Databases

BBSRC Cereals Collection

These collections are the largest and most authoritative in the UK, formed through the amalgamation of working collections from a range of institutions including barley stocks from the James Hutton institute (formerly known as the Scottish Crops Research Institute at Invergowrie, dundee), wheat from the former Plant Breeding Institute in Cambridge and oats from the Institute of Grassland and Environmental Research at Aberystwyth (now IBERS of the University of Aberystwyth). The old reference collections of the National Institute of Agricultural Botany (NIAB) which were disbanded in the 1960's are also included.

The collections were formed alongside public sector breeding programmes to provide access to the broad genetic variation required to drive forward progress in pest and disease resistance, plant architecture as well as quality traits such as seed storage composition. They are thus very comprehensive in material bred and trailed in the UK and Western Europe. In addition they have also acted as long term home for holdings of material coming into the UK from collections and expeditions throughout this century which has resulted in a large body of land races from different parts of the world. Over the years research lines from more basic science programmes have been accepted including key reference stocks, mutation stocks, near isogenic lines and precise genetic stocks. In more recent time the collections have become independent of breeding programmes which has allowed them to broaden their remit and focus but their links to the breeding sector have remained strong.

Summary statistics for the collections are as follows:-

  • Triticum - 9526 accessions. UK holdings 520 cultivars and 782 breeders lines. Bread wheat types 7971 accessions including 1787 named varieties, 2135 breeders lines, 3658 landraces or selections from landraces. Durum types 200 accessions including 89 named cultivars, 49 breeders lines and 45 landraces or selections from landraces.
  • Hordeum -10908 accessions. UK holdings 710 named varieties, 924 breeders lines. 1954 named varieties, 2038 breeders lines. 4500 landraces or selections from landraces. 330 genetic stocks.
  • Avena - 3000 accessions. UK holding 276 cultivars and 182 breeders lines A. sativa 1845 accessions incudes 1047 named cultivars, 454 breeders lines and 160 landraces. A.sativa nuda 168 accessions includes 30 named varieties, 75 breeders lines and 28 landraces. A. byzantina 158 accessions includes 30 named varieties, 118 landraces or selections from land races.

(As of November 2009 we have uploaded listings of WGIN wheat germplasm maintained at RRes-Rothampsted into our searchable database. Currently these consist of accession of Triticum monococcum and have been allocated accession numbers > 40000. )

The John Innes Pisum Collection

 The collection is broad based and comprises 3582 accessions including a wide range of wild and semi-cultivated material in addition to landraces and cultivars from many regions around the world. The collection also includes near-isogenic series for a number of genes as well as sets of host differentials for all major pea diseases. The collection incorporates the International collection of mutation stocks on behalf of the Pisum Genetics Association in collaboration with the Nordic Gene Bank which serves as the base collection and backup for the work at the JIC. A web searchable catalogue (PGene) of genetic stocks for Pisum is maintained and can be accessed via the link listed below. A number of recombinant inbred populations used for the mapping programmes at the JIC are also maintained as part of the collection.

For further information relating to the collections please contact: Mike Ambrose, John Innes Centre, Norwich Research Park Colney Lane, Norwich, NR4 7UH. TEL: +01603 450630. Email mike.ambrose@jic.ac.uk

We gratefully acknowledge financial support for the pea collection from 

NEW in 2012: The John Innes Pisum Collection works closely with other organisations and has had a number of successful collaborations that have resulted in the development of important data sets that add value to the collection and enhance its utility. Over the coming year we will be working to enhance the available data that have arisen from these outputs as we move towards flagging and developing ‘community Resources’.

The first is an output of a long standing collaboration between Noel Ellis of the JIC and Andy Flavell based at the University of Edinburgh to explore and develop molecular markers to gain an understanding of the genetic diversity within Pisum and its origins and to apply them to genotype complete collections. This was achieved over a long time period and several funding grants. The culmination of the work came with the following paper;

Jing R, Vershinin A, Grzebyta J, Shaw P, Smýkal P, Marshall D, Ambrose MJ , Ellis THN, Flavell AJ (2010) The genetic diversity and evolution of field pea (Pisum) studied by high throughput retrotransposon based insertion polymorphism (RBIP) marker analysis. BMC Evolutionary Biology 10:44doi:10.1186/1471-2148-10-44

Original data sources, microarray and map data can all be found on the JI Pisum Collection Germinate Database

This work has provided a whole new baseline description for the collection which is the basis of further study as we look to target particular sections of the diversity for particular traits of interest. Early in 2010 Noel Ellis left the John Innes to take up a Chair at the Institute of Biological, Environmental and Rural Sciences (IBERS) at the University of Aberystwyth where he continues to maintain very valuable web resources relating to pisum mutants, genetic maps and diversity studies.

Links to output to further collaborations and resources will be provided over the coming months.

