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The Defra Pulse Crop Genetic Improvement Network - AR0711

Description
Pulse crops and Defra policy objectives:Crop diversification and lowering inputs are major drivers for sustainable agricultural policy. Pulse crops can contribute positively to these two policy goals because, as a consequence of biological nitrogen fixation, they require minimal inputs while acting as a very effective break crop in a cereal dominated rotation. Pulse crops are also an efficient source of plant-derived protein for food and animal feed, and thus meet a need that has grown since the BSE crisis. However, pulse crops are currently under-represented in the UK, and throughout Europe, despite their being essential for sustainability in agriculture. A major cause of this limited contribution is farmers’ perception that these crops have erratic performance and that their end product value is low. Yield potential of pulse crops is high but average yields are about half of the best achieved, and the best UK yields fall short of current yield potential by about 25%. There are many causes for this, but efforts to improve yield consistency through genetics and breeding have the potential to achieve an increase in pulse production in the UK. The pulse crops, especially pea, can benefit from their association with the vegetable market where vining peas are a high value product. As the same species is involved in both markets (that are approximately of equivalent monetary value) the development of basic genetic tools can be a common resource, and the costs of their deployment can be shared. Objectives of the Network:The Defra Pulse Crop Genetic Improvement Network (PCGIN) will establish a platform that serves the process of legume crop improvement in the UK. It will:a) formally establish the route by which scientific resources, results and knowledge will be delivered to breeders, producers and end users, providing a link between these groups and the research base to achieve added value for pulse crops, b) provide resources, expertise and understanding that will be drawn upon by both public and commercial sectors in breeding, analysis, and in the definition and improvement of product quality relating to both commercial and public goods,c) promote and execute the translation of genomic research tools to crop improvement, consistent with both the needs of UK industry, and Defra objectives relating to sustainable agriculture,d) provide a direct link with, and involvement in, European pulse crop research programmes.The PCGIN will be managed by JIC, PGRO, NIAB and Defra, with ex officio input provided by the commercial sector, initially Unilever plc and Advanta Seeds UK. Core scientific research underpinning pulse crop genetics will be performed jointly by the first three organisations in projects that combine phenotypic and performance character assessment with genetic tool development. The Management Group will oversee an integrated set of related projects that exploit the activity of the core programme.
Objective
Objective 1: Communication and DeliveryTo establish and promote effective communication between the major players responsible for the genetic improvement of pulse crops. This first objective is not a scientific activity per se but it is essential to the relevance, application and delivery of the scientific activities of the PCGIN. Its activities are toa) establish and promote good communication between UK breeders in the pulse crops and the research base, both basic and applied, and ensure all have the opportunity to provide feedback throughout the projectb) establish a close liaison with SASA to ensure coordination and integration of our activitiesc) establish a database of ongoing research in the area of pulse crops especially in the UK, but also at an international leveld) establish a web site, updated every 4 months and linked to the other Defra crop improvement networkse) enable interaction days for management and stakeholders groups, providing opportunities to view and discuss genetic material (O1/03)f) develop associated projects linking participantsObjective 2: PhenotypingPhenotypic characterisation of novel legume germplasmThis will involvea) evaluating priority traits for different species by members of the PCGIN, taking account of the assessment of priorities already indicated by the breeders' surveyb) making informed choices on the species, germplasm, traits and specific biotic stresses to be studied, to include the use of exotic germplasmc) developing a series of protocols for assessment of the traits required, with rapid and reproducible scoring techniques and reliable methodology for G x E interactions established at three sites (NIAB, JIC, PGRO)d) correlating genetic marker data, where available, with phenotypic charactersObjective 3: PerformanceExtant varietal performance data will be associated with genotype dataThis will be based on a) selection of maximally informative databases for UK pulse crop characters, site characteristics, history and yearly recordsb) selecting a set of 50 cultivars that are differential for the traits identified in the assessment of breeders’ priorities (yield, standing ability, disease resistance), based on maximally informative databasesc) genotyping selected cultivars with genetic markers (200 each)d) selecting three cultivars that are maximally informative on the basis of phenotypic data and marker analysis for the generation of segregating populationse) establishing recombinant inbred lines (RILs) to F6 from crosses between the chosen lines (150 lines per population).Objective 4: Reverse geneticsTILLING for genes that regulate the development of the aerial part of the legume plantThis will involvea) Access to ca. 5000 pea cDNA sequences (ESTs).b) annotating sequences and identifying targets for TILLING, based on database mining and identity of orthologous genes involved in plant shoot architecturec) designing primers based on candidate genes, derived from a) and b) and from databases developed within the EU project (Grain Legumes)d) TILLING for mutants in these genes, using the platform developed within the EU project (Grain Legumes) and assessing phenotypes of mutants.Objective 5: Genetic mapping in crop legumes5a Provide novel germplasm for trait analysis (Fast Neutron mutant analysis and mapping)5b Integrated Genetic MapsObjective 5a will be achieved bya) selecting a set of 12 independent M3 individuals from a novel legume genetic resource [fast neutron (FN) deletion pea population]b) performing cDNA-AFLP analysis of gene transcripts from total plants of these individuals and determining the number of genes deleted per FN linec) sequencing the cDNA-AFLP fragments corresponding to the missing transcripts and identifying the corresponding genes d) performing marker analysis of the deleted fragments by mapping identified genes in extant mapping RI populationsObjective 5b will involvee) identifying the most effective strategy for relating the genetic maps of pea, field bean and lupin for UK usef) establishing genetic mapping populations for bean and lupin within UK through coordination with the EU Grain Legumes projectg) designing a comprehensive set of gene-based markers (at least 100) to enable integration of gene maps across crop speciesh) defining a set of molecular markers for priority traits that can be exploited by breeders Objective 6: Genetics of Seed Quality TraitsThis will involvea) expansion of Objective 1 to include industrial end users within the range of interested partiesb) wide consultation with a wide range of industries to define priority seed quality traitsc) development of tools and definition of protocols for analysis of these traits d) establishment and analysis of recombinant inbred populations that segregate for key traits in relation to seed and protein quality, as defined by these end-userse) de novo satellite projects with industry to exploit this variation
Project Documents
• Final Report : The Defra Pulse Crop Genetic Improvement Network   (4189k)
Time-Scale and Cost
From: 2005

To: 2009

Cost: £1,287,709
Contractor / Funded Organisations
John Innes Centre (BBSRC), National Institute of Agricultural Botany, Processors and Growers Research Organisation
Keywords
Arable              
Arable Farming              
Biotechnology              
Crop Improvement              
Crops              
Farming              
Genetics              
Genomics              
Molecular Biology              
Sustainable Farming and Food              
Fields of Study
Arable Crops