Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)
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. caro...
| Main Authors: | , , , , |
|---|---|
| Format: | Artículo |
| Language: | Inglés |
| Published: |
Springer Nature
2020
|
| Subjects: | |
| Online Access: | https://repositorio.inia.gob.pe/handle/20.500.12955/1129 https://doi.org/10.1186/s12862-016-0806-x |
| _version_ | 1855490486828007424 |
|---|---|
| author | Arbizu Berrocal, Carlos Irvin Ellison, Shelby L. Senalik, Douglas Simon, Philipp W. Spooner, David M. |
| author_browse | Arbizu Berrocal, Carlos Irvin Ellison, Shelby L. Senalik, Douglas Simon, Philipp W. Spooner, David M. |
| author_facet | Arbizu Berrocal, Carlos Irvin Ellison, Shelby L. Senalik, Douglas Simon, Philipp W. Spooner, David M. |
| author_sort | Arbizu Berrocal, Carlos Irvin |
| collection | Repositorio INIA |
| description | 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 |
| format | Artículo |
| id | INIA1129 |
| institution | Institucional Nacional de Innovación Agraria |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Springer Nature |
| publisherStr | Springer Nature |
| record_format | dspace |
| spelling | INIA11292022-11-21T20:35:13Z Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae) Arbizu Berrocal, Carlos Irvin Ellison, Shelby L. Senalik, Douglas Simon, Philipp W. Spooner, David M. Carrot Daucus carota Genotyping-by-sequencing (GBS) Phylogeny Single nucleotide polymorphisms (SNPs) Biotecnología agrícola, Biotecnología alimentaria 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 Background. Methods. Results. Discussion. Conclusions. Additional files. 2020-09-11T04:17:45Z 2020-09-11T04:17:45Z 2016-10-28 info:eu-repo/semantics/article Arbizu, C.I., Ellison, S.L., Senalik, D. et al. Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae). BMC Evol Biol 16, 234 (2016). doi: 10.1186/s12862-016-0806-x https://repositorio.inia.gob.pe/handle/20.500.12955/1129 BMC Evolutionary Biology https://doi.org/10.1186/s12862-016-0806-x eng BMC Evolutionary Biology (2016) 16:234 https://doi.org/10.1186/s12862-016-0806-x info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ application/pdf application/pdf Estados Unidos Springer Nature Estados Unidos Instituto Nacional de Innovación Agraria Repositorio Institucional - INIA |
| spellingShingle | Carrot Daucus carota Genotyping-by-sequencing (GBS) Phylogeny Single nucleotide polymorphisms (SNPs) Biotecnología agrícola, Biotecnología alimentaria Arbizu Berrocal, Carlos Irvin Ellison, Shelby L. Senalik, Douglas Simon, Philipp W. Spooner, David M. 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) |
| 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_short | 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 |
| topic | Carrot Daucus carota Genotyping-by-sequencing (GBS) Phylogeny Single nucleotide polymorphisms (SNPs) Biotecnología agrícola, Biotecnología alimentaria |
| url | https://repositorio.inia.gob.pe/handle/20.500.12955/1129 https://doi.org/10.1186/s12862-016-0806-x |
| work_keys_str_mv | AT arbizuberrocalcarlosirvin genotypingbysequencingprovidesthediscriminatingpowertoinvestigatethesubspeciesofdaucuscarotaapiaceae AT ellisonshelbyl genotypingbysequencingprovidesthediscriminatingpowertoinvestigatethesubspeciesofdaucuscarotaapiaceae AT senalikdouglas genotypingbysequencingprovidesthediscriminatingpowertoinvestigatethesubspeciesofdaucuscarotaapiaceae AT simonphilippw genotypingbysequencingprovidesthediscriminatingpowertoinvestigatethesubspeciesofdaucuscarotaapiaceae AT spoonerdavidm genotypingbysequencingprovidesthediscriminatingpowertoinvestigatethesubspeciesofdaucuscarotaapiaceae |