAsís, RamónFernie, Alisdair R.Van Sluys, M.A.Carrari, FernandoRossi, MagdalenaTomateLoci de Rasgos CuantitativosVariación GenéticaMarcadores GenéticosTomatoesQuantitative Trait LociGenetic VariationGenetic MarkersQTL (quantitative trait loci)Marcadores MolecularesIn tomato, numerous wild-related species have been demonstrated to be untapped sources of valuable genetic variability, including pathogen-resistance genes, nutritional, and industrial quality traits. From a collection of S. pennellii introgressed lines, 889 fruit metabolic loci (QML) and 326 yield-associated loci (YAL), distributed across the tomato genome, had been identified previously. By using a combination of molecular marker sequence analysis, PCR amplification and sequencing, analysis of allelic variation, and evaluation of co-response between gene expression and metabolite composition traits, the present report, provides a comprehensive list of candidate genes co-localizing with a subset of 106 QML and 20 YAL associated either with important agronomic or nutritional characteristics. This combined strategy allowed the identification and analysis of 127 candidate genes located in 16 regions of the tomato genome. Eighty-five genes were cloned and partially sequenced, totalling 45 816 and 45 787 bases from S. lycopersicum and S. pennellii, respectively. Allelic variation at the amino acid level was confirmed for 37 of these candidates. Furthermore, out of the 127 gene-metabolite co-locations, some 56 were recovered following correlation of parallel transcript and metabolite profiling. Results obtained here represent the initial steps in the integration of genetic, genomic, and expressional patterns of genes co-localizing with chemical compositional traits of the tomato fruit.Instituto de BiotecnologíaFil: Bermúdez, Luisa. Universidade de Sao Paulo. Instituto de Biociências. Departamento de Botânica; BrasilFil: Urias, Ursula. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Universidade de Sao Paulo. Instituto de Biociências. Departamento de Botânica; BrasilFil: Milstein, D. Universidade de Sao Paulo. Instituto de Biociências. Departamento de Botânica; BrasilFil: Kamenetzky, Laura. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Asis, Ramón. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas; ArgentinaFil: Fernie, Alisdair R. Max Planck Institute for Molecular Plant Physiology; AlemaniaFil: Van Sluys, M.A. Universidade de Sao Paulo. Instituto de Biociências. Departamento de Botânica; BrasilFil: Carrari, Fernando Oscar. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Rossi, Magdalena. Universidade de São Pablo. Instituto de Biociências. Departamento de Botânica; BrasilSociety for Experimental Biology2020-06-30T14:39:05Z2020-06-30T14:39:05Z2008-07info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/7493https://academic.oup.com/jxb/article/59/10/2875/4422810022-09571460-2431https://doi.org/10.1093/jxb/ern146Journal of Experimental Botany 59 (10) : 2875–2890 (July 2008)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2025-09-29T13:44:58Zoai:localhost:20.500.12123/7493instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-29 13:44:58.624INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv A candidate gene survey of quantitative trait loci affecting chemical composition in tomato fruit
title A candidate gene survey of quantitative trait loci affecting chemical composition in tomato fruit
spellingShingle A candidate gene survey of quantitative trait loci affecting chemical composition in tomato fruit
Bermúdez, Luisa
Tomate
Loci de Rasgos Cuantitativos
Variación Genética
Marcadores Genéticos
Tomatoes
Quantitative Trait Loci
Genetic Variation
Genetic Markers
QTL (quantitative trait loci)
Marcadores Moleculares
title_short A candidate gene survey of quantitative trait loci affecting chemical composition in tomato fruit
title_full A candidate gene survey of quantitative trait loci affecting chemical composition in tomato fruit
title_fullStr A candidate gene survey of quantitative trait loci affecting chemical composition in tomato fruit
title_full_unstemmed A candidate gene survey of quantitative trait loci affecting chemical composition in tomato fruit
title_sort A candidate gene survey of quantitative trait loci affecting chemical composition in tomato fruit
dc.creator.none.fl_str_mv Bermúdez, Luisa
Urias, Ursula
Milstein, D.
Kamenetzky, Laura
Asís, Ramón
Fernie, Alisdair R.
Van Sluys, M.A.
Carrari, Fernando
Rossi, Magdalena
author Bermúdez, Luisa
author_facet Bermúdez, Luisa
Urias, Ursula
Milstein, D.
Kamenetzky, Laura
Asís, Ramón
Fernie, Alisdair R.
Van Sluys, M.A.
Carrari, Fernando
Rossi, Magdalena
author_role author
author2 Urias, Ursula
Milstein, D.
Kamenetzky, Laura
Asís, Ramón
Fernie, Alisdair R.
Van Sluys, M.A.
