Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae

Autores
Cavagnaro, Pablo Federico; Chung, Sang Min; Manin, Sylvie; Yildiz, Mehtap; Ali, Aamir; Alessandro, María Soledad; Iorizzo, Massimo; Senalik, Douglas A.; Simon, Philipp W.
Año de publicación
2011
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background: The Apiaceae family includes several vegetable and spice crop species among which carrot is the most economically important member, with ~21 million tons produced yearly worldwide. Despite its importance, molecular resources in this species are relatively underdeveloped. The availability of informative, polymorphic, and robust PCR-based markers, such as microsatellites (or SSRs), will facilitate genetics and breeding of carrot and other Apiaceae, including integration of linkage maps, tagging of phenotypic traits and assisting positional gene cloning. Thus, with the purpose of isolating carrot microsatellites, two different strategies were used; a hybridization-based library enrichment for SSRs, and bioinformatic mining of SSRs in BAC-end sequence and EST sequence databases. This work reports on the development of 300 carrot SSR markers and their characterization at various levels. Results: Evaluation of microsatellites isolated from both DNA sources in subsets of 7 carrot F2 mapping populations revealed that SSRs from the hybridization-based method were longer, had more repeat units and were more polymorphic than SSRs isolated by sequence search. Overall, 196 SSRs (65.1%) were polymorphic in at least one mapping population, and the percentage of polymophic SSRs across F2 populations ranged from 17.8 to 24.7. Polymorphic markers in one family were evaluated in the entire F2, allowing the genetic mapping of 55 SSRs (38 codominant) onto the carrot reference map. The SSR loci were distributed throughout all 9 carrot linkage groups (LGs), with 2 to 9 SSRs/LG. In addition, SSR evaluations in carrot-related taxa indicated that a significant fraction of the carrot SSRs transfer successfully across Apiaceae, with heterologous amplification success rate decreasing with the target-species evolutionary distance from carrot. SSR diversity evaluated in a collection of 65 D. carota accessions revealed a high level of polymorphism for these selected loci, with an average of 19 alleles/locus and 0.84 expected heterozygosity. Conclusions: The addition of 55 SSRs to the carrot map, together with marker characterizations in six other mapping populations, will facilitate future comparative mapping studies and integration of carrot maps. The markers developed herein will be a valuable resource for assisting breeding, genetic, diversity, and genomic studies of carrot and other Apiaceae
Fil: Cavagnaro, Pablo Federico. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Cuyo Mendoza-san Juan. Estación Experimental Agropecuaria la Consulta; Argentina. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentina
Fil: Chung, Sang Min. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. Dongguk University. Department of Life Science; Estados Unidos
Fil: Manin, Sylvie. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. Yuzuncu Yil University. Faculty of Agriculture, Department of Horticulture; Turquía
Fil: Yildiz, Mehtap. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. Yuzuncu Yil University. Faculty of Agriculture. Department. of Horticulture; Corea del Sur
Fil: Ali, Aamir. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. University of Sargodha. Department of Biological Sciences; Pakistán
Fil: Alessandro, María Soledad. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-san Juan. Estación Experimental Agropecuaria la Consulta; Argentina
Fil: Iorizzo, Massimo. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos
Fil: Senalik, Douglas A.. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. University of Wisconsin-Madison. Department of Horticulture. USDA-ARS. Vegetable Crops Unit; Estados Unidos
Fil: Simon, Philipp W.. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. University of Wisconsin-Madison. Department of Horticulture. USDA-ARS. Vegetable Crops Unit; Estados Unidos
Materia
CARROT
MICROSATELLITES
GENETIC MAP
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:11336/20450

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network_name_str CONICET Digital (CONICET)
