scholarly journals Linking Agrobiodiversity Data through Metadata Standards

2020 ◽  
Vol 4 ◽  
Author(s):  
Filipi Soares ◽  
Antonio Saraiva ◽  
Debora Drucker
Keyword(s):  
Genetic Marker ◽  
Food Production ◽  
Biological Diversity ◽  
Agricultural Research ◽  
Crop Wild Relatives ◽  
Wild Relatives ◽  
Food And Agriculture ◽  
Darwin Core ◽  
Metadata Standards

Agrobiodiversity, or biodiversity for food and agriculture, plays a major role in the sustainability of food production. As stated by FAO 2019, agrobiodiversity can provide food production systems and society with a variety of services as ecosystem services, crops resilience to threats, sustainable intensification, livelihoods, food security and nutrition. The official definition of the concept has been given by CBD 2000 as "a broad term that includes all components of biological diversity of relevance to food and agriculture, and all components of biological diversity that constitute the agroecosystem: the variety and variability of animals, plants and micro-organisms, at the genetic, species and ecosystem levels, which are necessary to sustain key functions of the agro-ecosystem, its structure and processes". Thus, agrobiodiversity is primarily based on species and their function in agroecosystems. Many projects for sharing agrobiodiversity data in a structured way have emerged over the years. One realizes in looking at the Bioversity International (2018) crop descriptors list that the earliest groups of descriptors for crops and some associated data emerged back in the 1970s. In the same list, there are four multi-crop descriptors and derived standards, which are broad standards for crop-related data, namely: Core descriptors for in situ conservation of crop wild relatives v.1 (Thormann et al. 2013); FAO/Bioversity multi-crop passport descriptors V.2.1 (Alercia et al. 2015); Descriptors for farmers' knowledge of plants (Aknazarov et al. 2009); Descriptors for Genetic Marker Technologies (Vicente et al. 2004). Core descriptors for in situ conservation of crop wild relatives v.1 (Thormann et al. 2013); FAO/Bioversity multi-crop passport descriptors V.2.1 (Alercia et al. 2015); Descriptors for farmers' knowledge of plants (Aknazarov et al. 2009); Descriptors for Genetic Marker Technologies (Vicente et al. 2004). These standards share some core elements in common, as taxon, location, a period of collecting, and were intended to be used in the context of data on the occurrence of species in nature. Darwin Core, a TDWG standard commonly used for sharing data of taxon occurrence in nature (Wieczorek et al. 2012), is a globally used metadata standard, representing "a large majority of the 1.4 billion of species occurrence records shared by the Global Biodiversity Information Facility (GBIF), published by more than 1561 organizations in 59 countries in January 2020" (Body et al. 2020). Darwin Core is a standardized language that applies unique Internationalized Resource Identifiers (IRIs) to each element assigned as a metadata element, plus a label and a definition. It improves the interoperability between databases in the context of the Semantic Web (Duerst and Suignard 2005). We believe it is possible to use Darwin Core to represent agrobiodiversity data if a metadata extension is developed to enroll the agrobiodiversity concepts missing in Darwin Core. Thus, a research project held at the University of São Paulo in partnership with Brazilian Agricultural Research Corporation started to map concepts and descriptors from the literature for agrobiodiversity data representation. This project is the sequence of the research initiated by Soares et al. 2019. The crop descriptors published by Bioversity International (2018) may be integrated into the metadata extension, but also other standards like Global Genome Biodiversity Network (GGBN) Data Standard v1 (Droege et al. 2016) and the Darwin Core germplasm extension (DwC-germplasm). At the moment, we are designing a mind map to organize the agrobiodiversity concepts. We expect the metadata extension will be useful for the scientific community to share agrobiodiversity data as linked data, applying Resource Description Framework (RDF) as a resource relationship model, for example.

Conservation gap analysis of crop wild relatives in Turkey

2019 ◽  
Vol 17 (2) ◽  
pp. 164-173 ◽  
Author(s):  
Necla Tas ◽  
George West ◽  
Gun Kircalioglu ◽  
S. Boyraz Topaloglu ◽  
Jade Phillips ◽  
...  
Keyword(s):  
Gap Analysis ◽  
Agricultural Research ◽  
Crop Wild Relatives ◽  
Wild Relatives ◽  
Ex Situ ◽  
Wild Plant ◽  
Taxon Richness ◽  
Central Research ◽  
Research Institute

