Plant genetic resources – Enrichment Index

Figure 1: Cumulative Enrichment Index of plant genetic resource collections held in the UK and annual number of accessions, 1960 to 2018

Figure 2: Number of accessions contributing to the Enrichment Index added per year at selected UK holding institutes, 1960 to 2018

Relevance

The UK is relatively rich in wild relatives of crops, landraces of cereal, vegetable and fruit crops, and traditional orchard trees. Maintaining genetic diversity of UK plants is important for conservation of biological diversity, as well as for economic and cultural reasons. The UK is a Party to the International Treaty on Plant Genetic Resources for Food and Agriculture, and has also committed to a five-point action plan in response to the Foresight (2011) report on the future of food and farming (Environmental Audit Committee 2011) which includes actions on conserving plant genetic resources.

International/domestic reporting

The UK Biodiversity Indicators have been reviewed in response to the latest goals and targets agreed under the Kunming-Montreal Global Biodiversity Framework (GBF) of the Convention on Biological Diversity (CBD). The indicators are being adapted, with some new indicators being developed, to better align them with the monitoring framework for the GBF. The suite of biodiversity indicators is therefore expected to change ready for forthcoming UK national reports to CBD in 2026 and 2029.

Web links for further information

• EURISCO Catalogue website
• Defra United Kingdom: Country Report on Plant Genetic Resources for Food and Agriculture (2010) (PDF, 430kb)
• Commonwealth Potato Collection, The James Hutton Institute Home page
• Genetic Resources Unit, Institute of Biological Environmental & Rural Sciences, Aberystwyth University Home page
• Garden Organic – the Organic Organisation, Heritage Seed Library Home page
• Nottingham Arabidopsis Stock Centre Home page
• John Innes Centre Germplasm Resources Unit
• University of Reading National Fruit Collection
• Royal Botanic Gardens, Kew Millennium Seed Bank Partnership Seed Bank
• Royal Botanic Gardens, Kew Seed collection manual
• Royal Botanic Gardens, Kew UK Native Seed Hub
• Science and Advice for Scottish Agriculture, Scottish Government Home page
• Warwick Crop Centre, Genetic Resources Unit Home page
• Joint Nature Conservation Committee Vascular Plant Red List
• Convention on Biological Diversity Global Strategy for Plant Conservation
• Food and Agriculture Organisation of the United Nations Commission on Genetic Resources for Food and Agriculture

Methodology

The number of accessions (germplasm samples) per taxon is often used as a proxy for the level of genetic diversity in ex situ germplasm collections taking into account the threat of losing reference material through reduced seed viability. However, the Enrichment Index provides a better reflection of genetic diversity held in gene banks than the number of accessions as reduced weight is given to samples of taxa already present in the collection, particularly those originating from the same country.

It is assumed that there are positive relationships between the level of genetic diversity and the: - number of accessions held; - number of taxa held; and - geographical distribution of collection sites.

The Enrichment Index first identifies duplicate accessions, that is, samples belonging to the same taxon with the same collection date and country of origin. Each subsequent duplication is given a reduced weight. For each taxon present, the number of samples is weighted, with accessions from the same country of origin being given a reduced weight depending on the land area of the country of origin (duplicates from smaller countries of origin are given less weight than those from larger countries of origin). The weights of the accessions are compared with those of preceding years and summed to produce an assessment of the genetic diversity present in the collections each year.

This index can be applied to UK accessions, filtering data by relevant taxa and country of holding institute, as was carried out through the following steps (further details are available in the technical document accompanying the 2023 publication; note that there has been no update to this indicator since the 2018 publication data where data were accessed on 7 June 2018):

Obtaining Data for the Index:

1. Data from EURISCO was accessed, including current policy for viability and the following data fields: accession number, acquisition date, country of origin, collection date, genus, species, subspecies, holding institute, donor description, collection site, latitude and longitude.

Preparing the Data:

1. Data was filtered by taxa of interest.

2. Gaps were identified in acquisition date. Where the donor name existed, the collection date could be used to fill gaps in the acquisition date field.

3. Gaps identified in country of origin. Collection site, latitude and longitude could be used to fill some gaps in the country of origin field.

4. Country of origin information compared to collection site information to identify errors.

5. As a final check, all records needed to have a value for the following fields: INSTCODE, ACCENUMB, ORIGCTY (either all ISO codes, or all country names), YEAR, TAXON. Any records not having all of these fields needed to be removed before continuing.

6. Two tables were created in Microsoft Access: a Collection table with data on accessions and a Country table with data on each country.