spelling Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across ApiaceaeCavagnaro, Pablo FedericoChung, Sang MinManin, SylvieYildiz, MehtapAli, AamirAlessandro, María SoledadIorizzo, MassimoSenalik, Douglas A.Simon, Philipp W.CARROTMICROSATELLITESGENETIC MAPhttps://purl.org/becyt/ford/4.4https://purl.org/becyt/ford/4Background: The Apiaceae family includes several vegetable and spice crop species among which carrot is the most economically important member, with ~21 million tons produced yearly worldwide. Despite its importance, molecular resources in this species are relatively underdeveloped. The availability of informative, polymorphic, and robust PCR-based markers, such as microsatellites (or SSRs), will facilitate genetics and breeding of carrot and other Apiaceae, including integration of linkage maps, tagging of phenotypic traits and assisting positional gene cloning. Thus, with the purpose of isolating carrot microsatellites, two different strategies were used; a hybridization-based library enrichment for SSRs, and bioinformatic mining of SSRs in BAC-end sequence and EST sequence databases. This work reports on the development of 300 carrot SSR markers and their characterization at various levels. Results: Evaluation of microsatellites isolated from both DNA sources in subsets of 7 carrot F2 mapping populations revealed that SSRs from the hybridization-based method were longer, had more repeat units and were more polymorphic than SSRs isolated by sequence search. Overall, 196 SSRs (65.1%) were polymorphic in at least one mapping population, and the percentage of polymophic SSRs across F2 populations ranged from 17.8 to 24.7. Polymorphic markers in one family were evaluated in the entire F2, allowing the genetic mapping of 55 SSRs (38 codominant) onto the carrot reference map. The SSR loci were distributed throughout all 9 carrot linkage groups (LGs), with 2 to 9 SSRs/LG. In addition, SSR evaluations in carrot-related taxa indicated that a significant fraction of the carrot SSRs transfer successfully across Apiaceae, with heterologous amplification success rate decreasing with the target-species evolutionary distance from carrot. SSR diversity evaluated in a collection of 65 D. carota accessions revealed a high level of polymorphism for these selected loci, with an average of 19 alleles/locus and 0.84 expected heterozygosity. Conclusions: The addition of 55 SSRs to the carrot map, together with marker characterizations in six other mapping populations, will facilitate future comparative mapping studies and integration of carrot maps. The markers developed herein will be a valuable resource for assisting breeding, genetic, diversity, and genomic studies of carrot and other ApiaceaeFil: Cavagnaro, Pablo Federico. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Cuyo Mendoza-san Juan. Estación Experimental Agropecuaria la Consulta; Argentina. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; ArgentinaFil: Chung, Sang Min. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. Dongguk University. Department of Life Science; Estados UnidosFil: Manin, Sylvie. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. Yuzuncu Yil University. Faculty of Agriculture, Department of Horticulture; TurquíaFil: Yildiz, Mehtap. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. Yuzuncu Yil University. Faculty of Agriculture. Department. of Horticulture; Corea del SurFil: Ali, Aamir. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. University of Sargodha. Department of Biological Sciences; PakistánFil: Alessandro, María Soledad. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-san Juan. Estación Experimental Agropecuaria la Consulta; ArgentinaFil: Iorizzo, Massimo. University of Wisconsin-Madison. Department. of Horticulture; Estados UnidosFil: Senalik, Douglas A.. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. University of Wisconsin-Madison. Department of Horticulture. USDA-ARS. Vegetable Crops Unit; Estados UnidosFil: Simon, Philipp W.. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. University of Wisconsin-Madison. Department of Horticulture. USDA-ARS. Vegetable Crops Unit; Estados UnidosBiomed Central2011-08-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/20450Cavagnaro, Pablo Federico; Chung, Sang Min; Manin, Sylvie; Yildiz, Mehtap; Ali, Aamir; et al.; Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae; Biomed Central; Bmc Genomics; 12; 1-8-2011; 386-4061471-2164CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-386info:eu-repo/semantics/altIdentifier/doi/10.1186/1471-2164-12-386info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T09:51:22Zoai:ri.conicet.gov.ar:11336/20450instacron: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 09:51:22.536CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae
title Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae
spellingShingle Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae
Cavagnaro, Pablo Federico
CARROT
MICROSATELLITES
GENETIC MAP
title_short Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae
title_full Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae
title_fullStr Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae
title_full_unstemmed Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae
title_sort Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae
dc.creator.none.fl_str_mv Cavagnaro, Pablo Federico
Chung, Sang Min
Manin, Sylvie
Yildiz, Mehtap
Ali, Aamir
Alessandro, María Soledad
Iorizzo, Massimo
Senalik, Douglas A.
