The ImageCLEF 2013 Plant Identification Task

International audienceThe ImageCLEF's plant identification task provides a testbed for a system-oriented evaluation of plant identification about 250 species trees and herbaceous plants based on detailed views of leaves, flowers, fruits, stems and bark or some entire views of the plants. Two types of image content are considered: SheetAsBackgroud which contains only leaves in a front of a generally white uniform background, and NaturalBackground which contains the 5 kinds of detailed views with unconstrained conditions, directly photographed on the plant. The main originality of this data is that it was specifically built through a citizen sciences initiative conducted by Tela Botanica, a French social network of amateur and expert botanists. This makes the task closer to the conditions of a real-world application. This overview presents more precisely the resources and assessments of task, summarizes the retrieval approaches employed by the participating groups, and provides an analysis of the main evaluation results. With a total of twelve groups from nine countries and with a total of thirty three runs submitted, involving distinct and original methods, this third year task confirms Image Retrieval community interest for biodiversity and botany, and highlights further challenging studies in plant identification

Examination of morphological and habitat variation within Stenanthium gramineum (Eastern Featherbells, Melanthiaceae)

Stenanthium gramineum (Ker. Gawler) Morong (Melanthiaceae) has historically been an understudied species. This species is generally considered to consist of two varieties: var. gramineum, a habitat generalist, occurring on grassy balds, rock outcrops, and in dry and mesic woodlands, and var. robustum, a habitat specialist, occurring in mountain bogs and wet meadows. A third variety, var. micranthum is not formally recognized, but was described on the basis of its small stature and unique granitic dome habitat. However, many taxonomists do not recognize any of the varieties, suggesting that they are indistinct and sympatric. The purpose of this study was to determine if the three varieties of Stenanthium gramineum should be recognized as distinct entities, and at what taxonomic rank each should be recognized. I performed morphological and ecological analyses of the three varieties of S. gramineum, including taking macro and micro morphological measurements from the field and from herbarium specimens, as well as measuring ecological characters of the field sites I visited. I then ran univariate and multivariate statistical analyses on the data collected to aid in clarifying the taxonomy of S. gramineum varieties. Results suggest that var. robustum should be elevated to species level, based on morphological separation, while var. micranthum should be recognized as a taxon discrete from the typical var. gramineum. The findings in this study emphasize the need for conservation of all varieties, as anthropogenically caused changes threaten their habitats. This is especially critical in the case of var. robustum, a mountain bog specialist of the Appalachians

The ImageCLEF 2013 Plant Identification Task

International audienceThe ImageCLEF's plant identification task provides a testbed for a system-oriented evaluation of plant identification about 250 species trees and herbaceous plants based on detailed views of leaves, flowers, fruits, stems and bark or some entire views of the plants. Two types of image content are considered: SheetAsBackgroud which contains only leaves in a front of a generally white uniform background, and NaturalBackground which contains the 5 kinds of detailed views with unconstrained conditions, directly photographed on the plant. The main originality of this data is that it was specifically built through a citizen sciences initiative conducted by Tela Botanica, a French social network of amateur and expert botanists. This makes the task closer to the conditions of a real-world application. This overview presents more precisely the resources and assessments of task, summarizes the retrieval approaches employed by the participating groups, and provides an analysis of the main evaluation results. With a total of twelve groups from nine countries and with a total of thirty three runs submitted, involving distinct and original methods, this third year task confirms Image Retrieval community interest for biodiversity and botany, and highlights further challenging studies in plant identification

Genetic and Phenotypic Variation in Tree Crops Biodiversity

Recently, there has been a dramatic increase in the use of DNA-derived data and innovative phenotyping to obtain insights into the causative genes underlying traits of agronomical interest or to characterize tree genetic resources. The latter, in particular, could represent an important source of genetic diversity that can be readily used to enhance the adaptability to limiting environmental factors and resistance to biotic stresses or to promote novel genotypes with improved agronomic traits. On the whole, the studies collected in this book report on tree crop biodiversity characterization that could provide the essential building blocks to ensure future improvements in production and quality, as well as for innovations in tree crop development and utilization

Breeding for resilience: a strategy for organic and low-input farming systems?