Calculating the Index:

1. Data were added to the MS-Access application produced by FAO.

2. Quality control macros were performed on the Collection and Country tables.

3. The Enrichment Index macro was run to calculate the index.

4. Any results that were to be kept were exported before re-running the index macro.

Caveats and limitations

The Index is a valuable method for assessing the efforts made to conserve genetic diversity of target plants through ex situ storage. However, the following points should be taken into consideration when interpreting it:

• The indicator does not assess the effectiveness of conservation in the field and therefore overlooks the importance of in situ conservation (that is, conserving genetic diversity in the wild), which not only includes species but also the habitats in which they live.
• The indicator makes the assumption that the number of accessions per taxon is positively related to the level of genetic diversity stored ex situ. However, this relationship may not always exist, particularly for commercial cultivars, since many cultivars are bred for the same market and hence are phenotypically and probably genetically very similar. Crop wild relative populations are considered to contain far more genetic diversity than crops themselves (Hopkins and Maxted, 2010). Without detailed investigation it is difficult to assess how much genetic variation is present in a collection.
• The indicator focuses on ex situ conservation in germplasm collections, which will represent only a small proportion of the total genetic diversity of UK crops and their wild relatives. The EURISCO catalogue is the most comprehensive database available, containing more than half of the ex situ accessions maintained in Europe (EURISCO 2012). However, it is not a comprehensive data set for the UK.
• Not all genetic resource collections are stored as seed. For example, the National Fruit Collection (NFC; of more than 3,900 named apple, pear, plum, cherry, bush fruit, vine and cob nut cultivars owned by Defra) is kept as a field collection. Consequently, a value for country of origin is often not available. This is a required field for calculating the Enrichment Index; resources without a country of origin are therefore under-represented.
• The genetic diversity of crop wild relatives is expected to be higher than for cultivated plants. Ideally a separate enrichment index would be produced separately for cultivated plants and crop wild relatives. However, it is not possible to determine in every case whether an accession is wild sourced or from a cultivated stock, so the indicator currently considers them together. A consequence of this is that the indicator potentially underrepresents the crop based genetic resource collections.
• Wild relatives of cultivated plants are those falling within taxon groups one to three as defined in the taxon group concept (Maxted et al. 2006). In this indicator a slightly broader scope based on genus of the taxa is used, as within the taxon group concept, groups one to three goes to subgenus (which would add to the complexity of filtering the results downloaded from EURISCO).

Supplementary data on the Millennium Seed Bank

This section provides supplementary information of the conservation of plant resources in the Millennium Seed Bank project managed by the Royal Botanic Gardens, Kew. The Millennium Seed Bank (MSB) is one of the largest ex situ conservation projects in the World. It aims to collect seeds, herbarium specimens and data from species worldwide, including the entire UK seed-bearing flora, and to conserve these collections to international standards. These include the rarest, most threatened and most useful species.

The MSB already holds seeds from species thought to be extinct in the wild. In addition, seed banks provide a controlled source of plant material for research, education and public awareness.

The Millennium Seed Bank manages an active UK seed banking programme. The current strategy is to maintain, augment and improve the UK collections held in the MSB, to make them more genetically comprehensive and of sufficient number to be of use for UK science and conservation.

The UK Flora Project seeks to add to the MSB UK species which are currently missing, particularly targeting rare and threatened species which may be confined to just a handful of isolated locations. In addition, new provenance collections for species already banked at the MSB, for which better geographic coverage and hence genetic diversity are required are being sought.

The MSB is also leading a new initiative, the UK National Tree Seed Project, which undertakes in-depth sampling of the UK woody flora. For each target species multi- provenance seed collections are being made from right across its UK distribution. In many cases seeds from individual trees are being stored separately. These seeds will be available to research organisations working on solutions to the threats facing UK trees, such as the control of pests and diseases and to help foresters and conservationists develop woodland more resilient to environmental change.

Kew’s UK Native Seed Hub aims to increase the quality, quantity and diversity of native plants and seeds available for conservation and habitat restoration by providing high quality UK native plant material. The initiative supplies seeds and plugs, with a focus on species which are not easily available through commercial native seed suppliers, and supports other UK native seed and plant producers and conservation organisations.

Figure 3 shows the number of distinct geographic areas (hectads) from which collections of threatened seed-bearing plants have been made across the UK. A hectad is an area of 10 km by 10 km. Threatened seed-bearing plants are those listed as critically endangered, endangered or vulnerable in the Great Britain Vascular Plant Red List (PDF, 950kb). This is a measure of the conservation of genetic diversity of UK threatened species because the greater the number of hectads, the wider the sampling area and the more likely it is that the total sample contains greater genetic diversity. The number of sampled hectads almost doubled between 1995 and 2000 as a result of a lot of collecting effort in the run-up to the millennium, and has subsequently increased by 24% since 2010.

Figure 3: Number of populations (based on hectads) from which collections of threatened seed-bearing plants have been made across UK and conserved in the Millennium Seed Bank, 1995 to 2017

Figure 4: Number of UK Seed Collections in the Millennium Seed Bank, 1995 to 2017

Development plan

Since our previous publication we have adapted the language and visualisations used in this indicator. We are keen to hear from our users about these changes, as well as our published development plan, please email us.

If this indicator is retained within the UK Biodiversity Indicators suite, revisions will be considered, as informed by discussions with the UK Plant Genetic Resources Group. Revisions could potentially include widening the range of data sources used to include other organisations, factoring in the loss of genetic sample material from holding institutes and tracking how samples are used.