Germplasm is a term used to describe living genetic resources such as seeds or tissue, maintained for the purpose of breeding, preservation, and other research uses because it contains the information for a species’ genetic makeup, a valuable natural resource of plant diversity.
Genetic diversity of germplasm gives plant breeders the sustained ability to develop new high yielding, high quality varieties that can resist constantly evolving pests, diseases and environmental stresses. Sexually compatible wild species and landraces – ancestral varieties of crop species- are the key to genetic diversity. This is why plant genetic resources programs gather, preserve, evaluate, catalogue and distribute germplasm for people all over the world. The germplasm banks use descriptors to describe the germplasm and keep associated records. Germplasm collections can range from collections of wild species to elite, domesticated breeding lines that have undergone extensive breeders’/farmers’ selection.
- Data format: use data matrices in csv or Excel (For example GnpIS, BMS)
- Metadata and vocabularies: use MCPD as metadata format for passport and other variables data required for characterization of germplasm.
1. Data formats
We recommend using data matrices in csv or Excel with minimum metadata as described in the FAO/IPGRI Multi-crop Passport Descriptors (MCPD) for passport and other variables data that are required for characterization of germplasm.
2. Metadata and vocabularies
The FAO/IPGRI Multi-crop Passport Descriptors (MCPD) is a recognized specification for identification and germplasm passport information exchange. It includes identification, managing institution, geographical information etc. The working group recommends using MCPD because it provides the most commonly used descriptors in the genetic resources programs across the world. To be applied, this specification must be implemented in databases, exchange format and metadata format. For instance, all the terms from the MCPD are described in the Multi-crop passport ontology with a unique identifier for each vocabulary and it can be used or implemented in databases/tools to make them interoperable.
The MCPD has been reused by several other crop descriptors published by Bioversity International and also by the FAO World Information and Early Warning System (WIEWS) on plant genetic resources (PGR), the GENESYS global portal, and the GRIN-Global. The Darwin Core extension for genebanks (DwC-Germplasm) is the result of mapping between Darwin Core (DwC) and MCPD.
For data managers, the working group recommends using DwC-Germplasm for database implementation, file formating, and data exposure as it covers MCPD.
Pay close attention to the level of identification dealt with. For instance, avoid the common mistake of declaring a variety as an accession.
|Accession number||Scientific name||Country of origin||Holding_institute||Accession name||Acquisition date|
|10056||Triticum durum||GEO||GEO013||tetri tavtukhi||19750700|
|01C0100654||Triticum aestivum||DEU||CZE122||DIPPES STURM||19540000|
|01C0100699||Triticum aestivum||AUT||CZE122||Marchfelder begrannter||19530000|
|01C0101523||Triticum aestivum||DNK||CZE122||OTOFTE 56||19650000|
|01C0101530||Triticum aestivum||FRA||CZE122||AA BLONDEAU||19650000|
|01C0102670||Triticum aestivum||HRV||CZE122||Zg 1477/69 (Zagreb)||19700000|
|01C0102700||Triticum aestivum||HUN||CZE122||Mv 102 (Martonvasar)||19760000|
|01C0105579||Triticum aestivum||UKR||CZE122||Scedraja polesja;Schedraya polesya||19930000|
|01C0105588||Triticum aestivum||CHE||CZE122||Oberkulmer Schwarzer||19950000|
|01C0105592||Triticum aestivum||CZE||CZE122||BR 1905b (Branisovice)||19950000|
|01C0105596||Triticum aestivum||SVK||CZE122||BU 51 (Bucany)||19950000|
|13210||Triticum aestivum||CHN||SVK001||Nongta 1||19900000|
|13212||Triticum aestivum||JPN||SVK001||NORIN 10||19900000|
|1326||Triticum aestivum||ARG||CHE001||SINVALOCHO MA||19520000|
|13260||Triticum aestivum||CAN||SVK001||Pioneer 4||19900000|
|G2153||Triticum aestivum||MEX002||CIMMYT SEL.KLEPPER||1986—-|
|IG 143517||Triticum turgidum||SYR002||2007/03|
|IWS 009 001 002 400||Triticum aestivum||BGR||BGR029||19970901|
Things to follow for the future
Identification of germplasm must be non ambiguous at the scale of the world wide web. To achieve this, consider using URI and mainly follow the work of the Divseek project.
Germplasm are now referenced using DOI: a Digital Object Identifier which allows a unambiguously and permanently identification of plant genetic resources for food and agriculture being exchanged across organizations. You can have a look at germplams into GnpIS which are all associated with a DOI: Apache example.
Written on: WDI working group
Published on: 02 October 2014
Updated on: 27 April 2015