Rationalization of a genebank cucumber collection with SSR markers

The CGN cucumber (Cucumis sativus) collection consists of 937 accessions. The majority of accessions originated from the working collection of the former Institute for Horticultural Plant Breeding (IVT), where they were used for breeding. The collection mainly includes old cultivars received from Dutch and foreign seed companies, and genebanks, but also contains landraces and accessions of the cropwild relative C. hardwickii. Passport data were updated in 2002, and used to rationalize the collection. In 2009, CGN participated in a project initiated by The Institute of Vegetables and Flowers of the Chinese Academy of Agricultural Sciences in Beijing (CAAS), China. The project aimed at developing a structured core collection of cucumber germplasm using well-distributed and highly polymorphic SSR markers. For this purpose, the collections of CAAS, of the USDA (United States) and of the CGN were used. A total of 3,318 accessions were analyzed with 23 highly polymorphic microsatellite (SSR) markers, resulting in a core set of 109 accessions (in preparation). In addition to the collaborative project, the SSR data of 752 CGN accessions were analyzed separately in order to find further options to rationalize the collection based on these markers. A phylogenetic tree was constructed based on Jaccard similarity values. Four distinct groups could be recognized, i.e. C. hardwickii, landraces from South Asia, varieties from Asia, and varieties predominantly from Europe and USA. The SSR data were also used to verify passport data, such as origin country, and to improve accession documentation. Twenty-seven groups of accessions with identical microsatellite profile were identified. Trials are planned to compare these potential duplicate accessions morphologically. In the past, a “cucumber” group and a “gherkin” group were recognized within the collection, based on morphological traits. However, this division was not supported by the SSR data and therefore abandoned

Global strategy for the conservation and use of eggplants

Common eggplant (Solanum melongena L.), also known as brinjal eggplant or aubergine, is a vegetable crop grown for its large soft fruits which are used in cooking. There are also two African eggplant species grown locally: scarlet eggplant (Solanum aethiop icum L.) and gboma eggplant (Solanum macrocarpon L.). According to the statistics of the United Nations Food and Agriculture Organization (FAO), eggplant is grown on 1.8 million hectares (ha) globally, and 90% of eggplant production takes place in Asia. Breeding and research on eggplant is carried out in many coun tries. Numerous germplasm collections of eggplant and its related species exist to provide plant materials for breeding and related research. In the present study, we overview the current status of eggplant germplasm conservation efforts and the use of eggplant diversity with the aim of providing a forward-looking strategy document. To do this, we surveyed the global databases Genesys and WIEWS (World Information and Early Warning System on Plant Genetic Resources for Food and Agriculture) to obtain information about existing eggplant ex situ collections. The most often represented species in these databases is brinjal eggplant with 12,715 acces sions conserved in total. This is followed by scarlet eggplant (886 accessions) and gboma eggplant (209 accessions). Wild relatives of eggplant are conserved in some collections, but some species are not well represented. In total, 109 eggplant collection holders were iden tified through the database searches. The collection holders were asked to complete an online survey on the status of their collections and the challenges that they faced. Responses were received from 32 collec tion holders, 27 of which provided sufficient data for further analyses. Most of the collection holders that responded were governmental organizations or publicly funded institutions. Two respondents were non-governmental organizations (NGOs). Several challenges related to the sustainability of eggplant conservation and use were identified. Shortages of funds and staff were reported as major threats to collection viability and security by many of the collec tion holders. Opportunities for improvement included recruiting new and/or young people interested in eggplant conservation, and increased collaborations across national borders and among institutions. Improved documentation of existing plant materials and increased information sharing were also identi fied as areas for improvement.publishedVersio

Untargeted metabolic profiling in dried blood spots identifies disease fingerprint for pyruvate kinase deficiency

The diagnostic evaluation and clinical characterization of rare hereditary anemia (RHA) is to date still challenging. In particular, there is little knowledge of the broad metabolic impact of many of the molecular defects underlying RHA. In this study we explored the potential of untargeted metabolomics to diagnose a relatively common type of RHA: pyruvate kinase deficiency (PKD). In total, 1,903 unique metabolite features were identified in dried blood spot samples from 16 PKD patients and 32 healthy controls. A metabolic fingerprint was identified using a machine learning algorithm, and subsequently a binary classification model was designed. The model showed high performance characteristics (AUC 0.990, 95% CI: 0.981-0.999) and an accurate class assignment was achieved for all newly added control (n=13) and patient samples, (n=6) with the exception of one patient (accuracy 94%). Important metabolites in the metabolic fingerprint included glycolytic intermediates, polyamines and several acyl carnitines. In general, the application of untargeted metabolomics in dried blood spots is a novel functional tool that holds promise for the diagnostic stratification and studies on the disease pathophysiology in RHA

