Germplasm

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.

Recommendations

Summary

  1. Data format: use data matrices in csv or Excel (For example GnpIS, BMS) 
  2. 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.

3. Databases

Best practices

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
1 Triticum turgidum ITA ITA266 ersa1
10056 Triticum durum GEO GEO013 tetri tavtukhi 19750700
01C0100654 Triticum aestivum DEU CZE122 DIPPES STURM 19540000
01C0100665 Triticum aestivum POL CZE122 EPP 19310000
01C0100699 Triticum aestivum AUT CZE122 Marchfelder begrannter 19530000
01C0101523 Triticum aestivum DNK CZE122 OTOFTE 56 19650000
01C0101526 Triticum aestivum FIN CZE122 Hutte 19660000
01C0101530 Triticum aestivum FRA CZE122 AA BLONDEAU 19650000
01C0101552 Triticum aestivum USA CZE122 CHEYENNE 19660000
01C0101569 Triticum aestivum YUG CZE122 Backa 19660000
01C0102670 Triticum aestivum HRV CZE122 Zg 1477/69 (Zagreb) 19700000
01C0102693 Triticum aestivum NLD CZE122 Anouska;Anouk 19760000
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
1323 Aegilops cylindrica ARM ARM005
1324 Triticum aestivum SWE CHE001 Svenno 19520000
1326 Triticum aestivum ARG CHE001 SINVALOCHO MA 19520000
13260 Triticum aestivum CAN SVK001 Pioneer 4 19900000
B7225 Triticum aestivum MEX002 MOULIN
BW13360 Triticum aestivum MEX002 1986—-
G2153 Triticum aestivum MEX002 CIMMYT SEL.KLEPPER 1986—-
G2166 Triticum aestivum MEX002 1988—-
G9758 Triticum aestivum MEX002 1992—-
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.

 

Written on: WDI working group
Published on:  02 October 2014
Updated on: 27 April 2015

 

 

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