CWR In Situ Strategy Helpdesk

Data sources

Taxonomic data

The first stage in the CWR conservation strategy process is to delineate the taxa to be conserved. To do this, the first step is to make a decision on which taxonomic classification to adopt. For some crop gene pools or national floras, there may be a classification that is generally widely accepted by specialists in that group, while for others, there may not be general agreement.

To find out which classifications are available, a number of online resources can be consulted, as well as monographs, Floras, journal articles and grey literature. Whichever classification is chosen, a reference should be provided and synonyms and authorities listed for all taxa in the gene pool/national inventory. This is important for users of the information who recognize an alternative classification.

Part of the second stage in the crop gene pool conservation process (selection of target taxa) involves classification of the taxa according to their degree of relationship to the crop. To find this information, it is necessary to search the literature, as online databases do not generally provide information about genetic or taxonomic relatedness. For the major crops, this information is likely to be fairly easy to find, while for the minor crops it can prove more difficult as there is likely to have been less research carried out. Whatever the crop, it is worth undertaking thorough bibliographic searches to obtain the information required. Note that taxonomic databases generally do not include the taxonomic hierarchy below genus and above species in their structure (i.e., sections and series may be included, but there are generally no links between these levels and the species); therefore, when applying the Taxon Group concept, it is necessary to refer to printed publications (usually monographs or Floras) containing the classification.

Some key sources of taxonomic data are listed below, along with a brief outline of the scope of the resource and how to access the data required.

Online resources

Crop Wild Relative Catalogue for Europe and the Mediterranean –http://www.pgrforum.org/cwris/cwris.asp

For Euro-Mediterranean taxa, the Crop Wild Relative Catalogue for Europe and the Mediterranean (Kell et al., 2005) can be consulted to find the accepted classification used by the Euro+Med PlantBase project (version August 2005). Euro+Med PlantBase is currently not fully accessible online for direct use, as taxonomists are currently reviewing and refining the data*. However, the taxonomic data in Euro+Med PlantBase (version August 2005) form the taxonomic core of the Crop Wild Relative Catalogue, which can be accessed via CWRIS (the Crop Wild Relative Information System).

To access the taxonomic data:

  • Follow the link above and click on the link 'PGR Forum CWR Catalogue for Europe and the Mediterranean'
  • To view a list of genera contained in the Catalogue, click on 'taxonomy', then 'genera'
  • Click on the genus of interest to find a list of species—subspecies can be viewed by clicking on a species

All the information needed can be found here, including synonyms and authorities (except that authorities are not available for some subspecies and will have to be looked up elsewhere), but if you wish to view the original source of taxonomic data (Euro+Med PlantBase), click on the link shown to 'original data source'. Here you will find the nomenclatural reference for individual taxa.

If the Crop Wild Relative Catalogue is used to delineate the taxa, the taxonomic reference should be the original source of taxonomic data, which is Euro+Med PlantBase version August 2005, while also referencing the Catalogue as the point of access. In this case, the reference might read:

'Euro+Med PlantBase (2005) Euro+Med PlantBase: The Information Resource for Euro-Mediterranean Plant Diversity. Dipartimento di Scienze botaniche ed Orto botanico, Università degli Studi di Palermo. Available at: http://www.emplantbase.org/home.html, accessed via the Crop Wild Relative Catalogue for Europe and the Mediterranean, available online via the Crop Wild Relative Information System (http://www.pgrforum.org/cwris/cwris.asp), 11 March 2008.'

*Note that as of October 2009, taxonomic and distribution data for several families contained in Euro+Med PlantBase are now available directly from: http://ww2.bgbm.org/EuroPlusMed/query.asp. For the families that have been updated, it is recommended that data are checked directly from this source as the CWR Catalogue for Europe and the Mediterranean has not yet been updated with the revised data set.

GBIF (Global Biodiversity Information Facility) – http://data.gbif.org/welcome.htm

As well as providing access to taxon occurrence records (see page ‘distribution data’), GBIF provides information on nomenclature and classification. To access this information:

  • Enter the crop genus name into the search facility and follow the link provided to access information on that taxon
  • Click on the link ‘names and classification’ to reveal a list of taxa in the genus. At the top of the page, you will see a reference for this classification: ‘according to: The Global Biodiversity Information Facility: GBIF Data Portal Classification (based on Catalogue of Life Annual Checklist, with provisional additions from specimen and observation data resources)'
  • Click on ‘classifications of <taxon name>' to find information on alternative classifications

A list of classifications will be presented. Follow the link provided for information on the classification. In each case, the reference for the classification will be shown at the top of the page.

GRIN Taxonomy for Plants– http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl

GRIN taxonomic data provide the structure and nomenclature for accessions of the National Plant Germplasm System (NPGS), part of the National Genetic Resources Program (NGRP) of the United States Department of Agriculture's (USDA's) Agricultural Research Service (ARS). In GRIN Taxonomy for Plants, all families and genera of vascular plants and over 40,000 species from throughout the world are represented—especially economic plants and their relatives. Information on scientific and common names, classification, distribution, references and economic impacts are provided.

GRIN Taxonomy for Plants can be used as a taxonomic reference, as well as to delimit taxa geographically.

