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
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/167545
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CONICET Digital (CONICET) |
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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 Técnicas2025-09-29T09:41:24Zoai: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:34982025-09-29 09:41:25.139CONICET 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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1844613308411281408 |
score |
13.070432 |