Genomic analysis of wild tomato introgressions determining metabolism-and yield-associated traits

Autores
Kamenetzky, Laura; Asis, Ramón; Bassi, Sebastián; de Godoy, Fabiana; Bermúdez, Luisa; Fernie, Alisdair R.; van Sluys, Marie Anne; Vrebalov, Julia; Giovannoni, James J.; Rossi, Magdalena; Carrari, Fernando Oscar
Año de publicación
2010
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
With the aim of determining the genetic basis of metabolic regulation in tomato fruit, we constructed a detailed physical map of genomic regions spanning previously described metabolic quantitative trait loci of a Solanum pennellii introgression line population. Two genomic libraries from S. pennellii were screened with 104 colocated markers from five selected genomic regions, and a total of 614 bacterial artificial chromosome (BAC)/cosmids were identified as seed clones. Integration of sequence data with the genetic and physical maps of Solanum lycopersicum facilitated the anchoring of 374 of these BAC/ cosmid clones. The analysis of this information resulted in a genome-wide map of a nondomesticated plant species and covers 10% of the physical distance of the selected regions corresponding to approximately 1% of the wild tomato genome. Comparative analyses revealed that S. pennellii and domesticated tomato genomes can be considered as largely colinear. A total of 1,238,705 bp from both BAC/cosmid ends and nine large insert clones were sequenced, annotated, and functionally categorized. The sequence data allowed the evaluation of the level of polymorphism between the wild and cultivated tomato species. An exhaustive microsynteny analysis allowed us to estimate the divergence date of S. pennellii and S. lycopersicum at 2.7 million years ago. The combined results serve as a reference for comparative studies both at the macrosyntenic and microsyntenic levels. They also provide a valuable tool for fine-mapping of quantitative trait loci in tomato. Furthermore, they will contribute to a deeper understanding of the regulatory factors underpinning metabolism and hence defining crop chemical composition. © 2010 American Society of Plant Biologists.
Fil: Kamenetzky, Laura. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina
Fil: Asis, Ramón. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina
Fil: Bassi, Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina
Fil: de Godoy, Fabiana. Universidade de Sao Paulo; Brasil
Fil: Bermúdez, Luisa. Universidade de Sao Paulo; Brasil
Fil: Fernie, Alisdair R.. Max Planck Institute for Molecular Plant Physiology; Alemania
Fil: van Sluys, Marie Anne. Universidade de Sao Paulo; Brasil
Fil: Vrebalov, Julia. Cornell University; Estados Unidos
Fil: Giovannoni, James J.. Cornell University; Estados Unidos
Fil: Rossi, Magdalena. Universidade de Sao Paulo; Brasil
Fil: Carrari, Fernando Oscar. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina
Materia
Tomato
Physical map
Metabolism
Introgression lines
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:11336/67777
Acceder
id CONICETDig_b278f052b0af8613cbd691db1a0284f6
oai_identifier_str oai:ri.conicet.gov.ar:11336/67777
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Genomic analysis of wild tomato introgressions determining metabolism-and yield-associated traitsKamenetzky, LauraAsis, RamónBassi, Sebastiánde Godoy, FabianaBermúdez, LuisaFernie, Alisdair R.van Sluys, Marie AnneVrebalov, JuliaGiovannoni, James J.Rossi, MagdalenaCarrari, Fernando OscarTomatoPhysical mapMetabolismIntrogression lineshttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1With the aim of determining the genetic basis of metabolic regulation in tomato fruit, we constructed a detailed physical map of genomic regions spanning previously described metabolic quantitative trait loci of a Solanum pennellii introgression line population. Two genomic libraries from S. pennellii were screened with 104 colocated markers from five selected genomic regions, and a total of 614 bacterial artificial chromosome (BAC)/cosmids were identified as seed clones. Integration of sequence data with the genetic and physical maps of Solanum lycopersicum facilitated the anchoring of 374 of these BAC/ cosmid clones. The analysis of this