Global change is increasingly affecting agricultural production and threatening food security. Organic and low-input farming systems are less demanding in fossil energy and might thus contribute to moderating global carbon missions. Moreover, under increased uncertainty and variability in environmental conditions, these systems offer solutions for buffering against climatic extremes, disease epidemics, changing nutrient availability, and other stresses that will add to already heterogeneous environmental conditions. 2010 has been designated the Biodiversity Target year by Parties to the Convention on Biological Diversity. Yet, it is clear that biological diversity in agroecosystems, measured as the number and abundance of species as well as genetic diversity within cultivated plants, is still decreasing, largely due to the negative impacts of intensive industrial agriculture. Overall, ecosystem services delivered by biodiversity such as plant disease control, soil fertility and pollination are jeopardized by its decline. These threats present an opportunity for the organic sector to develop original and innovative strategies for biodiversity preservation and increased resilience in the field. The second EUCARPIA meeting of the Section Organic plant breeding and low-input agriculture organised in Paris, France, from the 1st to the 3rd of December 2010, by INRA – UMR Génétique Végétale Le Moulon and ITAB, wishes to take inspiration from the ecological sciences to highlight the use of biodiversity in agriculture while taking advantage of the new tools coming from genomics. Therefore, the symposium will deal with breeding strategies for organic and low-input farming systems with a special emphasis on approaches that allow for more resilience in response to global change. Some 130 participants representing 20 countries will attend the symposium, including students, researchers and other professionals from universities, institutes, breeding companies, governemental institutions, Non Governemental Organizations and farmers. The programme features 30 oral and 37 poster presentations, covering the following areas: · Improving resilience of agro-ecosystems · Utilizing and conserving agrobiodiversity in agricultural landscape · Global change and adaptability · New insights into the mechanisms of adaptation to local conditions and organic farming · Breeding for diverse environments and products · Regional participatory plant breedin

Moorland and bracken change in the North York Moors : an investigation using remote sensing.

SIGLEAvailable from British Library Document Supply Centre- DSC:D89387 / BLDSC - British Library Document Supply CentreGBUnited Kingdo

Breeding F1 Hybrid Varieties of Leaf Chicory Through Marker-Assisted Selection Schemes

