Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)
Descripción del Articulo
This work is supported by the USDA Agricultural Research Service. C. Arbizu is partly funded by the National Council of Science and Technology of Perú (Concytec).
| Autores: | , , , , |
|---|---|
| Formato: | artículo |
| Fecha de Publicación: | 2016 |
| Institución: | Consejo Nacional de Ciencia Tecnología e Innovación |
| Repositorio: | CONCYTEC-Institucional |
| Lenguaje: | inglés |
| OAI Identifier: | oai:repositorio.concytec.gob.pe:20.500.12390/1206 |
| Enlace del recurso: | https://hdl.handle.net/20.500.12390/1206 https://doi.org/10.1186/s12862-016-0806-x |
| Nivel de acceso: | acceso abierto |
| Materia: | Single nucleotide polymorphisms (SNPs) Carrot Daucus carota Genotyping-by-sequencing (GBS) Phylogeny https://purl.org/pe-repo/ocde/ford#4.01.01 |
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| dc.title.none.fl_str_mv |
Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae) |
| title |
Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae) |
| spellingShingle |
Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae) Arbizu, CI Single nucleotide polymorphisms (SNPs) Carrot Daucus carota Genotyping-by-sequencing (GBS) Phylogeny https://purl.org/pe-repo/ocde/ford#4.01.01 |
| title_short |
Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae) |
| title_full |
Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae) |
| title_fullStr |
Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae) |
| title_full_unstemmed |
Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae) |
| title_sort |
Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae) |
| author |
Arbizu, CI |
| author_facet |
Arbizu, CI Ellison, SL Senalik, D Simon, PW Spooner, DM |
| author_role |
author |
| author2 |
Ellison, SL Senalik, D Simon, PW Spooner, DM |
| author2_role |
author author author author |
| dc.contributor.author.fl_str_mv |
Arbizu, CI Ellison, SL Senalik, D Simon, PW Spooner, DM |
| dc.subject.none.fl_str_mv |
Single nucleotide polymorphisms (SNPs) |
| topic |
Single nucleotide polymorphisms (SNPs) Carrot Daucus carota Genotyping-by-sequencing (GBS) Phylogeny https://purl.org/pe-repo/ocde/ford#4.01.01 |
| dc.subject.es_PE.fl_str_mv |
Carrot Daucus carota Genotyping-by-sequencing (GBS) Phylogeny |
| dc.subject.ocde.none.fl_str_mv |
https://purl.org/pe-repo/ocde/ford#4.01.01 |
| description |
This work is supported by the USDA Agricultural Research Service. C. Arbizu is partly funded by the National Council of Science and Technology of Perú (Concytec). |
| publishDate |
2016 |
| dc.date.accessioned.none.fl_str_mv |
2024-05-30T23:13:38Z |
| dc.date.available.none.fl_str_mv |
2024-05-30T23:13:38Z |
| dc.date.issued.fl_str_mv |
2016 |
| dc.type.none.fl_str_mv |
info:eu-repo/semantics/article |
| format |
article |
| dc.identifier.uri.none.fl_str_mv |
https://hdl.handle.net/20.500.12390/1206 |
| dc.identifier.doi.none.fl_str_mv |
https://doi.org/10.1186/s12862-016-0806-x |
| dc.identifier.isi.none.fl_str_mv |
386313500002 |
| url |
https://hdl.handle.net/20.500.12390/1206 https://doi.org/10.1186/s12862-016-0806-x |
| identifier_str_mv |
386313500002 |
| dc.language.iso.none.fl_str_mv |
eng |
| language |
eng |
| dc.relation.ispartof.none.fl_str_mv |
BMC Evolutionary Biology |
| dc.rights.none.fl_str_mv |
info:eu-repo/semantics/openAccess |
| dc.rights.uri.none.fl_str_mv |
https://creativecommons.org/licenses/by/4.0/ |
| eu_rights_str_mv |
openAccess |
| rights_invalid_str_mv |
https://creativecommons.org/licenses/by/4.0/ |
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BMC |
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BMC |
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reponame:CONCYTEC-Institucional instname:Consejo Nacional de Ciencia Tecnología e Innovación instacron:CONCYTEC |
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Consejo Nacional de Ciencia Tecnología e Innovación |
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CONCYTEC |
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CONCYTEC |
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CONCYTEC-Institucional |
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CONCYTEC-Institucional |
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Repositorio Institucional CONCYTEC |
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repositorio@concytec.gob.pe |
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1839175546416660480 |
