Cryopreservation and long-term storage of pear germplasm

Summary Germplasm collections of vegetatively propagated crops are usually maintained as plants in fields or potted in greenhouses or screened enclosures. Safety duplication of these collections, as duplicate plants or separate collections, is costly and requires large amounts of space. Cryopreservation techniques which were recently developed for long-term storage of pear germalasm may offer an efficient alternative to conventional germplasm collection maintenance. Pear (Pyrus L.) germplasm may now be stored as seeds (species), dormant buds or pollen from field-grown trees, or shoot tips fromin vitro-grown plants (cultivars). Pear germplasm may now be cryopreserved and stored for long periods (> 100 yr) utilizing slow-freezing or vitrification ofin vitro-grown shoot-tips. Dormant bud freezing, pollen, and seed cryopreservation of other lines are being developed to complete the base collection forPyrus. This cryopreserved collection provides base (long-term) storage for the field-grown pear germplasm collection at the National Clonal Germplasm Repository, Corvallis, Oregon. Based on a presentation at the 1997 Congress on In Vitro Biology held in Washington, D.C., June 14–18, 1997.     

Methods of developing a core collection of annual Medicago species

A core collection is a subset of a large germplasm collection that contains accessions chosen to represent the genetic variability of the germplasm collection. The purpose of the core collection is to improve management and use of a germplasm collection. Core collections are usually assembled by grouping accessions and selecting from within these groups. The objective of this study was to compare 11 methods of assembling a core collection of the U.S. National collection of annual Medicago species. These methods differed in their use of passport and evaluation data as well as their selection strategy. Another objective was to compare core collections with sample sizes of 5%, 10% and 17% of the germplasm collection. Core collections assembled with evaluation data and cluster analysis better represented the germplasm collection than core collections assembled based solely on passport data and random selection of accessions, The Relative Diversity and the logarithm methods generated better core collections than the proportional method. The 5% and 10% sample size core collection were judged insufficient to represent the germplasm collection.     

Autonomous recovery in componentized Internet applications

In this paper we show how to reduce downtime of J2EE applications by rapidly and automatically recovering from transient and intermittent software failures, without requiring application modifications. Our prototype combines three application-agnostic techniques: macroanalysis for fault detection and localization, microrebooting for rapid recovery, and external management of recovery actions. The individual techniques are autonomous and work across a wide range of componentized Internet applications, making them well-suited to the rapidly changing software of Internet services. The proposed framework has been integrated with JBoss, an open-source J2EE application server. Our prototype provides an execution platform that can automatically recover J2EE applications within seconds of the manifestation of a fault. Our system can provide a subset of a system's active end users with the illusion of continuous uptime, in spite of failures occurring behind the scenes, even when there is no functional redundancy in the system.     

RETRACTED ARTICLE: An analysis of population structure and linkage disequilibrium using multilocus data in 187 maize inbred lines

This study analyzes population structure and linkage disequilibrium (LD) among 187 commonly used Chinese maize inbred lines, representing the genetic diversity among public, commercial and historically important lines for corn breeding. Seventy SSR loci, evenly distributed over 10 chromosomes, were assayed for polymorphism. The identified 290 alleles served to estimate population structure and analyze the genome-wide LD. The population of lines was highly structured, showing 6 subpopulations: BSSS (American BSSS including Reid), PA (group A germplasm derived from modern U.S. hybrids in China), PB (group B germplasm derived from modern U.S. hybrid in China), Lan (Lancaster Surecrop), LRC (derivative lines from Lvda Reb Cob, a Chinese landrace) and SPT (derivative lines from Si-ping-tou, a Chinese landrace). Forty lines, which formerly had an unknown and/or miscellaneous origin and pedigree record, were assigned to the appropriate group. Relationship estimates based on SSR marker data were quantified in a Q matrix, and this information will inform breeder’s decisions regarding crosses. Extensive inter- and intra-chromosomal LD was detected between 70 microsatellite loci for the investigated maize lines (2109 loci pairs in LD with D′ > 0.1 and 93 out of them at P < 0.01).This suggests that rapidly evolving microsatellites may track recent population structure. Interlocus LD decay among the diverse maize germplasm indicated that association studies in QTLs and/or candidate genes might avoid nonfunctional and spurious associations since most of the LD blocks were broken between diverse germplasm. The defined population structure and the LD analysis present the basis for future association mapping. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Urban Wet Environment as Mosquito Habitat in the Upper Midwest

