Genetic diversity, population structure, and taxonomic confirmation in annual medic (Medicago spp.) collections from Crimea, Ukraine
Annual medic (Medicago spp.) germplasm was collected from the Crimean Peninsula of Ukraine in 2008 to fill gaps in geographic coverage in the United States department of Agriculture, Agricultural Research Service, National Plant Germplasm System (NPGS) temperate-adapted forage legume collection. A t...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2024-04-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2024.1339298/full |
| _version_ | 1827295699808550912 |
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| author | Dongyan Zhao Manoj Sapkota Meng Lin Craig Beil Moira Sheehan Stephanie Greene Brian M. Irish |
| author_facet | Dongyan Zhao Manoj Sapkota Meng Lin Craig Beil Moira Sheehan Stephanie Greene Brian M. Irish |
| author_sort | Dongyan Zhao |
| collection | DOAJ |
| description | Annual medic (Medicago spp.) germplasm was collected from the Crimean Peninsula of Ukraine in 2008 to fill gaps in geographic coverage in the United States department of Agriculture, Agricultural Research Service, National Plant Germplasm System (NPGS) temperate-adapted forage legume collection. A total of 102 accessions across 10 Medicago species were collected. To assess genetic diversity, population structure, and to confirm taxonomic identities, the collections were phenotypically and genetically characterized. Phenotyping included the use of 24 descriptor traits while genetic characterization was accomplished using a 3K Diversity Array Technologies (DArTag) panel developed for alfalfa (Medicago sativa L.). For both field and molecular characterizations, a reference set of 92 geographically diverse and species-representative accessions were obtained from the NPGS collection. Phenotypic descriptors showed consistency among replicated plants within accessions, some variation across accessions within species, and evident distinctions between species. Because the DArTag panel was developed for cultivated alfalfa, the transferability of markers to the species being evaluated was limited, resulting in an average of ~1,500 marker loci detected per species. From these loci, 448 markers were present in 95% of the samples. Principal component and phylogenetic analysis based on a larger set of 2,396 selected markers clustered accessions by species and predicted evolutionary relationships among species. Additionally, the markers aided in the taxonomic identity of a few accessions that were likely mislabeled. The genotyping results also showed that sampling individual plants for these mostly self-pollinating species is sufficient due to high reproducibility between single (n=3) and pooled (n=7) biological replicate leaf samples. The phenotyping and the 2,396 Single Nucleotide Polymorphism (SNP) marker set were useful in estimating population structure in the Crimean and reference accessions, highlighting novel and unique genetic diversity captured in the Crimean accessions. This research not only demonstrated the utility of the DArTag marker panel in evaluating the Crimean germplasm but also highlighted its broader application in assessing genetic resources within the Medicago genus. Furthermore, we anticipate that our findings will underscore the importance of leveraging genetic resources and advanced genotyping tools for sustainable crop improvement and biodiversity conservation in annual medic species. |
| first_indexed | 2024-04-24T14:24:50Z |
| format | Article |
| id | doaj.art-9a0b0b7dc7b64ecc9f42678c29fc815d |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-24T14:24:50Z |
| publishDate | 2024-04-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-9a0b0b7dc7b64ecc9f42678c29fc815d2024-04-03T05:11:07ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2024-04-011510.3389/fpls.2024.13392981339298Genetic diversity, population structure, and taxonomic confirmation in annual medic (Medicago spp.) collections from Crimea, UkraineDongyan Zhao0Manoj Sapkota1Meng Lin2Craig Beil3Moira Sheehan4Stephanie Greene5Brian M. Irish6Breeding Insight, Cornell University, Ithaca, NY, United StatesBreeding Insight, Cornell University, Ithaca, NY, United StatesBreeding Insight, Cornell University, Ithaca, NY, United StatesBreeding Insight, Cornell University, Ithaca, NY, United StatesBreeding Insight, Cornell University, Ithaca, NY, United StatesAgricultural Genetic Resources Preservation Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Prosser, WA, United StatesPlant Germplasm Introduction and Testing Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Prosser, WA, United StatesAnnual medic (Medicago spp.) germplasm was collected from the Crimean Peninsula of Ukraine in 2008 to fill gaps in geographic coverage in the United States department of Agriculture, Agricultural Research Service, National Plant Germplasm System (NPGS) temperate-adapted forage legume collection. A total of 102 accessions across 10 Medicago species were collected. To assess genetic diversity, population structure, and to confirm taxonomic identities, the collections were phenotypically and genetically characterized. Phenotyping included the use of 24 descriptor traits while genetic characterization was accomplished using a 3K Diversity Array Technologies (DArTag) panel developed for alfalfa (Medicago sativa L.). For both field and molecular characterizations, a reference set of 92 geographically diverse and species-representative accessions were obtained from the NPGS collection. Phenotypic descriptors showed consistency among replicated plants within accessions, some variation across accessions within species, and evident distinctions between species. Because the DArTag panel was developed for cultivated alfalfa, the transferability of markers to the species being evaluated was limited, resulting in an average of ~1,500 marker loci detected per species. From these loci, 448 markers were present in 95% of the samples. Principal component and phylogenetic analysis based on a larger set of 2,396 selected markers clustered accessions by species and predicted evolutionary relationships among species. Additionally, the markers aided in the taxonomic identity of a few accessions that were likely mislabeled. The genotyping results also showed that sampling individual plants for these mostly self-pollinating species is sufficient due to high reproducibility between single (n=3) and pooled (n=7) biological replicate leaf samples. The phenotyping and the 2,396 Single Nucleotide Polymorphism (SNP) marker set were useful in estimating population structure in the Crimean and reference accessions, highlighting novel and unique genetic diversity captured in the Crimean accessions. This research not only demonstrated the utility of the DArTag marker panel in evaluating the Crimean germplasm but also highlighted its broader application in assessing genetic resources within the Medicago genus. Furthermore, we anticipate that our findings will underscore the importance of leveraging genetic resources and advanced genotyping tools for sustainable crop improvement and biodiversity conservation in annual medic species.https://www.frontiersin.org/articles/10.3389/fpls.2024.1339298/fulldiversityDArTag genotypingmarkergermplasmlegume |
| spellingShingle | Dongyan Zhao Manoj Sapkota Meng Lin Craig Beil Moira Sheehan Stephanie Greene Brian M. Irish Genetic diversity, population structure, and taxonomic confirmation in annual medic (Medicago spp.) collections from Crimea, Ukraine Frontiers in Plant Science diversity DArTag genotyping marker germplasm legume |
| title | Genetic diversity, population structure, and taxonomic confirmation in annual medic (Medicago spp.) collections from Crimea, Ukraine |
| title_full | Genetic diversity, population structure, and taxonomic confirmation in annual medic (Medicago spp.) collections from Crimea, Ukraine |
| title_fullStr | Genetic diversity, population structure, and taxonomic confirmation in annual medic (Medicago spp.) collections from Crimea, Ukraine |
| title_full_unstemmed | Genetic diversity, population structure, and taxonomic confirmation in annual medic (Medicago spp.) collections from Crimea, Ukraine |
| title_short | Genetic diversity, population structure, and taxonomic confirmation in annual medic (Medicago spp.) collections from Crimea, Ukraine |
| title_sort | genetic diversity population structure and taxonomic confirmation in annual medic medicago spp collections from crimea ukraine |
| topic | diversity DArTag genotyping marker germplasm legume |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2024.1339298/full |
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