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

The Treatment-Naive Microbiome in New-Onset Crohn\u27s Disease

Inflammatory bowel diseases (IBDs), including Crohn\u27s disease (CD), are genetically linked to host pathways that implicate an underlying role for aberrant immune responses to intestinal microbiota. However, patterns of gut microbiome dysbiosis in IBD patients are inconsistent among published studies. Using samples from multiple gastrointestinal locations collected prior to treatment in new-onset cases, we studied the microbiome in the largest pediatric CD cohort to date. An axis defined by an increased abundance in bacteria which include Enterobacteriaceae, Pasteurellacaea, Veillonellaceae, and Fusobacteriaceae, and decreased abundance in Erysipelotrichales, Bacteroidales, and Clostridiales, correlates strongly with disease status. Microbiome comparison between CD patients with and without antibiotic exposure indicates that antibiotic use amplifies the microbial dysbiosis associated with CD. Comparing the microbial signatures between the ileum, the rectum, and fecal samples indicates that at this early stage of disease, assessing the rectal mucosal-associated microbiome offers unique potential for convenient and early diagnosis of CD

Investigation of Vapor-Phase Lubrication in a Gas Turbine Engine,"

ABSTRACT The liquid oil lubrication system of current aircraft jet engines accounts for approximately 10-15% of the total weight of the engine. It has long been a koal of the aircraft gas turbine industry to reduce this weight. Vapor-Phase Lubrication (VPL) is a promising technology to eliminate liquid oil lubrication. The current investigation resulted in the first gas turbine to operate in the absence of conventional liquid lubrication. A phosphate ester, commercially known as DURAD 6208, was chosen for the test. Extensive research at Wright Laboratory demonstrated that this lubricant could reliably lubricate rolling element bearings in the gas turbine engine environment. The Allison T63 engine was selected as the test vehicle because of its small size and bearing configuration. Specifically, VPL was evaluated in the number eight bearing because it is located in a relatively hot environment, in line with the combustor discharge, and it can be isolated from the other bearings and the liquid lubrication system. The bearing was fully instrumented and its performance with standard oil lubrication was documented. Results of this baseline study were used to develop a thermodynamic model to predict the bearing temperature with VPL. The engine was then operated at a ground idle condition with VPL with the lubricant misted into the #8 bearing at 13 ml/hr. The bearing temperature stabilized at 283°C within 10 minutes. Engine operation was continued successfully for a total of one hour. No abnormal wear of the rolling contact surfaces was found when the bearing was later examined. Bearing temperatures after engine shutdown indicated the bearing had reached thermodynamic equilibrium with its surroundings during the test. After shutdown bearing temperatures steadily decreased without the soakback effect seen after shutdown in standard lubricated bearings. In contrast, the oil lubricated bearing ran at a considerably lower operating temperature (83°C) and was significantly heated by its surroundings after engine shutdown. In the baseline tests, the final bearing temperatures never reached that of the operating VPL system. NOMENCLATUR

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

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

Heterozygosity increases microsatellite mutation rate, linking it to demographic history

<p>Abstract</p> <p>Background</p> <p>Biochemical experiments in yeast suggest a possible mechanism that would cause heterozygous sites to mutate faster than equivalent homozygous sites. If such a process operates, it could undermine a key assumption at the core of population genetic theory, namely that mutation rate and population size are indpendent, because population expansion would increase heterozygosity that in turn would increase mutation rate. Here we test this hypothesis using both direct counting of microsatellite mutations in human pedigrees and an analysis of the relationship between microsatellite length and patterns of demographically-induced variation in heterozygosity.</p> <p>Results</p> <p>We find that microsatellite alleles of any given length are more likely to mutate when their homologue is unusually different in length. Furthermore, microsatellite lengths in human populations do not vary randomly, but instead exhibit highly predictable trends with both distance from Africa, a surrogate measure of genome-wide heterozygosity, and modern population size. This predictability remains even after statistically controlling for non-independence due to shared ancestry among populations.</p> <p>Conclusion</p> <p>Our results reveal patterns that are unexpected under classical population genetic theory, where no mechanism exists capable of linking allele length to extrinsic variables such as geography or population size. However, the predictability of microsatellite length is consistent with heterozygote instability and suggest that this has an important impact on microsatellite evolution. Whether similar processes impact on single nucleotide polymorphisms remains unclear.</p

Towards an optimal sampling strategy for assessing genetic variation within and among white clover (Trifolium repens L.) cultivars using AFLP

Cost reduction in plant breeding and conservation programs depends largely on correctly defining the minimal sample size required for the trustworthy assessment of intra- and inter-cultivar genetic variation. White clover, an important pasture legume, was chosen for studying this aspect. In clonal plants, such as the aforementioned, an appropriate sampling scheme eliminates the redundant analysis of identical genotypes. The aim was to define an optimal sampling strategy, i.e., the minimum sample size and appropriate sampling scheme for white clover cultivars, by using AFLP data (283 loci) from three popular types. A grid-based sampling scheme, with an interplant distance of at least 40 cm, was sufficient to avoid any excess in replicates. Simulations revealed that the number of samples substantially influenced genetic diversity parameters. When using less than 15 per cultivar, the expected heterozygosity (He) and Shannon diversity index (I) were greatly underestimated, whereas with 20, more than 95% of total intra-cultivar genetic variation was covered. Based on AMOVA, a 20-cultivar sample was apparently sufficient to accurately quantify individual genetic structuring. The recommended sampling strategy facilitates the efficient characterization of diversity in white clover, for both conservation and exploitation