Genotype and Phenotype data

Genetic diversity, population structure, and taxonomic confirmation in annual medic (Medicago spp.) collections from Crimea, Ukrainedoi: 10.3389/fpls.2024.1339298Annual 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.Description of the data and file structureCrimea_MADC.csv: MADC report of all the genotypes obtained from DArT after genotypingCrimea_phenotype.XLSX: phenotype data observed for all the accessions.Sharing/Access informationThis is a section for linking to other ways to access the data, and for linking to sources the data is derived from, if any.Links to other publicly accessible locations of the data:https://www.frontiersin.org/articles/10.3389/fpls.2024.1339298/full#supplementary-materialGenotype data was derived from the following sources:DArTag sequencing乌克兰克里米亚地区一年生苜蓿（Medicago spp.）采集样本的遗传多样性、种群结构与分类学验证 doi: 10.3389/fpls.2024.1339298 2008年，为填补美国农业部（United States Department of Agriculture, USDA）农业研究服务局（Agricultural Research Service, ARS）国家植物种质系统（National Plant Germplasm System, NPGS）温带适应性饲用豆科种质资源库的地理覆盖空白，研究团队从乌克兰克里米亚半岛采集了一年生苜蓿（Medicago spp.）种质资源。本次共采集到10个苜蓿属物种的102份种质。 为评估该批种质的遗传多样性、种群结构并验证其分类学身份，研究团队从表型与遗传两个层面开展了特征解析。表型鉴定采用24项标准化描述性状；遗传鉴定则依托专为紫花苜蓿（Medicago sativa L.）开发的3K多样性阵列技术（Diversity Array Technologies, DArTag）分型面板完成。 在表型与分子特征分析中，研究团队从NPGS种质库获取了92份地理分布广泛、物种代表性强的种质作为参照集。表型鉴定结果显示，同一份种质内的重复植株表型一致性优异，同一物种种质间存在一定表型变异，且不同物种间表型差异显著。 由于该DArTag分型面板专为栽培紫花苜蓿开发，其标记序列在待测物种中的可转移性有限，最终每个物种平均检测到约1500个标记位点。其中，在95%的受试样本中均可稳定检测到的标记位点共计448个。基于筛选出的2396个标记位点开展主成分分析与系统发育分析，结果可按物种对种质进行精准聚类，并准确预测出物种间的进化亲缘关系。此外，该标记面板还协助纠正了数份疑似存在标签错误的种质的分类学身份。 基因分型结果同时表明，对于这些以自花授粉为主的物种而言，仅采集单株样本即可满足分析需求，因为单株（n=3）与混合样本（n=7）的生物学重复叶片样品间具有高度的重现性。 表型数据与2396个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记集可有效用于评估克里米亚种质与参照种质的种群结构，凸显出克里米亚种质中蕴含的新颖且独特的遗传多样性。 本研究不仅验证了DArTag分型面板在克里米亚苜蓿种质评估中的应用价值，还揭示了其在苜蓿属物种遗传资源评价中的更广泛应用前景。此外，本研究结果亦强调了利用遗传资源与先进基因分型工具开展一年生苜蓿属物种可持续作物改良与生物多样性保护的重要性。 ### 数据与文件结构 1. Crimea_MADC.csv：经DArT基因分型后获取的所有基因型的MADC分析报告 2. Crimea_phenotype.XLSX：所有受试种质的表型观测数据集 ### 共享与获取说明 本章节用于链接数据的其他公开获取渠道，以及数据来源说明。 数据的其他公开获取链接：https://www.frontiersin.org/articles/10.3389/fpls.2024.1339298/full#supplementary-material 基因型数据来源：DArTag测序