As noted in GRIN Taxonomy:

'National Germplasm Resources Laboratory (NGRL) botanists are responsible for maintaining the taxonomic and nomenclatural integrity of the scientific names in GRIN. Through ongoing research into all current taxonomic literature, consultations with taxonomic botanists, and systematic reviews of GRIN scientific names for various plant families, the most recent taxonomy and nomenclature are incorporated into GRIN. For major crop genera, GRIN taxonomic work may often involve interaction with other USDA scientists for those crops and their Crop Germplasm Committees (CGC). The taxonomic and nomenclatural decisions accepted in GRIN are based on various considerations. Ideally, the taxonomy reflects the views of recognized taxonomic specialists for various plant groups as determined from published literature, such as monographs, revisions, or contributed treatments to Floras, or from direct consultation for review of GRIN taxonomic information. When a specialist or specialist-generated literature is lacking, taxonomic decisions must be based on the floristic literature. Floras are generally assigned greater weight than checklists, and modern Floras are given greater consideration than older ones in preparing the GRIN treatment. Other considerations being equal, when there are differences in taxonomic treatment or nomenclatural disputes, the GRIN treatment would generally be guided by current usage. In serving the agricultural scientists of NPGS, it is necessary to consider usage among agronomists and horticulturalists in addition to that of taxonomists. A requirement, however, is that all nomenclature adhere to the rules of the International Code of Botanical Nomenclature (Greuter et al., 2000).'

Data in GRIN Taxonomy can be searched online or downloaded.

Onine searches: To access taxonomic data via GRIN, click on the 'queries' link in the menu bar to search for information on your taxon of interest. At genus level, if you use the ‘simple queries – species data, single criterion’ search facility, you will see a list of all names contained in the database within that genus. Accepted names according to GRIN Taxonomy are highlighted in bold. You can refine your search using the 'advanced queries – species data, multiple criteria' option.  Here, you can limit the results to only provide accepted names within the genus.

Data downloads: GRIN Taxonomy data can be downloaded to your hard drive and searched using a suitable database. To do this, click on the 'downloads' link on the menu bar and follow the instructions given. The data are provided as zip files and for each one, a 'last modified' date is provided.

A standalone version of the GRIN database called pcGRIN is also available for individual crops. To use pcGRIN go to: http://www.ars-grin.gov/npgs/pcgrin.html and follow the instructions provided. You will download and install the software and then select and install the crop datasets separately. The individual crop datasets show a last modfied date.

The disadvantage of using downloaded data is that if searches are required at a later date, it may be necessary to refresh the data by downloading updated files.

Mansfeld’s World Database of Agricultural and Horticultural Crops – http://mansfeld.ipk-gatersleben.de/

Mansfeld’s World Database of Agricultural and Horticultural Crops (Hanelt and IPK Gatersleben, 2001; IPK Gatersleben, 2003) contains more than 6100 cultivated species of agricultural and horticultural plants worldwide, including medicinal and aromatic plants, but with the exception of ornamental and forestry plants. The database also includes cultivated algae and fungi, pteridophyta and gymnosperms.

Mansfeld’s Database can be used as a taxonomic reference, following the accepted taxonomy in Mansfeld’s Encyclopedia of Agricultural and Horticultural Crops (Hanelt and IPK Gatersleben, 2001).

To find a list of taxa in the crop genus:

  • Follow the link above and select ‘database query’
  • Select ‘query for names’
  • Enter the genus name under ‘scientific name’ and press ‘search’—a list of all taxa in the genus will be returned, with authorities—you can also limit the search to include accepted names only
  • Click on the links to the taxon names to find a list of synonyms and references

Kew Bibliographic Databases (KBD) – http://kbd.kew.org/kbd/searchpage.do

KBD provides access to three databases: Kew Record of Taxonomic Literature, Economic Botany and Plant Micromorphology. To find taxonomic references, enter the taxon name into the search field and refine the search to ‘Kew Record of taxonomic Literature’ and ‘Economic Botany’.

This is a useful resource for obtaining information on taxonomic classifications used as well as genetic and/or taxonomic relatedness.

Other taxonomic data sources

It may be necessary to consult Floras, monographs and journal articles to obtain the taxonomic information needed on the crop gene pool. This is particularly the case for minor crops, but also for obtaining information on the degree of relationship of the wild relatives to the crop (either taxonomic or genetic) for both major and minor crop groups.

To search for taxonomic references, use online library databases, such as:

Some of the larger universities also offer online library search facilities that can be useful for obtaining references. It is usually possible to read the abstract of the article, even if you do not have access to the full text of an e-journal. Open access materials are also increasingly available.

A further important resource is taxon experts. It is sometimes possible to contact a taxon expert directly for guidance (e.g., recent publications, the most recent generally accepted classification, genetic information etc.). Taxon experts can be found by contacting herbaria or gene banks containing major collections of the crop group, or via author contact details published in peer-reviewed journal articles or books, or by searching for a person via the institute they are associated with on the internet. Many large research organizations have personnel databases available online, which provide contact details—usually an email address and possibly a phone number.

Data sources introduction > Taxonomic data > Distribution data > Conservation data > Environmental data

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