information resulted in a genome-wide map of a nondomesticated plant species and covers 10% of the physical distance of the selected regions corresponding to approximately 1% of the wild tomato genome. Comparative analyses revealed that S. pennellii and domesticated tomato genomes can be considered as largely colinear. A total of 1,238,705 bp from both BAC/cosmid ends and nine large insert clones were sequenced, annotated, and functionally categorized. The sequence data allowed the evaluation of the level of polymorphism between the wild and cultivated tomato species. An exhaustive microsynteny analysis allowed us to estimate the divergence date of S. pennellii and S. lycopersicum at 2.7 million years ago. The combined results serve as a reference for comparative studies both at the macrosyntenic and microsyntenic levels. They also provide a valuable tool for fine-mapping of quantitative trait loci in tomato. Furthermore, they will contribute to a deeper understanding of the regulatory factors underpinning metabolism and hence defining crop chemical composition. © 2010 American Society of Plant Biologists.Fil: Kamenetzky, Laura. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; ArgentinaFil: Asis, Ramón. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; ArgentinaFil: Bassi, Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; ArgentinaFil: de Godoy, Fabiana. Universidade de Sao Paulo; BrasilFil: Bermúdez, Luisa. Universidade de Sao Paulo; BrasilFil: Fernie, Alisdair R.. Max Planck Institute for Molecular Plant Physiology; AlemaniaFil: van Sluys, Marie Anne. Universidade de Sao Paulo; BrasilFil: Vrebalov, Julia. Cornell University; Estados UnidosFil: Giovannoni, James J.. Cornell University; Estados UnidosFil: Rossi, Magdalena. Universidade de Sao Paulo; BrasilFil: Carrari, Fernando Oscar. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; ArgentinaAmerican Society of Plant Biologist2010-12info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/67777Kamenetzky, Laura; Asis, Ramón; Bassi, Sebastián; de Godoy, Fabiana; Bermúdez, Luisa; et al.; Genomic analysis of wild tomato introgressions determining metabolism-and yield-associated traits; American Society of Plant Biologist; Plant Physiology; 152; 4; 12-2010; 1772-17860032-0889CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1104/pp.109.150532info:eu-repo/semantics/altIdentifier/url/http://www.plantphysiol.org/content/152/4/1772info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T09:50:37Zoai:ri.conicet.gov.ar:11336/67777instacron: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 09:50:37.614CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Genomic analysis of wild tomato introgressions determining metabolism-and yield-associated traits
title Genomic analysis of wild tomato introgressions determining metabolism-and yield-associated traits
spellingShingle Genomic analysis of wild tomato introgressions determining metabolism-and yield-associated traits
Kamenetzky, Laura
Tomato
Physical map
Metabolism
Introgression lines
title_short Genomic analysis of wild tomato introgressions determining metabolism-and yield-associated traits
title_full Genomic analysis of wild tomato introgressions determining metabolism-and yield-associated traits
title_fullStr Genomic analysis of wild tomato introgressions determining metabolism-and yield-associated traits
title_full_unstemmed Genomic analysis of wild tomato introgressions determining metabolism-and yield-associated traits
title_sort Genomic analysis of wild tomato introgressions determining metabolism-and yield-associated traits
dc.creator.none.fl_str_mv Kamenetzky, Laura
Asis, Ramón
Bassi, Sebastián
de Godoy, Fabiana
Bermúdez, Luisa
Fernie, Alisdair R.
van Sluys, Marie Anne
Vrebalov, Julia
Giovannoni, James J.
Rossi, Magdalena
Carrari, Fernando Oscar
author Kamenetzky, Laura
author_facet Kamenetzky, Laura
Asis, Ramón
Bassi, Sebastián
de Godoy, Fabiana
Bermúdez, Luisa
Fernie, Alisdair R.
van Sluys, Marie Anne
Vrebalov, Julia
Giovannoni, James J.
Rossi, Magdalena
Carrari, Fernando Oscar
author_role author
author2 Asis, Ramón
Bassi, Sebastián
de Godoy, Fabiana
Bermúdez, Luisa
Fernie, Alisdair R.
van Sluys, Marie Anne
Vrebalov, Julia
Giovannoni, James J.