AbstractCrop wild relatives (CWR) are wild plant taxa relatively closely related to crops that can contribute beneficial traits for crop improvement, such as biotic and abiotic stress resistance. Turkey has a rich flora of approximately 11,000 higher plant taxa, has two Vavilov centres of crop diversity (i.e. the Mediterranean and the Near East), is recognized as the cradle of agriculture providing the northern boundary of the Fertile Crescent, and has recently been identified as the country with the highest concentration of CWR diversity. The objective of this paper is to present the results of a gap analysis of CWR genetic diversity in Turkey using existing data sources of 458 of the 764 priority CWR taxa with available georeferenced data. In total, 27,597 presence points were obtained from the Global Biodiversity Information Facility, Aegean Agricultural Research Institute in Menemen and Field Crops Central Research Institute, Ankara. Geographic Information System (GIS) software was used to identify taxon richness, sampling bias, future ex situ population collection and location where existing protected sites could form the basis of national network of in situ genetic reserves. CWR taxon richness was located along the Aegean Coast, Syrian border and southern Mediterranean coast. Current ex situ representation of CWR taxa is inadequate and further collection across the entire country is required. The highest priority in situ reserve location is found in Izmir, Sanliurfa and Antalya province, which reflects overall CWR richness.

scholarly journals Darwin Core for Agricultural Biodiversity: A metadata extension proposal

2019 ◽  
Vol 3 ◽  
Author(s):  
Filipi Soares ◽  
Benildes Maculan ◽  
Debora Drucker
Keyword(s):  
Biological Diversity ◽  
Agricultural Research ◽  
Convention On Biological Diversity ◽  
Biological Interactions ◽  
Agricultural Biodiversity ◽  
Biodiversity Data ◽  
Standard Format ◽  
Darwin Core ◽  
Metadata Standards ◽  
Biodiversity Information

Agricultural Biodiversity has been defined by the Convention on Biological Diversity as the set of elements of biodiversity that are relevant to agriculture and food production. These elements are arranged into an agro-ecosystem that compasses "the variability among living organisms from all sources including terrestrial, marine and other aquatic ecosystems and the ecological complexes of which they are part: this includes diversity within species, between species and of ecosystems" (UNEP 1992). As with any other field in Biology, Agricultural Biodiversity work produces data. In order to publish data in a way it can be efficiently retrieved on web, one must describe it with proper metadata. A metadata element set is a group of statements made about something. These statements have three elements, named subject (thing represented), predicate (space filled up with data) and object (data itself). This representation is called triples. For example, the title is a metadata element. A book is the subject; title is the predicate; and The Chronicles of Narnia is the object. Some metadata standards have been developed to describe biodiversity data, as ABCD Data Schema, Darwin Core (DwC) and Ecological Metadata Language (EML). The DwC is said to be the most used metadata standard to publish data about species occurrence worldwide (Global Biodiversity Information Facility 2019). "Darwin Core is a standard maintained by the Darwin Core maintenance group. It includes a glossary of terms (in other contexts these might be called properties, elements, fields, columns, attributes, or concepts) intended to facilitate the sharing of information about biological diversity by providing identifiers, labels, and definitions. Darwin Core is primarily based on taxa, their occurrence in nature as documented by observations, specimens, samples, and related information" (Biodiversity Information Standards (TDWG) 2014). Within this thematic context, a master research project is in progress at the Federal University of Minas Gerais in partnership with the Brazilian Agricultural Research Corporation (EMBRAPA). It aims to apply the DwC on Brazil’s Agricultural Biodiversity data. A pragmatic analysis of DwC and DwC Extensions demonstrated that important concepts and relations from Agricultural Biodiversity are not represented in DwC elements. For example, DwC does not have significant metadata to describe biological interactions, to convey important information about relations between organisms in an ecological perspective. Pollination is one of the biological interactions relevant to Agricultural Biodiversity, for which we need enhanced metadata. Given these problems, the principles of metadata construction of DwC will be followed in order to develop a metadata extension able to represent data about Agricultural Biodiversity. These principles are the Dublin Core Abstract Model, which present propositions for creating the triples (subject-predicate-object). The standard format of DwC Extensions (see Darwin Core Archive Validator) will be followed to shape the metadata extension. At the end of the research, we expect to present a model of DwC metadata record to publish data about Agricultural Biodiversity in Brazil, including metadata already existent in Simple DwC and the new metadata of Brazil’s Agricultural Biodiversity Metadata Extension. The resulting extension will be useful to represent Agricultural Diversity worldwide.

