Genetic and transcription profile analysis of tissue-specific anthocyanin pigmentation in carrot root phloem

Autores
Bannoud, Florencia; Carvajal, Sofia; Ellison, Shelby; Senalik, Douglas A.; Gómez Talquenca, Sebastián; Iorizzo, Massimo; Simon, Philipp W.; Cavagnaro, Pablo Federico
Año de publicación
2021
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
In purple carrots, anthocyanin pigmentation can be expressed in the entire root, or it can display tissue specific-patterns. Within the phloem, purple pigmentation can be found in the outer phloem (OP) (also called the cortex) and inner phloem (IP), or it can be confined exclusively to the OP. In this work, the genetic control underlying tissue-specific anthocyanin pigmentation in the carrot root OP and IP tissues was investigated by means of linkage mapping and transcriptome (RNAseq) and phylogenetic analyses; followed by gene expression (RT-qPCR) evaluations in two genetic backgrounds, an F2 population (3242) and the inbred B7262. Genetic mapping of ‘root outer phloem anthocyanin pigmentation’ (ROPAP) and inner phloem pigmentation (RIPAP) revealed colocalization of ROPAP with the P1 and P3 genomic regions previously known to condition pigmentation in different genetic stocks, whereas RIPAP co-localized with P3 only. Transcriptome analysis of purple OP (POP) vs. non-purple IP (NPIP) tissues, along with linkage and phylogenetic data, allowed an initial identification of 28 candidate genes, 19 of which were further evaluated by RT-qPCR in independent root samples of 3242 and B7262, revealing 15 genes consistently upregulated in the POP in both genetic backgrounds, and two genes upregulated in the POP in specific backgrounds. These include seven transcription factors, seven anthocyanin structural genes, and two genes involved in cellular transport. Altogether, our results point at DcMYB7, DcMYB113, and a MADS-box (DCAR_010757) as the main candidate genes conditioning ROPAP in 3242, whereas DcMYB7 and MADS-box condition RIPAP in this background. In 7262, DcMYB113 conditions ROPAP.
Fil: Bannoud, Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Carvajal, Sofia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentina
Fil: Ellison, Shelby. University of Wisconsin; Estados Unidos
Fil: Senalik, Douglas A.. United States Department of Agriculture. Agriculture Research Service; Estados Unidos. University of Wisconsin; Estados Unidos
Fil: Gómez Talquenca, Sebastián. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-San Juan. Estación Experimental Agropecuaria Mendoza; Argentina
Fil: Iorizzo, Massimo. North Carolina State University. Department Of Food, Bioprocessing And Nutrition Sciences. Plants For Human Health Institute.; Estados Unidos
Fil: Simon, Philipp W.. University of Wisconsin; Estados Unidos
Fil: Cavagnaro, Pablo Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-San Juan. Estación Experimental Agropecuaria La Consulta; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Departamento de Producción Agropecuaria. Cátedra de Horticultura y Floricultura; Argentina
Materia
ANTHOCYANIN
CANDIDATE GENES
DAUCUS CAROTA
GENETIC MAPPING
PHLOEM PIGMENTATION
RNA-SEQ
RT-QPCR
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/167545
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/167545
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Genetic and transcription profile analysis of tissue-specific anthocyanin pigmentation in carrot root phloemBannoud, FlorenciaCarvajal, SofiaEllison, ShelbySenalik, Douglas A.Gómez Talquenca, SebastiánIorizzo, MassimoSimon, Philipp W.Cavagnaro, Pablo FedericoANTHOCYANINCANDIDATE GENESDAUCUS CAROTAGENETIC MAPPINGPHLOEM PIGMENTATIONRNA-SEQRT-QPCRhttps://purl.org/becyt/ford/4.1https://purl.org/becyt/ford/4In purple carrots, anthocyanin pigmentation can be expressed in the entire root, or it can display tissue specific-patterns. Within the phloem, purple pigmentation can be found in the outer phloem (OP) (also called the cortex) and inner phloem (IP), or it can be confined exclusively to the OP. In this work, the genetic control underlying tissue-specific anthocyanin pigmentation in the carrot root OP and IP tissues was investigated by means of linkage mapping and transcriptome (RNAseq) and phylogenetic analyses; followed by gene expression (RT-qPCR) evaluations in two genetic backgrounds, an F2 population (3242) and the inbred B7262. Genetic mapping of ‘root outer phloem anthocyanin