Classification Binary Trees with SSR Allelic Sizes: Combining Regression Trees with Genetic Molecular Data in Order to Characterize Genetic Diversity between Cultivars of <i>Olea europaea</i> L.
During recent centuries, cultivated olive has evolved to one of the major tree crops in the Mediterranean Basin and lately expanded to America, Australia, and Asia producing an estimated global average value of over USD 18 billion. A long-term research effort has been established with the long-term...
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| Format: | Article |
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MDPI AG
2020-10-01
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| Series: | Agronomy |
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| Online Access: | https://www.mdpi.com/2073-4395/10/11/1662 |
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| author | Evangelia V. Avramidou Georgios C. Koubouris Panos V. Petrakis Katerina K. Lambrou Ioannis T. Metzidakis Andreas G. Doulis |
| author_facet | Evangelia V. Avramidou Georgios C. Koubouris Panos V. Petrakis Katerina K. Lambrou Ioannis T. Metzidakis Andreas G. Doulis |
| author_sort | Evangelia V. Avramidou |
| collection | DOAJ |
| description | During recent centuries, cultivated olive has evolved to one of the major tree crops in the Mediterranean Basin and lately expanded to America, Australia, and Asia producing an estimated global average value of over USD 18 billion. A long-term research effort has been established with the long-term goal to preserve biodiversity, characterize agronomic behavior, and ultimately utilize genotypes suitable for cultivation in areas of unfavorable environmental conditions. In the present study, a combination of 10 simple sequence repeat (SSR) markers with the classification binary tree (CBT) analysis was evaluated as a method for discriminating genotypes within cultivated olive trees, while <i>Olea europaea</i> subsp. <i>cuspidata</i> was also used as an outgroup. The 10 SSR loci employed in this study, were highly polymorphic and gave reproducible amplification patterns for all accessions analyzed. Genetic analysis indicated that the group of SSR loci employed was highly informative. A further analysis revealed that two sub populations and pairwise relatedness gave insight about synonymies. In conclusion, the CBT method which employed SSR allelic sizes proved to be a valuable tool in order to distinguish olive cultivars over the traditional unweighted pair group method with the arithmetic mean (UPGMA) algorithm. Further research which will combine phenotyping characterization of olive germplasm will have the potential to enable the utilization of existing, and breeding of new, superior cultivars. |
| first_indexed | 2024-03-10T15:17:25Z |
| format | Article |
| id | doaj.art-fdc4deb84ef8415da87307af78c89339 |
| institution | Directory Open Access Journal |
| issn | 2073-4395 |
| language | English |
| last_indexed | 2024-03-10T15:17:25Z |
| publishDate | 2020-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Agronomy |
| spelling | doaj.art-fdc4deb84ef8415da87307af78c893392023-11-20T18:52:28ZengMDPI AGAgronomy2073-43952020-10-011011166210.3390/agronomy10111662Classification Binary Trees with SSR Allelic Sizes: Combining Regression Trees with Genetic Molecular Data in Order to Characterize Genetic Diversity between Cultivars of <i>Olea europaea</i> L.Evangelia V. Avramidou0Georgios C. Koubouris1Panos V. Petrakis2Katerina K. Lambrou3Ioannis T. Metzidakis4Andreas G. Doulis5Laboratory of Silviculture, Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization DEMETER (ELGO DIMITRA), GR-115 28 Athens, GreeceLaboratory of Olive Cultivation, Institute of Olive Tree, Subtropical Crops & Viticulture, Hellenic Agricultural Organization (H.A.O.) “Demeter” (ELGO DIMITRA), Leoforos Karamanli 167, GR-73100 Chania, GreeceLaboratory of Forest Entomology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization “Demeter” (ELGO DIMITRA), GR-115 28 Athens, GreeceLaboratory of Plant Biotechnology & Genomic Resources, Institute