Sampling of Culex larval habitat plays an important role in West Nile virus surveillance and control programs. Although many cities have established mosquito sampling programs and abatement districts, there is relatively little information describing the extent and ecology of urban surface waters and stormwater systems in different geographic areas and how these parameters affect mosquito communities and control strategies. An aerial survey of the city of Madison, Wisconsin revealed 521 above-ground wet sites. These included both constructed stormwater systems (ditches, retention ponds, detention ponds) and natural wetlands (marshes, flood areas, creeks, and rivers). Repeat sampling of 351 of these sites was conducted during 2004 and 2005. The majority of sites, 58% in 2004 and 72% in 2005, yielded no mosquito larvae, suggesting that physical and biological features of these wet sites limit the development of mosquito larvae. For both years, analysis of the positive samples revealed that less than 25% of sites produced Culex spp. while a small number of ditches and detention ponds were consistent “superproducers” of Culex larvae from year to year. This information will facilitate comparisons across geographical areas and provides insight into local variation in the public health risk due to mosquito transmission of human disease agents. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpress

ArrayExpress is a public microarray repository founded on the Minimum Information About a Microarray Experiment (MIAME) principles that stores MIAME-compliant gene expression data. Plant-based data sets represent approximately one-quarter of the experiments in ArrayExpress. The majority are based on Arabidopsis (Arabidopsis thaliana); however, there are other data sets based on Triticum aestivum, Hordeum vulgare, and Populus subsp. AtMIAMExpress is an open-source Web-based software application for the submission of Arabidopsis-based microarray data to ArrayExpress. AtMIAMExpress exports data in MAGE-ML format for upload to any MAGE-ML-compliant application, such as J-Express and ArrayExpress. It was designed as a tool for users with minimal bioinformatics expertise, has comprehensive help and user support, and represents a simple solution to meeting the MIAME guidelines for the Arabidopsis community. Plant data are queryable both in ArrayExpress and in the Data Warehouse databases, which support queries based on gene-centric and sample-centric annotation. The AtMIAMExpress submission tool is available at http://www.ebi.ac.uk/at-miamexpress/. The software is open source and is available from http://sourceforge.net/projects/miamexpress/. For information, contact miamexpress@ebi.ac.uk.     

Biological Control of <Emphasis Type="Italic">Melanaspis Obscura</Emphasis> on Oaks in Northern California

In 1988, Encarsia aurantii (Howard) (Hymenoptera: Aphelinidae) was introduced into northern California to control an isolated infestation of obscure scale, Melanaspis obscura (Comstock) (Coccoidea: Diaspididae), on native and exotic oaks (Quercus spp.) in Sacramento’s Capitol Park. By 2002, there was no longer any need for chemical control of the scale (i.e., complete biological control). Both parasite and host are univoltine; peak emergence of adult parasites coincides with the peak of newly settled, first-instar scales. Increase of the parasite and concomitant decline of the scale from 1992 to 2004 are documented for one native and one exotic oak tree. During spring of 2004, mean density of female scales (based on 100 twigs per tree) on 12 previously infested oak trees was generally low, ranging from <1 (eight trees) to ∼15 (single tree) scales/twig. Mean percentage parasitization (per twig) ranged from ∼30 to ∼85%, and was density independent (spatial context) for each of five trees. Two refuges for the scale population were noted: some scale crawlers settled and developed under the parental scale cover (spatial refuge) and some female scales continued to produce crawlers into late summer and early fall, when adult parasites were no longer available (temporal refuge). This case illustrates how an introduction strategy (i.e., single-species release of E. aurantii), which was derived from an analysis of the parasite guild of the pest, was executed in the field and ultimately led to successful biological control.     

Varietal identification and assessment of genetic relationships in Hippeastrum using RAPD markers

The National Botanical Research Institute (NBRI) in Lucknow, India, maintains germplasm of Hippeastrum, a beautiful summer blooming ornamental. Germplasm collections comprise NBRI hybrids developed through selective breeding, hybrids with unknown parentage, local species, and Dutch hybrids for research purposes. Considering the importance of protecting plant breeders’ rights for commercial exploitation of hybrids, a PCR-based technique (random amplified polymorphic DNA—RAPD) was used to correctly identify known and unknown hybrids and to determine cultivar relatedness. RAPD profiles were used very successfully to trace and confirm the parentage of all the hybrids tested and to determine clear molecular relationships among varieties.     