PGene

Accompanying notes

The database works on the basis of submitting a search which results in a summary listing of entries. Record details are returned when the magnifying glass on the summary listing line is clicked. No report facilities are available at the present time. Individual pages can be printed off in the usual way.

Search Options

The searches have been organised on the basis of users requirements and organised in such a way as to be extracting manageable subsets of entries. This should help maintain good response times over the web.

Four search routines are currently available. The use of Locus for the default search may be reviewed on the basis of feedback from users. For those familiar with pea genetics this should present few problems. A better search for those less familiar would be either the class or sub-class searches. The Phenotype search option performs an ‘approximate string search’ of the phenotype description data eg. the search ‘orange’ would report back records for orange cotyleodns (Orc), orange leaves (Orl) and orange pods (Orp).

*A note on gene symbols*

Gene symbols are in the process of revision. The guidelines for the registration of gene symbols were laid down by Stig Blixt. 1977. The Gene Symbols of Pisum. Pisum Newsletter 9, supplement. Symbols in the database have been revised for consistency and integrity of the database on the basis of a consensus over the use of the hyphen (Murfet, I.C. 1997, Pisum Genetics, vol. 30: 47 and Ellis, T.N. and Ambrose M.J. Pea. Ed. Wood, R. In: Genetic Nomenclature Guide. West Sussex ( UK ), Elsevier, 1998, S.22-23). Historically hyphens were used between the base symbol and number. Current use of hyphens for morphological characters is restricted to allele designations. Hyphens in extant names have been dropped. For the two genes er-1 and er-2 are now designated er1 and er2.

The use of hyphens in isozyme locus names is used to designate cellular compartmentalisation where appropriate (e.g. -p indicates plastid).

1. Locus - The input of symbols should be on the basis of current symbols.

2. Linkage Group - Revised in accordance to the current consensus map. Pisum Genetics Volume 30, pages 1-4.

3. Class -Gene symbols are assigned to a mutation class on the basis of the initial description of a mutant. In a number of cases further effects of the gene are noted which may be quite different. Searching on class alone does not guarantee that all genes of interested will be selected. An example is the case for bronze leaves brz. The gene was first isolated in a screen for low nodulation with the pleiotrophic effect of bronze spots on leaves. The gene is classified under 6. Root system and would not be picked up on a search on 4. Foliage and emergences.

The list of classes is as follows;

  1.   Physiological characters
  2.   Seed characters
  3.   Shoot system
  4.   Foliage and emergences
  5.   Chlorophyll mutations
  6.   Root system
  7.   Flower and generative apparatus
  8.   Pods
  9.   Complex mutants
  10.   Chromosome mutation

4. Sub-class - All ten classes are sub-divided to allow for refining of searches. The pick list presents the class description as a header.

Search Coverage

Gene symbols are classified into a series of categories (Valid, Provisional, Invalid, Synonyms, Homonyms, Extinct and Base). The default for all searches is on Valid and Provisional symbols only. By clicking in the box marked Select all genes, the search is extended to include Synonyms, Invalid, Extinct and Base symbols.

*Please note* The Previous gene symbol for Synonyms is the one first published. The Current gene symbol for Synonyms is the Valid symbol. Look through list or do a new search for the Valid symbol record details.

Invalid gene symbols have no Current Valid symbol.

Descriptions - The main description field is being reformatted to remove details referring to interaction, pleiotrophy, complementary and hypostatic actions. Editing of these new fields is still in progress.

Bibliography - References are listed by author and year. The inclusion of references covers three main classes. The first mention of the mutation, the first defining of a gene symbol and the first genetic analysis. It has been an active policy to include further references that provide substantial additional details of a mutation and any gene interactions, the physiological and biochemical basis of the gene and any sequencing work.

Images - Images are stored in two sizes. The first as a thumb nail on the record detail. Clicking on the image will bring up a larger version where they are maintained. Good images that illustrate the characters well will be considered for inclusion.

Genetic Stocks - Information on all lines is presented whether or not the lines have been registered in the John Innes Pisum Collection. Any authors of mutants are urged to consider sending samples of lines appearing in the Gene List to the reference collection. While a number of mutants have been successfully traced in recent years, many have been lost. This is tragic loss and the deposition of a safety duplicate in the reference collection should be considered essential to ensuring that no further losses occur.

Progenitor - New field. The line from which a mutant has been derived. Resulted in the inclusion of progenitor lines as representative lines.

Mutagenic Agent - New field.

Example screenshots

Screen view at start of session

Description: New Picture

 

tl entered into ‘locus/Gene symbol’ box and click on search

Description: New Picture

Click on magnifying glass to expand full record

Description: New Picture

Description: New Picture

Enquiries 

Any enquiries or feedback relating to this application please contact:

Mike Ambrose
John Innes Centre, Norwich Research Park, Norwich, NR4 7UH
Tel: +01603 450630, email: mike.ambrose@jic.ac.uk