of Olive Tree, Subtropical Crops & Viticulture, Hellenic Agricultural Organization “Demeter” (ELGO DIMITRA), Kastorias 32A, GR-71307 Heraklion, GreeceLaboratory of Olive Cultivation, Institute of Olive Tree, Subtropical Crops & Viticulture, Hellenic Agricultural Organization (H.A.O.) “Demeter” (ELGO DIMITRA), Leoforos Karamanli 167, GR-73100 Chania, GreeceLaboratory of Plant Biotechnology & Genomic Resources, Institute of Olive Tree, Subtropical Crops & Viticulture, Hellenic Agricultural Organization “Demeter” (ELGO DIMITRA), Kastorias 32A, GR-71307 Heraklion, GreeceDuring recent centuries, cultivated olive has evolved to one of the major tree crops in the Mediterranean Basin and lately expanded to America, Australia, and Asia producing an estimated global average value of over USD 18 billion. A long-term research effort has been established with the long-term goal to preserve biodiversity, characterize agronomic behavior, and ultimately utilize genotypes suitable for cultivation in areas of unfavorable environmental conditions. In the present study, a combination of 10 simple sequence repeat (SSR) markers with the classification binary tree (CBT) analysis was evaluated as a method for discriminating genotypes within cultivated olive trees, while <i>Olea europaea</i> subsp. <i>cuspidata</i> was also used as an outgroup. The 10 SSR loci employed in this study, were highly polymorphic and gave reproducible amplification patterns for all accessions analyzed. Genetic analysis indicated that the group of SSR loci employed was highly informative. A further analysis revealed that two sub populations and pairwise relatedness gave insight about synonymies. In conclusion, the CBT method which employed SSR allelic sizes proved to be a valuable tool in order to distinguish olive cultivars over the traditional unweighted pair group method with the arithmetic mean (UPGMA) algorithm. Further research which will combine phenotyping characterization of olive germplasm will have the potential to enable the utilization of existing, and breeding of new, superior cultivars.https://www.mdpi.com/2073-4395/10/11/1662clustergenetic analysiscultivargermplasm management<i>Olea europaea</i> L. |
| spellingShingle | Evangelia V. Avramidou Georgios C. Koubouris Panos V. Petrakis Katerina K. Lambrou Ioannis T. Metzidakis Andreas G. Doulis Classification Binary Trees with SSR Allelic Sizes: Combining Regression Trees with Genetic Molecular Data in Order to Characterize Genetic Diversity between Cultivars of <i>Olea europaea</i> L. Agronomy cluster genetic analysis cultivar germplasm management <i>Olea europaea</i> L. |
| title | Classification Binary Trees with SSR Allelic Sizes: Combining Regression Trees with Genetic Molecular Data in Order to Characterize Genetic Diversity between Cultivars of <i>Olea europaea</i> L. |
| title_full | Classification Binary Trees with SSR Allelic Sizes: Combining Regression Trees with Genetic Molecular Data in Order to Characterize Genetic Diversity between Cultivars of <i>Olea europaea</i> L. |
| title_fullStr | Classification Binary Trees with SSR Allelic Sizes: Combining Regression Trees with Genetic Molecular Data in Order to Characterize Genetic Diversity between Cultivars of <i>Olea europaea</i> L. |
| title_full_unstemmed | Classification Binary Trees with SSR Allelic Sizes: Combining Regression Trees with Genetic Molecular Data in Order to Characterize Genetic Diversity between Cultivars of <i>Olea europaea</i> L. |
| title_short | Classification Binary Trees with SSR Allelic Sizes: Combining Regression Trees with Genetic Molecular Data in Order to Characterize Genetic Diversity between Cultivars of <i>Olea europaea</i> L. |
| title_sort | classification binary trees with ssr allelic sizes combining regression trees with genetic molecular data in order to characterize genetic diversity between cultivars of i olea europaea i l |
| topic | cluster genetic analysis cultivar germplasm management <i>Olea europaea</i> L. |
| url | https://www.mdpi.com/2073-4395/10/11/1662 |
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