More efficient conservation and use of vegetable genetic resources in Europe: ECPGR achievement and perspectives

The European Cooperative Programme for Plant Genetic Resources (ECPGR) is a regional network funded by the European countries and coordinated by Bioversity International. The Vegetables Network with representatives of 42 countries, is one of the crop specific ECPGR networks (http://www.ecpgr.cgiar.org/ networks/vegetables.html). It consists of six Working Groups (WGs), i.e., on Allium, Brassica, Cucurbits, Leafy Vegetables, Solanaceae and Umbellifer Crops. Sharing responsibilities for the ex situ conservation of European vegetable crops genetic resources is the highest priority of the Vegetables Network. It is foreseen that the rationalization of the collections will lead to higher cost-efficiency, and improvement of plant genetic resources documentation and quality. These efforts will be continued within the framework of the AEGIS initiative (A European Genebank Integrated System) (http://www.aegis.cgiar.org/). Challenges for the Vegetables Network include the identification of the so-called Most Appropriate Accessions (MAA) for each crop for their inclusion in the decentrally managed European Collection, and the development of agreed crop specific technical standards for conservation. Achievements of the Network in recent years include the development of European Central Crop Databases (ECCDBs), quality standards for collection man-agement of seed-propagated crops and cryopreserved material, safety duplication improvement and definition of minimum characterization descriptors. Several EU-funded projects have initiated and accelerated the activities of the WGs. Apart from further improvements within the framework of AEGIS, the Network is planning a number of other initiatives, such as improving collaboration at the global level (Allium), developing molecular characterization protocols (lettuce), filling the gaps in the conservation of wild relatives (Brassica and Umbellifer Crops), and improving the Network’s communication with the scientific community and the public at large

Clinical implementation of artificial-intelligence-assisted detection of breast cancer metastases in sentinel lymph nodes: the CONFIDENT-B single-center, non-randomized clinical trial

Pathologists' assessment of sentinel lymph nodes (SNs) for breast cancer (BC) metastases is a treatment-guiding yet labor-intensive and costly task because of the performance of immunohistochemistry (IHC) in morphologically negative cases. This non-randomized, single-center clinical trial (International Standard Randomized Controlled Trial Number:14323711) assessed the efficacy of an artificial intelligence (AI)-assisted workflow for detecting BC metastases in SNs while maintaining diagnostic safety standards. From September 2022 to May 2023, 190 SN specimens were consecutively enrolled and allocated biweekly to the intervention arm (n = 100) or control arm (n = 90). In both arms, digital whole-slide images of hematoxylin-eosin sections of SN specimens were assessed by an expert pathologist, who was assisted by the 'Metastasis Detection' app (Visiopharm) in the intervention arm. Our primary endpoint showed a significantly reduced adjusted relative risk of IHC use (0.680, 95% confidence interval: 0.347-0.878) for AI-assisted pathologists, with subsequent cost savings of ~3,000 €. Secondary endpoints showed significant time reductions and up to 30% improved sensitivity for AI-assisted pathologists. This trial demonstrates the safety and potential for cost and time savings of AI assistance

Genetic diversity and population structure of cucumber (Cucumis sativus L.)

Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also includes melon, watermelon, pumpkin and squash. Previous isozyme studies revealed a low genetic diversity in cucumber, but detailed insights into the crop's genetic structure and diversity are largely missing. We have fingerprinted 3,342 accessions from the Chinese, Dutch and U.S. cucumber collections with 23 highly polymorphic Simple Sequence Repeat (SSR) markers evenly distributed in the genome. The data reveal three distinct populations, largely corresponding to three geographic regions. Population 1 corresponds to germplasm from China, except for the unique semi-wild landraces found in Xishuangbanna in Southwest China and East Asia; population 2 to Europe, America, and Central and West Asia; and population 3 to India and Xishuangbanna. Admixtures were also detected, reflecting hybridization and migration events between the populations. The genetic background of the Indian germplasm is heterogeneous, indicating that the Indian cucumbers maintain a large proportion of the genetic diversity and that only a small fraction was introduced to other parts of the world. Subsequently, we defined a core collection consisting of 115 accessions and capturing over 77% of the SSR alleles. Insight into the genetic structure of cucumber will help developing appropriate conservation strategies and provides a basis for population-level genome sequencing in cucumber