pigmentation’ (ROPAP) and inner phloem pigmentation (RIPAP) revealed colocalization of ROPAP with the P1 and P3 genomic regions previously known to condition pigmentation in different genetic stocks, whereas RIPAP co-localized with P3 only. Transcriptome analysis of purple OP (POP) vs. non-purple IP (NPIP) tissues, along with linkage and phylogenetic data, allowed an initial identification of 28 candidate genes, 19 of which were further evaluated by RT-qPCR in independent root samples of 3242 and B7262, revealing 15 genes consistently upregulated in the POP in both genetic backgrounds, and two genes upregulated in the POP in specific backgrounds. These include seven transcription factors, seven anthocyanin structural genes, and two genes involved in cellular transport. Altogether, our results point at DcMYB7, DcMYB113, and a MADS-box (DCAR_010757) as the main candidate genes conditioning ROPAP in 3242, whereas DcMYB7 and MADS-box condition RIPAP in this background. In 7262, DcMYB113 conditions ROPAP.Fil: Bannoud, Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Carvajal, Sofia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; ArgentinaFil: Ellison, Shelby. University of Wisconsin; Estados UnidosFil: Senalik, Douglas A.. United States Department of Agriculture. Agriculture Research Service; Estados Unidos. University of Wisconsin; Estados UnidosFil: Gómez Talquenca, Sebastián. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-San Juan. Estación Experimental Agropecuaria Mendoza; ArgentinaFil: Iorizzo, Massimo. North Carolina State University. Department Of Food, Bioprocessing And Nutrition Sciences. Plants For Human Health Institute.; Estados UnidosFil: Simon, Philipp W.. University of Wisconsin; Estados UnidosFil: Cavagnaro, Pablo Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-San Juan. Estación Experimental Agropecuaria La Consulta; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Departamento de Producción Agropecuaria. Cátedra de Horticultura y Floricultura; ArgentinaMultidisciplinary Digital Publishing Institute2021-10info: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/11336/167545Bannoud, Florencia; Carvajal, Sofia; Ellison, Shelby; Senalik, Douglas A.; Gómez Talquenca, Sebastián; et al.; Genetic and transcription profile analysis of tissue-specific anthocyanin pigmentation in carrot root phloem; Multidisciplinary Digital Publishing Institute; Genes; 12; 10; 10-2021; 1464-14832073-4425CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.mdpi.com/2073-4425/12/10/1464info:eu-repo/semantics/altIdentifier/doi/10.3390/genes12101464info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-22T11:09:59Zoai:ri.conicet.gov.ar:11336/167545instacron: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:34982025-10-22 11:10:00.273CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Genetic and transcription profile analysis of tissue-specific anthocyanin pigmentation in carrot root phloem
title Genetic and transcription profile analysis of tissue-specific anthocyanin pigmentation in carrot root phloem
spellingShingle Genetic and transcription profile analysis of tissue-specific anthocyanin pigmentation in carrot root phloem
Bannoud, Florencia
ANTHOCYANIN
CANDIDATE GENES
DAUCUS CAROTA
GENETIC MAPPING
PHLOEM PIGMENTATION
RNA-SEQ
RT-QPCR
title_short Genetic and transcription profile analysis of tissue-specific anthocyanin pigmentation in carrot root phloem
title_full Genetic and transcription profile analysis of tissue-specific anthocyanin pigmentation in carrot root phloem
title_fullStr Genetic and transcription profile analysis of tissue-specific anthocyanin pigmentation in carrot root phloem
title_full_unstemmed Genetic and transcription profile analysis of tissue-specific anthocyanin pigmentation in carrot root phloem
title_sort Genetic and transcription profile analysis of tissue-specific anthocyanin pigmentation in carrot root phloem
dc.creator.none.fl_str_mv Bannoud, Florencia
Carvajal, Sofia
Ellison, Shelby
Senalik, Douglas A.
Gómez Talquenca, Sebastián
Iorizzo, Massimo
Simon, Philipp W.
Cavagnaro, Pablo Federico
author Bannoud, Florencia
author_facet Bannoud, Florencia
Carvajal, Sofia
Ellison, Shelby
Senalik, Douglas A.
Gómez Talquenca, Sebastián
Iorizzo, Massimo
Simon, Philipp W.
Cavagnaro, Pablo Federico
author_role author
author2 Carvajal, Sofia
Ellison, Shelby
Senalik, Douglas A.
Gómez Talquenca, Sebastián
Iorizzo, Massimo
Simon, Philipp W.