Rossi, Magdalena
Carrari, Fernando Oscar
author2_role author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Tomato
Physical map
Metabolism
Introgression lines
topic Tomato
Physical map
Metabolism
Introgression lines
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv With the aim of determining the genetic basis of metabolic regulation in tomato fruit, we constructed a detailed physical map of genomic regions spanning previously described metabolic quantitative trait loci of a Solanum pennellii introgression line population. Two genomic libraries from S. pennellii were screened with 104 colocated markers from five selected genomic regions, and a total of 614 bacterial artificial chromosome (BAC)/cosmids were identified as seed clones. Integration of sequence data with the genetic and physical maps of Solanum lycopersicum facilitated the anchoring of 374 of these BAC/ cosmid clones. The analysis of this information resulted in a genome-wide map of a nondomesticated plant species and covers 10% of the physical distance of the selected regions corresponding to approximately 1% of the wild tomato genome. Comparative analyses revealed that S. pennellii and domesticated tomato genomes can be considered as largely colinear. A total of 1,238,705 bp from both BAC/cosmid ends and nine large insert clones were sequenced, annotated, and functionally categorized. The sequence data allowed the evaluation of the level of polymorphism between the wild and cultivated tomato species. An exhaustive microsynteny analysis allowed us to estimate the divergence date of S. pennellii and S. lycopersicum at 2.7 million years ago. The combined results serve as a reference for comparative studies both at the macrosyntenic and microsyntenic levels. They also provide a valuable tool for fine-mapping of quantitative trait loci in tomato. Furthermore, they will contribute to a deeper understanding of the regulatory factors underpinning metabolism and hence defining crop chemical composition. © 2010 American Society of Plant Biologists.
Fil: Kamenetzky, Laura. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina
Fil: Asis, Ramón. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina
Fil: Bassi, Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina
Fil: de Godoy, Fabiana. Universidade de Sao Paulo; Brasil
Fil: Bermúdez, Luisa. Universidade de Sao Paulo; Brasil
Fil: Fernie, Alisdair R.. Max Planck Institute for Molecular Plant Physiology; Alemania
Fil: van Sluys, Marie Anne. Universidade de Sao Paulo; Brasil
Fil: Vrebalov, Julia. Cornell University; Estados Unidos
Fil: Giovannoni, James J.. Cornell University; Estados Unidos
Fil: Rossi, Magdalena. Universidade de Sao Paulo; Brasil
Fil: Carrari, Fernando Oscar. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina
description With the aim of determining the genetic basis of metabolic regulation in tomato fruit, we constructed a detailed physical map of genomic regions spanning previously described metabolic quantitative trait loci of a Solanum pennellii introgression line population. Two genomic libraries from S. pennellii were screened with 104 colocated markers from five selected genomic regions, and a total of 614 bacterial artificial chromosome (BAC)/cosmids were identified as seed clones. Integration of sequence data with the genetic and physical maps of Solanum lycopersicum facilitated the anchoring of 374 of these BAC/ cosmid clones. The analysis of this information resulted in a genome-wide map of a nondomesticated plant species and covers 10% of the physical distance of the selected regions corresponding to approximately 1% of the wild tomato genome. Comparative analyses revealed that S. pennellii and domesticated tomato genomes can be considered as largely colinear. A total of 1,238,705 bp from both BAC/cosmid ends and nine large insert clones were sequenced, annotated, and functionally categorized. The sequence data allowed the evaluation of the level of polymorphism between the wild and cultivated tomato species. An exhaustive microsynteny analysis allowed us to estimate the divergence date of S. pennellii and S. lycopersicum at 2.7 million years ago. The combined results serve as a reference for comparative studies both at the macrosyntenic and microsyntenic levels. They also provide a valuable tool for fine-mapping of quantitative trait loci in tomato. Furthermore, they will contribute to a deeper understanding of the regulatory factors underpinning metabolism and hence defining crop chemical composition. © 2010 American Society of Plant Biologists.
publishDate 2010
dc.date.none.fl_str_mv 2010-12
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/11336/67777
Kamenetzky, Laura; Asis, Ramón; Bassi, Sebastián; de Godoy, Fabiana; Bermúdez, Luisa; et al.; Genomic analysis of wild tomato introgressions determining metabolism-and yield-associated traits; American Society of Plant Biologist; Plant Physiology; 152; 4; 12-2010; 1772-1786
0032-0889
CONICET Digital
CONICET
url http://hdl.handle.net/11336/67777
identifier_str_mv Kamenetzky, Laura; Asis, Ramón; Bassi, Sebastián; de Godoy, Fabiana; Bermúdez, Luisa; et al.; Genomic analysis of wild tomato introgressions determining metabolism-and yield-associated traits; American Society of Plant Biologist; Plant Physiology; 152; 4; 12-2010; 1772-1786
0032-0889
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1104/pp.109.150532
info:eu-repo/semantics/altIdentifier/url/http://www.plantphysiol.org/content/152/4/1772
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
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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