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Publicationrp03422600rp03451600rp03450600rp03420600rp03421600Arbizu, CIEllison, SLSenalik, DSimon, PWSpooner, DM2024-05-30T23:13:38Z2024-05-30T23:13:38Z2016https://hdl.handle.net/20.500.12390/1206https://doi.org/10.1186/s12862-016-0806-x386313500002This work is supported by the USDA Agricultural Research Service. C. Arbizu is partly funded by the National Council of Science and Technology of Perú (Concytec).Background. The majority of the subspecies of Daucus carota have not yet been discriminated clearly by various molecular or morphological methods and hence their phylogeny and classification remains unresolved. Recent studies using 94 nuclear orthologs and morphological characters, and studies employing other molecular approaches were unable to distinguish clearly many of the subspecies. Fertile intercrosses among traditionally recognized subspecies are well documented. We here explore the utility of single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS) to serve as an effective molecular method to discriminate the subspecies of the D. carota complex. Results: We used GBS to obtain SNPs covering all nine Daucus carota chromosomes from 162 accessions of Daucus and two related genera. To study Daucus phylogeny, we scored a total of 10,814 or 38,920 SNPs with a maximum of 10 or 30 % missing data, respectively. To investigate the subspecies of D. carota, we employed two data sets including 150 accessions: (i) rate of missing data 10 % with a total of 18,565 SNPs, and (ii) rate of missing data 30 %, totaling 43,713 SNPs. Consistent with prior results, the topology of both data sets separated species with 2n = 18 chromosome from all other species. Our results place all cultivated carrots (D. carota subsp. sativus) in a single clade. The wild members of D. carota from central Asia were on a clade with eastern members of subsp. sativus. The other subspecies of D. carota were in four clades associated with geographic groups: (1) the Balkan Peninsula and the Middle East, (2) North America and Europe, (3) North Africa exclusive of Morocco, and (4) the Iberian Peninsula and Morocco. Daucus carota subsp. maximus was discriminated, but neither it, nor subsp. gummifer (defined in a broad sense) are monophyletic. Conclusions: Our study suggests that (1) the morphotypes identified as D. carota subspecies gummifer (as currently broadly circumscribed), all confined to areas near the Atlantic Ocean and the western Mediterranean Sea, have separate origins from sympatric members of other subspecies of D. carota, (2) D. carota subsp. maximus, on two clades with some accessions of subsp. carota, can be distinguished from each other but only with poor morphological support, (3) D. carota subsp. capillifolius, well distinguished morphologically, is an apospecies relative to North African populations of D. carota subsp. carota, (4) the eastern cultivated carrots have origins closer to wild carrots from central Asia than to western cultivated carrots, and (5) large SNP data sets are suitable for species-level phylogenetic studies in Daucus.Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica - ConcytecengBMCBMC Evolutionary Biologyinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/4.0/Single nucleotide polymorphisms (SNPs)Carrot-1Daucus carota-1Genotyping-by-sequencing (GBS)-1Phylogeny-1https://purl.org/pe-repo/ocde/ford#4.01.01-1Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)info:eu-repo/semantics/articlereponame:CONCYTEC-Institucionalinstname:Consejo Nacional de Ciencia Tecnología e Innovacióninstacron:CONCYTEC#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#20.500.12390/1206oai:repositorio.concytec.gob.pe:20.500.12390/12062024-05-30 15:23:55.097https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_14cbinfo:eu-repo/semantics/closedAccessmetadata only accesshttps://repositorio.concytec.gob.peRepositorio Institucional CONCYTECrepositorio@concytec.gob.pe#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#<Publication xmlns="https://www.openaire.eu/cerif-profile/1.1/" id="564f2be1-a22d-4c11-a25c-66cb56634837"> <Type xmlns="https://www.openaire.eu/cerif-profile/vocab/COAR_Publication_Types">http://purl.org/coar/resource_type/c_1843</Type> <Language>eng</Language> <Title>Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)</Title> <PublishedIn> <Publication> <Title>BMC Evolutionary Biology</Title> </Publication> </PublishedIn> <PublicationDate>2016</PublicationDate> <DOI>https://doi.org/10.1186/s12862-016-0806-x</DOI> <ISI-Number>386313500002</ISI-Number> <Authors> <Author> <DisplayName>Arbizu, CI</DisplayName> <Person