scholarly journals Status of the Ex Situ and In Situ Conservation of Brazilian Crop Wild Relatives of Rice, Potato, Sweet Potato, and Finger Millet: Filling the Gaps of Germplasm Collections

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 638
Author(s):  
Marcelo B. Medeiros ◽  
José F. M. Valls ◽  
Aluana G. Abreu ◽  
Gustavo Heiden ◽  
Suelma Ribeiro-Silva ◽  
...  
Keyword(s):  
Finger Millet ◽  
Ex Situ Conservation ◽  
Gap Analysis ◽  
In Situ Conservation ◽  
Germplasm Collection ◽  
Crop Wild Relatives ◽  
Wild Relatives ◽  
Ex Situ ◽  
The Status

This study presents the status of ex situ and in situ conservation for the crop wild relatives of rice, potato, sweet potato, and finger millet in Brazil, and the subsequent germplasm collection expeditions. This research is part of a global initiative entitled “Adapting Agriculture to Climate Change: Collecting, Protecting, and Preparing Crop Wild Relatives” supported by the Global Crop Diversity Trust. Species of the primary, secondary, and tertiary gene pools with occurrences reported in Brazil were included: Oryza alta Swallen, O. grandiglumis (Döll) Prod., O. latifolia Desv., O. glumaepatula Steud., Eleusine tristachya (Lam.) Lam., E. indica (L.) Gaertn., Solanum commersonii Dunal, S. chacoense Bitter, Ipomoea grandifolia (Dammer) O’Donell, I. ramosissima (Poir.) Choisy, I. tiliacea (Willd.) Choisy, I. triloba L., and I. cynanchifolia Meisn. The status of the ex situ and in situ conservation of each taxon was assessed using the gap analysis methodology, and the results were used to plan 16 germplasm collection expeditions. Seeds of the collected material were evaluated for viability, and the protocols for seed germination and cryopreservation were tested. The final conservation score, resulting from the gap analysis and including the average of the ex situ and in situ scores, resulted in a classification of medium priority of conservation for all the species, with the exception of I. grandifolia (high priority). The total accessions collected (174) almost doubled the total accessions of these crop wild relatives incorporated in Embrapa’s ex situ conservation system prior to 2015. In addition, accessions for practically absent species were collected for the ex situ conservation system, such as Ipomoea species, Eleusine indica, and Solanum chacoense. The methods used for dormancy breaking and low temperature conservation for the Oryza, Eleusine, and Ipomoea species were promising for the incorporation of accessions in the respective gene banks. The results show the importance of efforts to collect and conserve ex situ crop wild relatives in Brazil based on previous gap analysis. The complementarity with the in situ strategy also appears to be very promising in the country.

Spatial analyses of occurrence data of crop wild relatives (CWR) taxa as tools for selection of sites for conservation of priority CWR in Zambia

2019 ◽  
Vol 17 (2) ◽  
pp. 103-114 ◽  
Author(s):  
Dickson Ng'uni ◽  
Graybill Munkombwe ◽  
Godfrey Mwila ◽  
Hannes Gaisberger ◽  
Joana Magos Brehm ◽  
...  
Keyword(s):  
Crop Improvement ◽  
Sustainable Use ◽  
Crop Wild Relatives ◽  
Wild Relatives ◽  
Ex Situ ◽  
Relative Distribution ◽  
Spatial Analyses ◽  
Threat Status ◽  
Occurrence Data

AbstractCrop wild relatives (CWR) are valuable gene pools for crop improvement and offer unique potential and opportunity for enhancing food security and adaptation to climate change. However, current actions towards conservation of plant genetic resources in Zambia do not adequately cover CWR occurring in the country. The article describes the process leading to the development of a national strategic action plan (NSAP) for the conservation and sustainable use of priority CWR in Zambia. Based on 59 prioritized crops, a partial checklist of 459 CWR taxa was generated from the national flora checklist of 6305 taxa. The generated CWR taxa were prioritized based on the socio-economic value of the related crop, their utilization potential in crop improvement, relative distribution and threat status to produce 30 prioritized CWR taxa. Occurrence data were compiled for all CWR inventory taxa and used in spatial analyses to establish species distribution, species richness, gaps in in situ conservation and genebank collections, and to identify priority sites for in situ conservation and ex situ collecting. Consistent with the national developmental agenda, along with the contribution of national stakeholders, spatial analyses of occurrence data of priority CWR taxa are valuable input for the development of the NSAP for the conservation and sustainable use of the priority CWR.