Spatial Distribution of Genetic Variation in a Natural Beech Stand (Fagus sylvaticaL.) Based on Microsatellite Markers

The spatial distribution of alleles is described in a naturally regenerated, isolated pure beech (Fagus sylvaticaL.) stand consisting of 99 adult trees. After testing nine microsatellite loci originally developed for F. crenata, each tree was genotyped at four well-scorable microsatellite loci. Specific primers were developed for one locus of F. sylvaticaL. For the characterization of spatial genetic structures, two different statistics were used. One method is based on the mean genetic distance between trees in different spatial distance classes, and the other one is Moran's index I. The results show the same tendency of a strong family structure in the distance classes up to 30m in comparison with that expected for a spatially non-systematic distribution of genotypes. In general, microsatellites are more useful to detect spatial genetic structures than allozymes. Spatial genetic structures are influenced by unpredictable factors such as wind direction at anthesis and can therefore vary from year to year. We recommend that seed collections should cover large areas in order to prevent a preponderance of few families and a reduction of the adaptive potential of the next generation.     

Linking Temporal and Spatial Scales in the Study of an Argentine Ant Invasion

Our long-term study of an invasion of Argentine ants (Linepithema humile) in a 481-ha biological preserve in Northern California links multiple spatial and temporal scales. We have investigated, at local spatial scales of tens of meters, how nests spread and contract seasonally and from year to year. Microsatellite analysis shows population genetic structure on the scale of about 100 m. At the landscape scale, we have surveyed the spread and impact of Argentine ants in the biological preserve since 1993, and have found high variability both seasonally and from year to year. Here, we describe how seasonal patterns in nesting behavior at the local scale help to explain how the location of the invasion edge changes. Thus, the growth and spread of nests on the scale of tens of meters, from season to season, produce the dynamics of the invasion from year to year at the scale of hundreds of meters.     

WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration

Background

Imaging and image analysis advances are yielding increasingly complete and complicated records of cellular events in tissues and whole embryos. The ability to follow hundreds to thousands of cells at the individual level demands a spatio-temporal data infrastructure: tools to assemble and collate knowledge about development spatially in a manner analogous to geographic information systems (GIS). Just as GIS indexes items or events based on their spatio-temporal or 4D location on the Earth these tools would organize knowledge based on location within the tissues or embryos. Developmental processes are highly context-specific, but the complexity of the 4D environment in which they unfold is a barrier to assembling an understanding of any particular process from diverse sources of information. In the same way that GIS aids the understanding and use of geo-located large data sets, software can, with a proper frame of reference, allow large biological data sets to be understood spatially. Intuitive tools are needed to navigate the spatial structure of complex tissue, collate large data sets and existing knowledge with this spatial structure and help users derive hypotheses about developmental mechanisms.

Results

Toward this goal we have developed WormGUIDES, a mobile application that presents a 4D developmental atlas for Caenorhabditis elegans. The WormGUIDES mobile app enables users to navigate a 3D model depicting the nuclear positions of all cells in the developing embryo. The identity of each cell can be queried with a tap, and community databases searched for available information about that cell. Information about ancestry, fate and gene expression can be used to label cells and craft customized visualizations that highlight cells as potential players in an event of interest. Scenes are easily saved, shared and published to other WormGUIDES users. The mobile app is available for Android and iOS platforms.

Conclusion

WormGUIDES provides an important tool for examining developmental processes and developing mechanistic hypotheses about their control. Critically, it provides the typical end user with an intuitive interface for developing and sharing custom visualizations of developmental processes. Equally important, because users can select cells based on their position and search for information about them, the app also serves as a spatially organized index into the large body of knowledge available to the C. elegans community online. Moreover, the app can be used to create and publish the result of exploration: interactive content that brings other researchers and students directly to the spatio-temporal point of insight. Ultimately the app will incorporate a detailed time lapse record of cell shape, beginning with neurons. This will add the key ability to navigate and understand the developmental events that result in the coordinated and precise emergence of anatomy, particularly the wiring of the nervous system.     

