Inter-primer binding site (iPBS) retrotransposon markers provide insights into the genetic diversity and population structure of carrots (Daucus, Apiaceae)
Studies of genetic diversity and population structure are essential as an initial step in conservation and breeding programs for modern crops. Carrot (Daucus spp.) is among the ten most important vegetables worldwide, however, its genetic structure and phylogenetic relationships are not totally deci...
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| Format: | info:eu-repo/semantics/article |
| Language: | Inglés |
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TUBITAK
2022
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| Online Access: | https://hdl.handle.net/20.500.12955/1976 https://doi.org/10.55730/1300-011X.2972 |
| _version_ | 1855028474967752704 |
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| author | Yildiz, Mehtap Arbizu Berrocal, Carlos Irvin |
| author_browse | Arbizu Berrocal, Carlos Irvin Yildiz, Mehtap |
| author_facet | Yildiz, Mehtap Arbizu Berrocal, Carlos Irvin |
| author_sort | Yildiz, Mehtap |
| collection | Repositorio INIA |
| description | Studies of genetic diversity and population structure are essential as an initial step in conservation and breeding programs for modern crops. Carrot (Daucus spp.) is among the ten most important vegetables worldwide, however, its genetic structure and phylogenetic relationships are not totally deciphered. Here, we explored the utility of 21 inter-primer binding site (iPBS) retrotransposon markers to determine the genetic diversity and population structure of 38 accessions of Daucus and one accession of a related genus. The manual scoring revealed 309 bands based on their presence/absence. The dendrogram based on the UPGMA clustering algorithm and a principal coordinate analysis (PCoA) indicated the presence of four clusters. The Daucus species with 2n = 18 chromosome (subclade A´) separated from the other two species D. pusillus and D. muricatus, which were positioned into two individual clusters. The other clade includes the Daucus from the B group. It was also noticed that few accessions were intermixed amongst clusters. Different genetic diversity parameters were estimated based on the four clusters (populations) defined by STRUCTURE software, demonstrating that clusters 3 and 4 possessed the lowest and highest diversity values, respectively. AMOVA showed variation between and within clusters of 41.85% and 58.15%, respectively. The highest population divergence (Fst) was observed between clusters 2 and 3 (0.579), on the other hand, clusters 1 and 4 depicted the lowest Fst with 0.160. Our research highlighted that iPBS markers were successful and effective to study Daucus genetic diversity. These results will contribute to the genetic improvement of carrots and sustainable management of its diversity. |
| format | info:eu-repo/semantics/article |
| id | INIA1976 |
| institution | Institucional Nacional de Innovación Agraria |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | TUBITAK |
| publisherStr | TUBITAK |
| record_format | dspace |
| spelling | INIA19762022-11-21T19:50:24Z Inter-primer binding site (iPBS) retrotransposon markers provide insights into the genetic diversity and population structure of carrots (Daucus, Apiaceae) Yildiz, Mehtap Arbizu Berrocal, Carlos Irvin Carrot Daucus Genetics Germplasm iPBS https://purl.org/pe-repo/ocde/ford#4.04.00 Zanahoria Recursos genéticos Studies of genetic diversity and population structure are essential as an initial step in conservation and breeding programs for modern crops. Carrot (Daucus spp.) is among the ten most important vegetables worldwide, however, its genetic structure and phylogenetic relationships are not totally deciphered. Here, we explored the utility of 21 inter-primer binding site (iPBS) retrotransposon markers to determine the genetic diversity and population structure of 38 accessions of Daucus and one accession of a related genus. The manual scoring revealed 309 bands based on their presence/absence. The dendrogram based on the UPGMA clustering algorithm and a principal coordinate analysis (PCoA) indicated the presence of four clusters. The Daucus species with 2n = 18 chromosome (subclade A´) separated from the other two species D. pusillus and D. muricatus, which were positioned into two individual clusters. The other clade includes the Daucus from the B group. It was also noticed that few accessions were intermixed amongst clusters. Different genetic diversity parameters were estimated based on the four clusters (populations) defined by STRUCTURE software, demonstrating that clusters 3 and 4 possessed the lowest and highest diversity values, respectively. AMOVA showed variation between and within clusters of 41.85% and 58.15%, respectively. The highest population divergence (Fst) was observed between clusters 2 and 3 (0.579), on the other hand, clusters 1 and 4 depicted the lowest Fst with 0.160. Our research highlighted that iPBS markers were successful and effective to study Daucus genetic diversity. These results will contribute to the genetic improvement of carrots and sustainable management of its diversity. 2022-11-21T03:29:08Z 2022-11-21T03:29:08Z 2022-04-25 info:eu-repo/semantics/article Yildiz, M. & Arbizu, C. (2020). Inter-primer binding site (iPBS) retrotransposon markers provide insights into the genetic diversity and population structure of carrots (Daucus, Apiaceae). Turkish Journal of Agriculture and Forestry, 16(2), 214-223. doi: 10.55730/1300-011X.2972 1303-6173 https://hdl.handle.net/20.500.12955/1976 https://doi.org/10.55730/1300-011X.2972 eng Turkish Journal of Agriculture and Forestry https://journals.tubitak.gov.tr/agriculture/vol46/iss2/8/ info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ application/pdf application/pdf TUBITAK TR Instituto Nacional de Innovación Agraria Repositorio Institucional - INIA |
| spellingShingle | Carrot Daucus Genetics Germplasm iPBS https://purl.org/pe-repo/ocde/ford#4.04.00 Zanahoria Recursos genéticos Yildiz, Mehtap Arbizu Berrocal, Carlos Irvin Inter-primer binding site (iPBS) retrotransposon markers provide insights into the genetic diversity and population structure of carrots (Daucus, Apiaceae) |
| title | Inter-primer binding site (iPBS) retrotransposon markers provide insights into the genetic diversity and population structure of carrots (Daucus, Apiaceae) |
| title_full | Inter-primer binding site (iPBS) retrotransposon markers provide insights into the genetic diversity and population structure of carrots (Daucus, Apiaceae) |
| title_fullStr | Inter-primer binding site (iPBS) retrotransposon markers provide insights into the genetic diversity and population structure of carrots (Daucus, Apiaceae) |
| title_full_unstemmed | Inter-primer binding site (iPBS) retrotransposon markers provide insights into the genetic diversity and population structure of carrots (Daucus, Apiaceae) |
| title_short | Inter-primer binding site (iPBS) retrotransposon markers provide insights into the genetic diversity and population structure of carrots (Daucus, Apiaceae) |
| title_sort | inter primer binding site ipbs retrotransposon markers provide insights into the genetic diversity and population structure of carrots daucus apiaceae |
| topic | Carrot Daucus Genetics Germplasm iPBS https://purl.org/pe-repo/ocde/ford#4.04.00 Zanahoria Recursos genéticos |
| url | https://hdl.handle.net/20.500.12955/1976 https://doi.org/10.55730/1300-011X.2972 |
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