scholarly journals In situ and ex situ conservation gap analyses of crop wild relatives from Malawi

2020 ◽  
Author(s):  
Nolipher Khaki Mponya ◽  
Tembo Chanyenga ◽  
Joana Magos Brehm ◽  
Nigel Maxted
Keyword(s):  
Ex Situ Conservation ◽  
Plant Genetic Resources ◽  
Crop Wild Relatives ◽  
Wild Relatives ◽  
Conservation Strategy ◽  
Ex Situ ◽  
Grid Cells ◽  
Ex Situ Collections ◽  
Minimum Number

Abstract The study analysed the conservation gaps of the priority crop wild relatives (CWR) taxa for Malawi in order to contribute to the development of a harmonized conservation strategy that helps secure the priority CWR under in situ and ex situ. We used taxa distribution modelling, complementarity analysis and ecogeographic land characterization map to analyse spatial diversity and distribution of 123 priority taxa across different adaptive scenarios. We identified areas of observed and predicted richness, the minimum number of protected areas (PAs) that conserve the broadest ecogeographic diversity in situ and the minimum number of grid cells that capture highest diversity outside PAs to recommend the establishment of genetic reserves. We then analysed the representativeness of the conserved ecogeographic diversity of target taxa in ex situ collections to identify ex situ conservation gaps and advise for priority areas for ex situ collections. For the 123 taxa, 70.7% of the total diversity occurs in 36 PAs with 66.8% of the diversity captured in only 10 complementary PAs. Outside PAs, the broadest diversity was conserved in three grid cells of size 5 × 5 km. Fifty-three of 123 taxa have ex situ collections with only three taxa having ex situ collections at the Malawi Plant Genetic Resources Centre. The findings of this study will guide formulation of conservation actions for the priority taxa as well as lobbying for active conservation of the same under in situ and ex situ.

scholarly journals CROP WILD RELATIVES IN VOLOGDA PROVINCE, RECOMMENDED FOR IN SITU CONSERVATION

VAVILOVIA ◽  
2019 ◽  
Vol 2 (1) ◽  
pp. 12-30
Author(s):  
L. Yu. Shipilina
Keyword(s):  
In Situ Conservation ◽  
Crop Wild Relatives ◽  
Wild Relatives ◽  
Ex Situ ◽  
Endangered Plants ◽  
Economic Traits ◽  
Species Vulnerability ◽  
Priority Method ◽  
Rare And Endangered

Background. Preservation of crop wild relatives (CWR) as natural suppliers of genetic source material (GSM) is the foundation of food security. In situ conservation is considered the highest priority method. By preserving species in their natural communities, we safeguard all the genetic diversity that can be used as sources of valuable economic traits. The criteria developed by the International Union for Conservation of Nature and Natural Resources (IUCN) are unable to assess the significance of crop wild relatives at the regional level. With this in view, we have used the vulnerability status categories developed at VIR. Materials and methods. Crop wild relatives of Vologda Province were the target of the study. Research material was selected in VIR’s herbarium collection (WIR, LE), along with literary data and the results of the plant exploration surveys by VIR’s scientists. The species listed in the Red Books of Leningrad, Pskov and Novgorod Provinces, the Red Book of Karelia, and the list of rare and endangered plants (2015) of Vologda Province were analyzed. For the first time, plants were tested specifically to determine the species’ vulnerability degree. On the basis of such testing, CWR requiring special conservation measures were identified. Results and conclusions. Sixty-six CWR species that require in situ conservation occur in Vologda Province. The collected materials helped to develop databases of locations for the taxa studied. In total, we identified nine species with the vulnerability status of Category I (Corylus avellana L., Onobrychis arenaria (Kit.) Ser., Phleum phleoides (L.) Karst., Thymus talijevii Klok. Et Shost., Bistorta vivipara (L.) S.F. Gray, Gypsophila fastigiata L., Koeleria glauca (Spreng.) DC., Leymus arenarius (L.) Hochst., and Scorzonera glabra Rupr.). Maps of the species with the first vulnerability status category were made. Category II was assigned to 19 species; Category III, to 38 species. The species requiring special conservation efforts were identified: relicts (11 spp.) and endemics (1 sp.). Twenty-eight species are in the list of rare and endangered plants (2015) of Vologda Province. Nizhnesukhonsky floristic area stands out for its rich CWR diversity. In addition to in situ conservation within protected areas of various ranks, the species included into Categories I and II should be conserved ex situ in botanical gardens and genetic collections held by research institutes in the northwest of Russia.

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