July GRU Intern Rachel's Daily Blog
iHere in the GRU we’ve not got into social media as of yet, mostly because of time and, well it takes a particular style of communication to make it interesting and engaging. Not a problem for Rachel Taylor, an Intern from the University of Birmingham. Check out her daily blog of what she has been doing with us n the GRU and life in general.
June 2015 New SNP marker data on UK Heritage wheat accessions
As part of our commitment to increase the availability of maker sets on our materials we are releasing a dataset (SNP DATA: Set 1) based on 402 markers generated on a set of 109 heritage wheats from the BBSRC Small Grain Cereals Collection. Our thanks to all those concerned for enabling this action.
March 2015 Links made between PeaGerminate marker dataset and SeedStor
An important priority in genetic resources is the linking of datasets to germplasm collections. In 2000 the EU project ‘TEGERM’ resulted in the application of retro-element markers (RBIPS) to 3020 accessions of the John Innes Pisum Collection. The resulting structure analysis of JI Pisum Collection was published by Jing et al. 2010. The microarrays and molecular marker results of the project were uploaded into ‘Germinate Pea’ along with a further dataset of SSAP markers.
Links have been created between the two systems at the accession level to assist users in accessing enhanced data and requesting seed of these resources.
February 2015 New images added to SeedStor
A further 92 images have been added since the system went live in December last year. This brings the total to 1931 for the BBSRC Small Grain Cereal Collections from 1098 accessions and 209 for the JI Pisum Collection from 153 accessions.
December 2014 GRU new searchable database SeedStor goes live!
With the end of the year fast approaching we are very pleased to announce the public release of our new GRU database SeedStor. A year in development, this is a beta release of a LIMS and database system which we will continue to develop. The system enables users to browse across four our main collections and more will follow as we migrate data across. For the first time we are able to share extended data sets including phenotypic collection site data on these resources. The system is packed with useful browse and search facilities and there is a shopping cart to assist in the selection of lines. An extensive collection of images linked to these resources will be added early in the New Year along with further improvements. We are aware that there are a few browser specific issues with viewing images and reports which we are working to resolve. Happy browsing!
November 2014 Newly accessioned NIL’s for Ppd-1 alleles backcrossed into Alchemy and Robigus
We are pleased to announce the availability of a set of 37 BC2F4 lines for 8 insensitive Photoperiod 1 (Ppd-1) alleles from the B- and D- genomes of bread wheat and the A-genome of durum wheat. The NIL's were developed at NIAB, UK using the UK winter wheat cultivars Alchemy and Robigus as the recurrent BC parents. Further details of the lines and their response to short, natural and extended photoperiod are reported in Bentley et al. 2014 (doi: 10.1093/jxb/ert038). The lines have been accessioned into the BBSRC Small Grain Cereals Wheat collection as accessions 10237 - 10274. Find them using our search facility at http://data.jic.ac.uk/cgi-bin/germplasm/cereals.asp or Email JIC.email@example.com to request further information.
November 2014 Steve Reader retires after 41 years
On the 14th November, Steve Reader retired. One of the many contributions that Steve made in his long career was as Curator of the Triticeae and the Wheat Precise Genetic Stocks collections, formally at the Plant Breeding Institute in Cambridge before the materials and Steve moved up to the JIC in 1990.
Steve spent significant time over the past two years in updating the databases and training and transferring his extensive knowledge and skills in cytogenetic techniques to ensure that they remain part of the core competence here at the JIC. We wish Steve a long and well earned retirement. Adrian Turner of the GRU has now taken over as Curator of the Wheat Precise Genetic Stocks Collection. The Triticeae Collection will be curated by the GRU team as a whole. Please contact JIC.firstname.lastname@example.org for further information.
September 2014 Launch of the updated Crop Wild Relative database
The Crop Wild Relatives (CWR) are an important source of adaptive variation for crop improvement. The CRW database has recently been updated to include important information on ‘biodiversity hotspots’ by scientists at the University of Birmingham as potential targets for in situ conservation plans. It is the most comprehensive source of data of its type in the world and is the result of a truly global initiative organised by the FAO. The GRU has assisted in reviewing the data content for Pisum.
August 2014 SeedStor An information management System for Genebank Curators
SeedStor is being created by the team at the GRU and NBI Scientific Computing. Core functions include request processing, new accessions, stock control including regeneration and reporting. The system will integrate all our database systems and search functionalities. We are interested in collaborating and sharing the code and future development of this project which is targeted at Genebank curators and customer data and service provision.