Carrari, Fernando
Rossi, Magdalena
author2_role author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Tomate
Loci de Rasgos Cuantitativos
Variación Genética
Marcadores Genéticos
Tomatoes
Quantitative Trait Loci
Genetic Variation
Genetic Markers
QTL (quantitative trait loci)
Marcadores Moleculares
topic Tomate
Loci de Rasgos Cuantitativos
Variación Genética
Marcadores Genéticos
Tomatoes
Quantitative Trait Loci
Genetic Variation
Genetic Markers
QTL (quantitative trait loci)
Marcadores Moleculares
dc.description.none.fl_txt_mv In tomato, numerous wild-related species have been demonstrated to be untapped sources of valuable genetic variability, including pathogen-resistance genes, nutritional, and industrial quality traits. From a collection of S. pennellii introgressed lines, 889 fruit metabolic loci (QML) and 326 yield-associated loci (YAL), distributed across the tomato genome, had been identified previously. By using a combination of molecular marker sequence analysis, PCR amplification and sequencing, analysis of allelic variation, and evaluation of co-response between gene expression and metabolite composition traits, the present report, provides a comprehensive list of candidate genes co-localizing with a subset of 106 QML and 20 YAL associated either with important agronomic or nutritional characteristics. This combined strategy allowed the identification and analysis of 127 candidate genes located in 16 regions of the tomato genome. Eighty-five genes were cloned and partially sequenced, totalling 45 816 and 45 787 bases from S. lycopersicum and S. pennellii, respectively. Allelic variation at the amino acid level was confirmed for 37 of these candidates. Furthermore, out of the 127 gene-metabolite co-locations, some 56 were recovered following correlation of parallel transcript and metabolite profiling. Results obtained here represent the initial steps in the integration of genetic, genomic, and expressional patterns of genes co-localizing with chemical compositional traits of the tomato fruit.
Instituto de Biotecnología
Fil: Bermúdez, Luisa. Universidade de Sao Paulo. Instituto de Biociências. Departamento de Botânica; Brasil
Fil: Urias, Ursula. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Universidade de Sao Paulo. Instituto de Biociências. Departamento de Botânica; Brasil
Fil: Milstein, D. Universidade de Sao Paulo. Instituto de Biociências. Departamento de Botânica; Brasil
Fil: Kamenetzky, Laura. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.
Fil: Asis, Ramón. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas; Argentina
Fil: Fernie, Alisdair R. Max Planck Institute for Molecular Plant Physiology; Alemania
Fil: Van Sluys, M.A. Universidade de Sao Paulo. Instituto de Biociências. Departamento de Botânica; Brasil
Fil: Carrari, Fernando Oscar. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.
Fil: Rossi, Magdalena. Universidade de São Pablo. Instituto de Biociências. Departamento de Botânica; Brasil
description In tomato, numerous wild-related species have been demonstrated to be untapped sources of valuable genetic variability, including pathogen-resistance genes, nutritional, and industrial quality traits. From a collection of S. pennellii introgressed lines, 889 fruit metabolic loci (QML) and 326 yield-associated loci (YAL), distributed across the tomato genome, had been identified previously. By using a combination of molecular marker sequence analysis, PCR amplification and sequencing, analysis of allelic variation, and evaluation of co-response between gene expression and metabolite composition traits, the present report, provides a comprehensive list of candidate genes co-localizing with a subset of 106 QML and 20 YAL associated either with important agronomic or nutritional characteristics. This combined strategy allowed the identification and analysis of 127 candidate genes located in 16 regions of the tomato genome. Eighty-five genes were cloned and partially sequenced, totalling 45 816 and 45 787 bases from S. lycopersicum and S. pennellii, respectively. Allelic variation at the amino acid level was confirmed for 37 of these candidates. Furthermore, out of the 127 gene-metabolite co-locations, some 56 were recovered following correlation of parallel transcript and metabolite profiling. Results obtained here represent the initial steps in the integration of genetic, genomic, and expressional patterns of genes co-localizing with chemical compositional traits of the tomato fruit.
publishDate 2008
dc.date.none.fl_str_mv 2008-07
2020-06-30T14:39:05Z
2020-06-30T14:39:05Z
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/20.500.12123/7493
https://academic.oup.com/jxb/article/59/10/2875/442281
0022-0957
1460-2431
https://doi.org/10.1093/jxb/ern146
url http://hdl.handle.net/20.500.12123/7493
https://academic.oup.com/jxb/article/59/10/2875/442281
https://doi.org/10.1093/jxb/ern146
identifier_str_mv 0022-0957
1460-2431
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Society for Experimental Biology
publisher.none.fl_str_mv Society for Experimental Biology
dc.source.none.fl_str_mv Journal of Experimental Botany 59 (10) : 2875–2890 (July 2008)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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