Cavagnaro, Pablo Federico
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv ANTHOCYANIN
CANDIDATE GENES
DAUCUS CAROTA
GENETIC MAPPING
PHLOEM PIGMENTATION
RNA-SEQ
RT-QPCR
topic ANTHOCYANIN
CANDIDATE GENES
DAUCUS CAROTA
GENETIC MAPPING
PHLOEM PIGMENTATION
RNA-SEQ
RT-QPCR
purl_subject.fl_str_mv https://purl.org/becyt/ford/4.1
https://purl.org/becyt/ford/4
dc.description.none.fl_txt_mv In purple carrots, anthocyanin pigmentation can be expressed in the entire root, or it can display tissue specific-patterns. Within the phloem, purple pigmentation can be found in the outer phloem (OP) (also called the cortex) and inner phloem (IP), or it can be confined exclusively to the OP. In this work, the genetic control underlying tissue-specific anthocyanin pigmentation in the carrot root OP and IP tissues was investigated by means of linkage mapping and transcriptome (RNAseq) and phylogenetic analyses; followed by gene expression (RT-qPCR) evaluations in two genetic backgrounds, an F2 population (3242) and the inbred B7262. Genetic mapping of ‘root outer phloem anthocyanin pigmentation’ (ROPAP) and inner phloem pigmentation (RIPAP) revealed colocalization of ROPAP with the P1 and P3 genomic regions previously known to condition pigmentation in different genetic stocks, whereas RIPAP co-localized with P3 only. Transcriptome analysis of purple OP (POP) vs. non-purple IP (NPIP) tissues, along with linkage and phylogenetic data, allowed an initial identification of 28 candidate genes, 19 of which were further evaluated by RT-qPCR in independent root samples of 3242 and B7262, revealing 15 genes consistently upregulated in the POP in both genetic backgrounds, and two genes upregulated in the POP in specific backgrounds. These include seven transcription factors, seven anthocyanin structural genes, and two genes involved in cellular transport. Altogether, our results point at DcMYB7, DcMYB113, and a MADS-box (DCAR_010757) as the main candidate genes conditioning ROPAP in 3242, whereas DcMYB7 and MADS-box condition RIPAP in this background. In 7262, DcMYB113 conditions ROPAP.
Fil: Bannoud, Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Carvajal, Sofia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentina
Fil: Ellison, Shelby. University of Wisconsin; Estados Unidos
Fil: Senalik, Douglas A.. United States Department of Agriculture. Agriculture Research Service; Estados Unidos. University of Wisconsin; Estados Unidos
Fil: Gómez Talquenca, Sebastián. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-San Juan. Estación Experimental Agropecuaria Mendoza; Argentina
Fil: Iorizzo, Massimo. North Carolina State University. Department Of Food, Bioprocessing And Nutrition Sciences. Plants For Human Health Institute.; Estados Unidos
Fil: Simon, Philipp W.. University of Wisconsin; Estados Unidos
Fil: Cavagnaro, Pablo Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-San Juan. Estación Experimental Agropecuaria La Consulta; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Departamento de Producción Agropecuaria. Cátedra de Horticultura y Floricultura; Argentina
description In purple carrots, anthocyanin pigmentation can be expressed in the entire root, or it can display tissue specific-patterns. Within the phloem, purple pigmentation can be found in the outer phloem (OP) (also called the cortex) and inner phloem (IP), or it can be confined exclusively to the OP. In this work, the genetic control underlying tissue-specific anthocyanin pigmentation in the carrot root OP and IP tissues was investigated by means of linkage mapping and transcriptome (RNAseq) and phylogenetic analyses; followed by gene expression (RT-qPCR) evaluations in two genetic backgrounds, an F2 population (3242) and the inbred B7262. Genetic mapping of ‘root outer phloem anthocyanin pigmentation’ (ROPAP) and inner phloem pigmentation (RIPAP) revealed colocalization of ROPAP with the P1 and P3 genomic regions previously known to condition pigmentation in different genetic stocks, whereas RIPAP co-localized with P3 only. Transcriptome analysis of purple OP (POP) vs. non-purple IP (NPIP) tissues, along with linkage and phylogenetic data, allowed an initial identification of 28 candidate genes, 19 of which were further evaluated by RT-qPCR in independent root samples of 3242 and B7262, revealing 15 genes consistently upregulated in the POP in both genetic backgrounds, and two genes upregulated in the POP in specific backgrounds. These include seven transcription factors, seven anthocyanin structural genes, and two genes involved in cellular transport. Altogether, our results point at DcMYB7, DcMYB113, and a MADS-box (DCAR_010757) as the main candidate genes conditioning ROPAP in 3242, whereas DcMYB7 and MADS-box condition RIPAP in this background. In 7262, DcMYB113 conditions ROPAP.
publishDate 2021
dc.date.none.fl_str_mv 2021-10
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/11336/167545
Bannoud, Florencia; Carvajal, Sofia; Ellison, Shelby; Senalik, Douglas A.; Gómez Talquenca, Sebastián; et al.; Genetic and transcription profile analysis of tissue-specific anthocyanin pigmentation in carrot root phloem; Multidisciplinary Digital Publishing Institute; Genes; 12; 10; 10-2021; 1464-1483
2073-4425
CONICET Digital
CONICET
url http://hdl.handle.net/11336/167545
identifier_str_mv Bannoud, Florencia; Carvajal, Sofia; Ellison, Shelby; Senalik, Douglas A.; Gómez Talquenca, Sebastián; et al.; Genetic and transcription profile analysis of tissue-specific anthocyanin pigmentation in carrot root phloem; Multidisciplinary Digital Publishing Institute; Genes; 12; 10; 10-2021; 1464-1483
2073-4425
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.mdpi.com/2073-4425/12/10/1464
info:eu-repo/semantics/altIdentifier/doi/10.3390/genes12101464
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute
publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute
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 12.982451

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