亚洲产Clavicorona的形态学及亲和性研究

中国产的Clavicorona pyxidata与北美的种样本间配对实验结果显示该种在不同的地理分布区内的种群之间完全性亲和或具有相同的交配型等位基因,表明中国产与北美产的该形态学种同属于一个生物种。日本产的标本与C. pyxidata在子实体外部形态及孢子尺度上有差异,虽然在日本被鉴定为该种。日本产的菌株与C. pyxidata菌株间配对实验证明二者之间完全不亲和,即属于不同的生物种。生殖隔离拌随着形态学变异。     

The genetic status and conservation management of two cultivated bulb species extinct in the wild: Tecophilaea cyanocrocus (Chile) and Tulipa sprengeri (Turkey)

Tecophilaea cyanocrocus and Tulipasprengeri are both extinct in the wild as aresult of overharvesting by commercialcollectors. Stocks of both species survive incultivation in amateur collections, commercialnurseries and botanic garden collections.Whilst both species share a similarconservation history, the distribution ofgenetic diversity within cultivated materialwas unknown. To support the long-termconservation of both species the geneticdiversity of the surviving stocks was assessedusing amplified fragment length polymorphisms(AFLPs). This study revealed different geneticstructures for the two bulb species. The Kewcollections of T. cyanocrocus, originallyobtained from a commercial nursery, VanTubergen, are genetically highly uniform andthe addition of samples from other collectionshas dramatically increased the level ofvariation. In contrast, the collections ofT. sprengeri held at Kew since the early20th century include representativegenotypes covering the whole range of geneticvariation found in this species and areprobably the source of all other cultivatedmaterial. The results are discussed in relationto the management of these species to ensuretheir continued survival in cultivation.     

The annotation and analysis of complex 3D plant organs using 3DCoordX

A fundamental question in biology concerns how molecular and cellular processes become integrated during morphogenesis. In plants, characterization of 3D digital representations of organs at single-cell resolution represents a promising approach to addressing this problem. A major challenge is to provide organ-centric spatial context to cells of an organ. We developed several general rules for the annotation of cell position and embodied them in 3DCoordX, a user-interactive computer toolbox implemented in the open-source software MorphoGraphX. 3DCoordX enables rapid spatial annotation of cells even in highly curved biological shapes. Using 3DCoordX, we analyzed cellular growth patterns in organs of several species. For example, the data indicated the presence of a basal cell proliferation zone in the ovule primordium of Arabidopsis (Arabidopsis thaliana). Proof-of-concept analyses suggested a preferential increase in cell length associated with neck elongation in the archegonium of Marchantia (Marchantia polymorpha) and variations in cell volume linked to central morphogenetic features of a trap of the carnivorous plant Utricularia (Utricularia gibba). Our work demonstrates the broad applicability of the developed strategies as they provide organ-centric spatial context to cellular features in plant organs of diverse shape complexity.

Spatial context is essential to draw biological insight from 3D image data, and 3DCoordX is an intuitive, open-source computational tool that provides this context for plant organs with complex shapes.     

Metabolite analysis for the comparison of irrigated and non-irrigated field grown tomato of varying genotype

Every year the consequences of water deficit on crop yield and quality are profound. The observation that many wild species relatives of cultivated crops display a greater stress tolerance and the fact that the cultivated species generally display only a fraction of the allelic diversity available within the tomato clade suggest that crossing of wild species with elite cultivars could improve the stress physiology of modern crops. To assess this from the basis of chemical composition we applied an established GC-MS based metabolite profiling method to fruits from irrigated and non-irrigated tomato plants either of the cultivated tomato (Solanum lycopersicum) or of its hybrid with its wild species relative (Solanum pennellii). Results are discussed in terms of both the metabolic response to drought stress and the potential of utilizing exotic germplasm as a means to improve agronomically important characteristics of crop species. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Assessment of genetic diversity patterns in Chilean quinoa (Chenopodium quinoa Willd.) germplasm using multiplex fluorescent microsatellite markers

Quinoa (Chenopodium quinoa Willd.) is a staple seed crop in the Andean region of South America. Improving quinoa productivity is a primary food-security issue for this region, and has been part of the impetus for the establishment of several new quinoa breeding programs throughout the Andean region. Chilean quinoa has been characterized as morphologically diverse and bifurcated into coastal and highland ecotypes. The success of emerging breeding programs will rely heavily on the development of core germplasm collections and germplasm evaluation—especially of the coastal quinoa ecotypes that are often neglected in traditional breeding programs. Thus, the objective of this study was to characterize and quantify the genetic diversity within 28 Altiplano and 31 coastal Chilean accessions of quinoa using microsatellite markers. To facilitate the analysis, we also report the development of seven sets of fluorescent multiplexed microsatellite PCR reactions that result in genetic information for 20 highly polymorphic microsatellite loci. A total of 150 alleles were detected among the quinoa accession, ranging from 2 to 20 alleles per locus and an average 7.5 allele/locus. Both cluster (UPGMA) and principal component analyses separated the accessions into two discrete groups. The first group contained quinoa accessions from the north (Andean highlands) and the second group consisted of accessions from the south (lowland or coastal). Three accessions from Europe were classified into the southern quinoa group. The data obtained in the diversity analyses highlights the relationships within and among northern and southern Chilean quinoa accessions and provides the quinoa scientific community with a new set of easy to use and highly informative genetic markers.     