July 2014 New publication on the genetic diversity and structure analysis of the A.E. Watkins landrace wheat collection
In the late 1920’s, A.E. Watkins assembled a collection of several thousand lines of diploid, tetraploid and hexaploid wheats from 32 countries around the world. This provides a useful snapshot of genetic variation in wheat prior to the green revolution. We are pleased to announce the publication of marker analysis used to explore the underlying structure and relationships of 826 stabilised SSD lines of hexaploid wheats from the original collection and how this knowledge is being used in the development of new resources for research and breeding which should accelerate the detection of new alleles for crop improvement.
May 2014 Listing of marker verified stocks for Major Gene Near-Isogenic Lines for Ppd1 and Rht
The development of Near Isogenic lines (NILs) involves crossing alleles of specific genes into a common genetic background by cycles of backcrossing and selection to end up with lines that differ only at the genomic region of interest. NILs represent powerful tools for the study and evaluation of particular alleles of combinations of alleles.
We are pleased to announce our listings of marker verified stocks of NILs for the Ppd1 (one set) and Rht series (fourteen sets) of lines in wheat. Over time we intend to extend this element of quality assurance to other important stocks across the collections.
March New publication on haplotype variation sheds light on the co-evolution of potyviruses and cultivated peas
The availability of DNA resources of germplasm collections is providing to be a game changer in the search for novel allelic variation in target genes of known sequence. This can be seen as offering a good return on investment on the cost and efforts of assembling and maintaining crop seed banks over the past 50 years.
DNA samples of 2803 pea accessions from 7 collections around the world including the JI Pisum Collection have helped establish a geographical gradient of 34 elF4E alleles involved in resistance to Potyviruses in pea. The broad screen found the elF4EA variant confers resistance to the P1 PSbMV pathotype to be exclusively found in cultivated landrace materials and not related crop wild relatives. The elF4F variants found in the Highlands of Central Asia, the Northern region of the Indian sub-continent, Eastern Africa and China were found to be tightly linked to the diversity of the pathogen raising interesting questions about the co-evolution of the potyviruses and the pea host. The full manuscript can be found at doi:10.1371/journal.pone.0090394.
January 2014 Bristol Cereals DB Stocks Collection open for requests
We are pleased to announce that bagged seed stocks of a set of sequenced lines from the Functional Genomics Group at the University of Bristol on the Wheat SNP Database are available on request. Details can be found under Germplasm Resources. We look forward to hearing from you.
December 2013 Best Year ever for the GRU
As the emails stop coming in and the phone falls silent and everyone starts to wind down for the end of year and being with family, the GRU Christmas elves are busy wrapping up the last of the seed lots to go off in the post (far safer than the sledge!). As we total up the number of enquires 2013 turns out to have been our busiest year ever by a big margin. We’ve enjoyed engaging with old friends and new and helping you with seed, advice and information and look forward to hearing from you in the New Year. BEST WISHES from the GRU team
December 2013 New graphical introduction to wheat aneuploid stocks
We are pleased to announce a new graphical aid to wheat aneuploid stocks which we hope will be of use to those working with these stocks.
November 2013 Impact of gene on crop development could boost cereal yieldsThe GRU helps to underpin the science of a number of UK Institutions with advice, germplasm and working visits. We are therefore pleased to announce a major publication arising from work at the James Hutton and the University of Dundee that appears in the current issue of PNAS. The work demonstrates that a gene encoding a protein called HvAPETLA2 (HvAP2) controls how closely grains are packed on the top of the barley stem or spike, an important agronomic trait called spike density. A press release of the work can be found at the James Hutton.
October 2013 Pulse Promise from Genetic Advances
This is the title of an article in the current issue of Crop Production Magazine. The report focuses on the UK research efforts at the John Innes Centre, PGRO and NIAB within the Defra supported Pulse Crop Genetic Improvement Network (PCGIN) and associated projects, and the impact of recent advances in genetics and biotechnology are aiding our understanding of development and seed quality and how these finding are being translated to crop improvement. The article also features the JI Pisum collection maintained by the GRU in providing the genetic variation and knowledge to help underpin the efforts of the research and breeding communities.
October 2013 Global Crop Diversity Trust Pea expert consultation workshop held at the JIC
The GRU has just hosted a productive 2 day meeting of experts to discuss the availability, conservation needs and utility of crop wild relatives for pre-breeding in pea. This was a small meeting with delegates from the USA, Czech Republic, Russia and a skype link to Australia. A report of the meeting will be made public. A longer manuscript to capture the current status of these issues is also planned.
August 2013 GRU field Harvesting Complete
A window of good weather has enabled us to complete the field harvest of all regeneration and demonstration materials. Plenty of demonstrations are planned for next year and we will keep you posted of what, where and when.