id="rp03422" /> <Affiliation> <OrgUnit> </OrgUnit> </Affiliation> </Author> <Author> <DisplayName>Ellison, SL</DisplayName> <Person id="rp03451" /> <Affiliation> <OrgUnit> </OrgUnit> </Affiliation> </Author> <Author> <DisplayName>Senalik, D</DisplayName> <Person id="rp03450" /> <Affiliation> <OrgUnit> </OrgUnit> </Affiliation> </Author> <Author> <DisplayName>Simon, PW</DisplayName> <Person id="rp03420" /> <Affiliation> <OrgUnit> </OrgUnit> </Affiliation> </Author> <Author> <DisplayName>Spooner, DM</DisplayName> <Person id="rp03421" /> <Affiliation> <OrgUnit> </OrgUnit> </Affiliation> </Author> </Authors> <Editors> </Editors> <Publishers> <Publisher> <DisplayName>BMC</DisplayName> <OrgUnit /> </Publisher> </Publishers> <License>https://creativecommons.org/licenses/by/4.0/</License> <Keyword>Single nucleotide polymorphisms (SNPs)</Keyword> <Keyword>Carrot</Keyword> <Keyword>Daucus carota</Keyword> <Keyword>Genotyping-by-sequencing (GBS)</Keyword> <Keyword>Phylogeny</Keyword> <Abstract>Background. The majority of the subspecies of Daucus carota have not yet been discriminated clearly by various molecular or morphological methods and hence their phylogeny and classification remains unresolved. Recent studies using 94 nuclear orthologs and morphological characters, and studies employing other molecular approaches were unable to distinguish clearly many of the subspecies. Fertile intercrosses among traditionally recognized subspecies are well documented. We here explore the utility of single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS) to serve as an effective molecular method to discriminate the subspecies of the D. carota complex. Results: We used GBS to obtain SNPs covering all nine Daucus carota chromosomes from 162 accessions of Daucus and two related genera. To study Daucus phylogeny, we scored a total of 10,814 or 38,920 SNPs with a maximum of 10 or 30 % missing data, respectively. To investigate the subspecies of D. carota, we employed two data sets including 150 accessions: (i) rate of missing data 10 % with a total of 18,565 SNPs, and (ii) rate of missing data 30 %, totaling 43,713 SNPs. Consistent with prior results, the topology of both data sets separated species with 2n = 18 chromosome from all other species. Our results place all cultivated carrots (D. carota subsp. sativus) in a single clade. The wild members of D. carota from central Asia were on a clade with eastern members of subsp. sativus. The other subspecies of D. carota were in four clades associated with geographic groups: (1) the Balkan Peninsula and the Middle East, (2) North America and Europe, (3) North Africa exclusive of Morocco, and (4) the Iberian Peninsula and Morocco. Daucus carota subsp. maximus was discriminated, but neither it, nor subsp. gummifer (defined in a broad sense) are monophyletic. Conclusions: Our study suggests that (1) the morphotypes identified as D. carota subspecies gummifer (as currently broadly circumscribed), all confined to areas near the Atlantic Ocean and the western Mediterranean Sea, have separate origins from sympatric members of other subspecies of D. carota, (2) D. carota subsp. maximus, on two clades with some accessions of subsp. carota, can be distinguished from each other but only with poor morphological support, (3) D. carota subsp. capillifolius, well distinguished morphologically, is an apospecies relative to North African populations of D. carota subsp. carota, (4) the eastern cultivated carrots have origins closer to wild carrots from central Asia than to western cultivated carrots, and (5) large SNP data sets are suitable for species-level phylogenetic studies in Daucus.</Abstract> <Access xmlns="http://purl.org/coar/access_right" > </Access> </Publication> -1 |
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13.439101 |
Nota importante:
La información contenida en este registro es de entera responsabilidad de la institución que gestiona el repositorio institucional donde esta contenido este documento o set de datos. El CONCYTEC no se hace responsable por los contenidos (publicaciones y/o datos) accesibles a través del Repositorio Nacional Digital de Ciencia, Tecnología e Innovación de Acceso Abierto (ALICIA).
La información contenida en este registro es de entera responsabilidad de la institución que gestiona el repositorio institucional donde esta contenido este documento o set de datos. El CONCYTEC no se hace responsable por los contenidos (publicaciones y/o datos) accesibles a través del Repositorio Nacional Digital de Ciencia, Tecnología e Innovación de Acceso Abierto (ALICIA).