Ex situ conservation of plant germplasm using biotechnology

Conservation of plant genetic resources attracts more and more public interest as the only way to guarantee adequate food supplies for future human generations. However, the conservation and subsequent use of such resources are complicated by cultural, economical, technical and political issues. Over the last 30 years, there have been significant increases in the number of plant collections and in accessions in ex situ storage centres throughout the World. The present review is of these ex situ collections and the contribution biotechnology has made and can make to conservation of plant germplasm. The applications and limitations of the new, molecular approaches to germplasm characterization are discussed. In vitro slow growth is used routinely for conserving germplasm of plants such as banana, plantain, cassava and potato. More recently, cryopreservation procedures have become more accessible for long-term storage. New cryopreservation techniques, such as encapsulation-dehydration, vitrification and desiccation, lengthen the list of plant species that can not only tolerate low temperatures but also give normal growth on recovery. Extensive research is still needed if these techniques are to be fully exploited.V.M. Villalobos is with the Food and Agriculture Organization of the United Nations, Viale delle Terme di Caracalia, 00100 Rome, Italy. F. Engelmann is with the International Plant Genetic Resources Institute (IPGRI), Via delle Sette Chiese 142, 00145 Rome, Italy.     

Strategies for agrobiodiversity conservation and promotion: a case from Yunnan, China

This paper deals with strategies for agrobiodiversity conservation and promotion based on studies on four plant groups (selected from 50 plant groups) occurring in the Yunnan Province of China. These plants are edible konjac (Amorphophallus), medicinal Paris, Musella lasiocarpa and wild tea (Camellia sinensis and its wild relatives), including their cultivars and wild populations. After analyzing the target plants, we conclude that the following strategies should be adopted to conserve and promote agrobiodiversity: (1) in situ conservation of agrobiodiversity, including habitat protection of wild populations, maintenance of native species and varieties in traditional agroecosystems, and relevant environmental education; (2) ex situ conservation and promotion of agrobiodiversity, including establishment of living collections and germplasm banks, and introduction of species and varieties into agroecosystems for agricultural practice; and (3) promotion and conservation of agrobiodiversity through sustainable uses, including technique development of propagation, cultivation, pest and disease control, on farm and off farm management, and other activities such as new variety breeding and scientific studies. Strategies developed here will be helpful to conserve and promote agrobiodiversity at agroecosystem, species, variety or landrace, and management system levels.     

The Fungal Genetics Stock Center in the context of a world wide community of ex situ fungal germplasm repositories

Most fungal biology researchers depend on culture collections, or more aptly, ex situ fungal germplasm repositories, either for the materials upon which they work, or as a long-term home for their materials after their projects are finished. These collections are broadly distributed and typically supported by the local government. The large number of collections, notwithstanding, some collections have greater impact than others. This review will discuss the fungal germplasm repositories around the world with special attention paid to the Fungal Genetics Stock Center. To facilitate their activities collections have joined together in networks, both locally and internationally. Additional information on public policy and how it impacts collections will be presented and the impact of collections will be highlighted.     

贵州特有植物长柱红山茶种群年龄结构及空间分布格局研究

为评估贵州特有植物长柱红山茶(Camellia mairei var.lapiden)的资源现状,采用样方法对其种群年龄结构和空间分布格局进行了研究。结果表明,长柱红山茶种群年龄结构为衰退型,种群密度以中龄树>老年树>幼龄树;不同发育阶段种群的空间分布格局不同,幼龄树和中龄树均呈显著集群分布,老年树接近集群分布或随机分布;种群的3个发育阶段之空间关系不密切,均表现为负相关或不相关。长柱红山茶由于其繁殖生物学特性和受其群落之种内、种间竞争及生境异质性的影响而趋于濒危和灭绝。因此,建立长柱红山茶就地保护区和开展引种栽培,扩大其栽培种植范围以增加种群数量是保护长柱红山茶种质资源的有效措施。