Cichorium (Cichorium intybus subsp. intybus var. foliosum L.) comprises diploid plant species (2n=18) belonging to the Asteraceae family. These species are biennial or, in the wild, perennial species. They are naturally allogamous due to an efficient sporophytic self-incompatibility system. In addition, outcrossing is promoted by a floral morpho-phenology unfavorable to selfing in the absence of pollen donors (i.e., proterandry, wherein the anthers mature before the pistils) and a favorable competition of allo-pollen grains and tubes (i.e., pollen that is genetically diverse from that produced by the seed parents, usually called auto-pollen). Long appreciated as medical plants by the ancient Greeks and Romans, Cichorium spp. are currently among the most important cultivated vegetable crops. They are generally used as components in fresh salads or, more rarely, cooked according to local traditions and alimentary habits. Although this crop does not contribute greatly to the total agricultural income of each country, it is very important at the local level, as it characterizes the agriculture of limited areas, where from 80 to 90% of the country’s production is concentrated. This is indeed the case of Italy, where the Veneto region accounts for 66% of the national acreage and 59% of the national production of the particular type of red or variegated chicory known as “Radicchio”. Radicchio production was for a long time based on farmer’s populations, which are yearly selected and maintained and whose seed is usually reutilized on farm but may also be sold through private and not officially registered transactions. All these populations, obtained by mass selection and maintained through the inter-crossing of selected parents, have to be considered highly heterozygous and genetically heterogeneous whose behaviour and level of adaptation to different environments and/or cultural conditions depend on the frequency of favourable genes or gene combinations. In each breeding program, selection schemes and methods that can be used and the varietal types than can be breed, depend on plant reproductive barriers (e.g. self-incompatibility) and pollination system (e.g. allogamous), and thus on the genetic structure of populations. As a matter of fact, the strong self-incompatibility system found in chicory hinders obtaining highly homozygous parents, made it generally difficult to propose an efficient F1 seed production scheme. Despite the difficulties encountered in obtaining inbred lines by repeated selfing, the recent discovery of spontaneous male-sterile mutants increased the interest towards the production of F1 hybrid varieties. Indeed, male-sterility, or the inability of plants to produce functional pollen, is needful to the commercial production of hybrid seed by crossing parental inbred lines appropriately selected through progeny tests for assessing their specific combining ability. In this project we developed a genotyping method using molecular markers, useful for assessing the homozygosity and genetic stability of single inbred lines and for measuring the specific combining ability between maternal and paternal inbred lines on the basis of their genetic diversity. This information could be exploited for planning crosses and predicting the heterosis of experimental F1 hybrids on the basis of the allelic divergence and genetic distance of the parental lines. Knowing the parental genotypes would enable not only to protect newly registered varieties but also to assess the genetic purity and identity of the seed stocks of commercial F1 hybrids, and to certificate the origin of their food derivatives. Modern marker-assisted breeding (MAB) technology based on traditional methods using molecular markers such as SSRs and SNPs, without relations to genetic modification (GM) techniques, will now be planned and adopted for breeding of vigorous and uniform F1 hybrids combining quality, uniformity, and productivity traits in the same genotypes. Furthermore, this research project deals with the discovery and genetic analysis of four male-sterile mutants in this species. These mutants, which to the best of our knowledge are the first spontaneous male-sterile mutants ever discovered and described in Radicchio, were characterized in great details for the developmental pathway of micro-sporogenesis and gametogenesis, and the inheritance pattern of the gene underlying the male-sterility trait. A quick molecular diagnostic assay was also developed for the early marker-assisted selection of the genotype associated to male-sterile plants. Hence, male-sterile mutants object of this PhD project were demonstrated to be controlled by a single nuclear gene (ms1) that acts at the recessive status. We were able to map the male-sterility gene on a well saturated and characterized linkage group in a chromosomal region spanning 7.3 cM and 5.8 cM from the ms1 locus. On the whole, this information was crucial to plan a Genotyping-by-Sequencing experiment based on BC1 progenies with the aim of narrowing down the genomic window containing the gene for male-sterility in leaf chicory. Finally, the sequencing and assembly of the first genome draft of leaf chicory, will contribute to increase and reinforce the reliability of Italian seed firms and local activities of the Veneto region associated with the cultivation and commercialization of Radicchio plant varieties and food products; the seed market of this species will have the chance to become highly professional and more competitive at the national and international levels. We assembled a genome draft of an estimated size of 760 Mb. We obtained 58,392,530 and 389,385,400 raw reads through the MySeq and HiSeq platforms, respectively. Overall, we identified 66,785 SSR containing regions. Original data from the bioinformatic assembly of the first genome draft of Radicchio, along with the most relevant findings that emerged from an extensive de novo gene prediction and in silico functional annotation of more than 18,000 unigenes are critically discussed. To uncover the sequence of a given genome means to gain a robust scientific background and technological knowhow, which in short time can play a crucial role in addressing and solving issues related to the cultivation and protection of modern Radicchio varieties. In fact, we are confident that our efforts will extend the current knowledge of the genome organization and gene composition of leaf chicories, which is crucial in the development of new tools and diagnostic markers useful for our breeding strategies, and allow researchers for more focused studies on chromosome regions controlling relevant agronomic traits of Radicchio. In conclusion, the present work is a sort of handbook to better understand the world of a non-model species, i.e. leaf chicory, and it is mainly directed to breeders and seed producers dealing with leaf chicory

Isolation and Analysis of Characteristic Compounds from Herbal and Plant Extracts

Herbal and plant extracts show diverse activities and have been used for centuries as natural medicines for many health problems and diseases. Through the isolation and analysis of the compounds in the extracts, it is possible to understand why the extracts exhibit those activities, as well as the chemical metabolism of compounds that occur in plants and herbs. Recently, there have been increasing attempts to develop herbal and plant extracts into functional foods and drugs, but the legal requirements are becoming stricter. We need sophisticatedly defined extracts through the isolation and analysis of compounds comprising them in order to meet the legal requirements and to pursue quality control strategies in the production of functional foods and drugs. This Special Issue Book compiled the 15 recent research and review articles that highlight the isolation, profiling, and analysis of compounds in herbal and plant extracts, as well as quality control and standardized processing strategies for extracts with characteristic compounds