Simon, Philipp W.
author Cavagnaro, Pablo Federico
author_facet Cavagnaro, Pablo Federico
Chung, Sang Min
Manin, Sylvie
Yildiz, Mehtap
Ali, Aamir
Alessandro, María Soledad
Iorizzo, Massimo
Senalik, Douglas A.
Simon, Philipp W.
author_role author
author2 Chung, Sang Min
Manin, Sylvie
Yildiz, Mehtap
Ali, Aamir
Alessandro, María Soledad
Iorizzo, Massimo
Senalik, Douglas A.
Simon, Philipp W.
author2_role author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv CARROT
MICROSATELLITES
GENETIC MAP
topic CARROT
MICROSATELLITES
GENETIC MAP
purl_subject.fl_str_mv https://purl.org/becyt/ford/4.4
https://purl.org/becyt/ford/4
dc.description.none.fl_txt_mv Background: The Apiaceae family includes several vegetable and spice crop species among which carrot is the most economically important member, with ~21 million tons produced yearly worldwide. Despite its importance, molecular resources in this species are relatively underdeveloped. The availability of informative, polymorphic, and robust PCR-based markers, such as microsatellites (or SSRs), will facilitate genetics and breeding of carrot and other Apiaceae, including integration of linkage maps, tagging of phenotypic traits and assisting positional gene cloning. Thus, with the purpose of isolating carrot microsatellites, two different strategies were used; a hybridization-based library enrichment for SSRs, and bioinformatic mining of SSRs in BAC-end sequence and EST sequence databases. This work reports on the development of 300 carrot SSR markers and their characterization at various levels. Results: Evaluation of microsatellites isolated from both DNA sources in subsets of 7 carrot F2 mapping populations revealed that SSRs from the hybridization-based method were longer, had more repeat units and were more polymorphic than SSRs isolated by sequence search. Overall, 196 SSRs (65.1%) were polymorphic in at least one mapping population, and the percentage of polymophic SSRs across F2 populations ranged from 17.8 to 24.7. Polymorphic markers in one family were evaluated in the entire F2, allowing the genetic mapping of 55 SSRs (38 codominant) onto the carrot reference map. The SSR loci were distributed throughout all 9 carrot linkage groups (LGs), with 2 to 9 SSRs/LG. In addition, SSR evaluations in carrot-related taxa indicated that a significant fraction of the carrot SSRs transfer successfully across Apiaceae, with heterologous amplification success rate decreasing with the target-species evolutionary distance from carrot. SSR diversity evaluated in a collection of 65 D. carota accessions revealed a high level of polymorphism for these selected loci, with an average of 19 alleles/locus and 0.84 expected heterozygosity. Conclusions: The addition of 55 SSRs to the carrot map, together with marker characterizations in six other mapping populations, will facilitate future comparative mapping studies and integration of carrot maps. The markers developed herein will be a valuable resource for assisting breeding, genetic, diversity, and genomic studies of carrot and other Apiaceae
Fil: Cavagnaro, Pablo Federico. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Cuyo Mendoza-san Juan. Estación Experimental Agropecuaria la Consulta; Argentina. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentina
Fil: Chung, Sang Min. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. Dongguk University. Department of Life Science; Estados Unidos
Fil: Manin, Sylvie. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. Yuzuncu Yil University. Faculty of Agriculture, Department of Horticulture; Turquía
Fil: Yildiz, Mehtap. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. Yuzuncu Yil University. Faculty of Agriculture. Department. of Horticulture; Corea del Sur
Fil: Ali, Aamir. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. University of Sargodha. Department of Biological Sciences; Pakistán
Fil: Alessandro, María Soledad. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-san Juan. Estación Experimental Agropecuaria la Consulta; Argentina
Fil: Iorizzo, Massimo. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos
Fil: Senalik, Douglas A.. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. University of Wisconsin-Madison. Department of Horticulture. USDA-ARS. Vegetable Crops Unit; Estados Unidos
Fil: Simon, Philipp W.. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. University of Wisconsin-Madison. Department of Horticulture. USDA-ARS. Vegetable Crops Unit; Estados Unidos
description Background: The Apiaceae family includes several vegetable and spice crop species among which carrot is the most economically important member, with ~21 million tons produced yearly worldwide. Despite its importance, molecular resources in this species are relatively underdeveloped. The availability of informative, polymorphic, and robust PCR-based markers, such as microsatellites (or SSRs), will facilitate genetics and breeding of carrot and other Apiaceae, including integration of linkage maps, tagging of phenotypic traits and assisting positional gene cloning. Thus, with the purpose of isolating carrot microsatellites, two different strategies were used; a hybridization-based library enrichment for SSRs, and bioinformatic mining of SSRs in BAC-end sequence and EST sequence databases. This work reports on the development of 300 carrot SSR markers and their characterization at various levels. Results: Evaluation of microsatellites isolated from both DNA sources in subsets of 7 carrot F2 mapping populations revealed that SSRs from the hybridization-based method were longer, had more repeat units and were more polymorphic than SSRs isolated by sequence search. Overall, 196 SSRs (65.1%) were polymorphic in at least one mapping population, and the percentage of polymophic SSRs across F2 populations ranged from 17.8 to 24.7. Polymorphic markers in one family were evaluated in the entire F2, allowing the genetic mapping of 55 SSRs (38 codominant) onto the carrot reference map. The SSR loci were distributed throughout all 9 carrot linkage groups (LGs), with 2 to 9 SSRs/LG. In addition, SSR evaluations in carrot-related taxa indicated that a significant fraction of the carrot SSRs transfer successfully across Apiaceae, with heterologous amplification success rate decreasing with the target-species evolutionary distance from carrot. SSR diversity evaluated in a collection of 65 D. carota accessions revealed a high level of polymorphism for these selected loci, with an average of 19 alleles/locus and 0.84 expected heterozygosity. Conclusions: The addition of 55 SSRs to the carrot map, together with marker characterizations in six other mapping populations, will facilitate future comparative mapping studies and integration of carrot maps. The markers developed herein will be a valuable resource for assisting breeding, genetic, diversity, and genomic studies of carrot and other Apiaceae
publishDate 2011
dc.date.none.fl_str_mv 2011-08-01
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/11336/20450
Cavagnaro, Pablo Federico; Chung, Sang Min; Manin, Sylvie; Yildiz, Mehtap; Ali, Aamir; et al.; Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae; Biomed Central; Bmc Genomics; 12; 1-8-2011; 386-406
1471-2164
CONICET Digital
CONICET
url http://hdl.handle.net/11336/20450
identifier_str_mv Cavagnaro, Pablo Federico; Chung, Sang Min; Manin, Sylvie; Yildiz, Mehtap; Ali, Aamir; et al.; Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae; Biomed Central; Bmc Genomics; 12; 1-8-2011; 386-406
1471-2164
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
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info:eu-repo/semantics/altIdentifier/doi/10.1186/1471-2164-12-386
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
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dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Biomed Central
publisher.none.fl_str_mv Biomed Central
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reponame_str CONICET Digital (CONICET)
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repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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