July 2013 Demonstration plots of heritage wheats and barley
The long cool spring has delayed crop growth by some 3 weeks compared to an average year. We are pleased to report that these Heritage Cereal plots are all in ear and ready for viewing. If you are interested in coming to see them either as an individual or with a group then please contact us to make an appointment.
July 2013 New Genetic Garden opens at the Dundee Botanic garden
The GRU is pleased to have supplied supporting materials to scientists from the University of Dundee and the James Hutton Institute who this week will unveil a new Genetic Garden explaining the role of genes and genetics in conjunction with College of Life Sciences Plant Division in the Botanic Garden which opened this month.
June 2013 GRU at the National Institutes of Biosciences (NIB) meeting
The GRU is presenting a poster during the session. The on our collections and services and how we can help at the forthcoming NIB’s meeting at Roslin, Edinburgh. This important meeting provides us with a chance to engage with a wide cross section of the scientific community as well as colleagues from BBSRC central office.
June 12-13 2013 Come and see us at Cereals 2013 near Lincoln
GRU has been involved in the John Innes display as part of the BBSRC stand. Our display is a growing demonstration of wheat evolution with highlights as to traits that have scientists and breeders have found in these ancient forms and incorporated into modern wheats.
April 2013 Focus on Biodiversity
Feburary 2013 New GRU Germplasm Manager
We are pleased to announce a new member of the GRU team. Dr Adrian Turner is a new Germplasm manager who will lead the development of our stock validation programme targeted primarily on specialist stocks where molecular marker and phenotype checks will provide valuable quality assurance to our operations and resources.
February 2013 GRU You Tube Channel tops 1000 views across 63 countries
In just under 6 months the 5 GRU information resource videos on guides to crossing in wheat and peas and explanations of different aspects of our work. The highest figures being for the UK, USA, India, Australia, Canada and with remarkably good figures from across South America and the Middle and Far East. We are delighted that these resources are proving useful to so many and will be adding more over the course of the year.
January 2013 New wheat resources from the Bristol Wheat Genomic Group
We are pleased to announce that following discussions with Prof. Keith Edwards at the University of Bristol, the GRU is set to become the stock distribution centre for seed of the high density mapping and exome capture targeted resequencing lines for the Bristol Group. The material is currently being multiplied under glass and will be available from the GRU from late summer 2013.
Welcome to our new Germplasm Resources Unit website.This site is still under development but we felt we wanted to share some of the new functionality and features with our users sooner rather than later. We have introduced a range of new pages, features and funtionality which we intend to build on further. If you have any comments on the new desig , we would be pleased to hear from you. Please email comments to Mike Ambrose (email@example.com). Also, don't forget to subscribe to our e-newsletter Seed Bank News
The GRU is involved in training and advising on procedures relating to germplasm management and related activities. We are aware that there is potentially a much wider audience for such resources so we have started to produce a range of practical guides which we are making available via the web.
The John Innes Centre is custodian of a number of key germplasm collections which serves academic, industrial and non-industrial groups both within the UK and internationally. They are the subject of research in their own right as well as being involved in a range of collaborative programmes and genetic resources networks.
The collections housed within a purpose built facility maintained at 1.5°C and 10%RH with some 600m3 of storage capacity.
Material from the collections is available on request to research, academic and commercial companies subject to availability. Material is also available for educational displays and demonstrations.
All materials are sent out accompanied by a material transfer agreement (MTA), the specific version being dependent on the particular material in question. The main public collections (JI Pisum collection and the BBSRC Small Grain Cereals Collections) form part of the UK’ contribution to the Multilateral System (MLS) of the International Treaty for Plant Genetic Resources for Food and Agriculture (ITPGRFA). The MTA issued for the use of these resources is the standard MTA (sMTA) of the ITPGRFA. This sMTA outlines the conditions of use and responsibilities of the recipient and should be retained for future reference for the following reasons;
- The sMTA is issued under the ITPGRFA. As such it provides the necessary evidence of ‘due diligence’ should you later be required to show the audit trail for the origin of the materials in further grant proposals or possible commercialisation of materials that have used any of these materials in their development.
- Materials covered by the sMTA of the ITPGRFA and is outside the scope of the Nagoya Protocol which covers access and benefit sharing for all other germplasm. Evidence of the exact terms under which your material was sourced might be important in answering any questions that might arise under either instrument.
Please not that passing on the material to further parties is done so under the same terms as they were received. Please email if you have any queries and for details of other agreements.
Seed Bank News is produced by the Germplasm Resources Unit (GRU) at the John Innes Centre as a further channel of communication with our user community and raise awareness of recent activities and to flag the work of the collections and what we can offer.
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