Proposal for a new COST Action: Exploiting genomics to understand - PowerPoint PPT Presentation

Proposal for a new COST Action: Exploiting genomics to understand plant-nematode interactions Nemagenics Main objective: To develop a coordinated approach to exploitation of genomics information that is appearing for plant parasitic nematodes and their hosts Nemagenics

Talk plan Plant parasitic nematodes Damage Interactions with hosts State of the art The need for a new COST Action Genomics Scientific programme Integration of activities Benefits to Europe Nemagenics

Nematodes – damage & cont rol Nematodes are damaging plant pathogens Nematodes are significant pathogens on almost all important crops grown worldwide � Cyst and root knot nemat odes are t he most import ant pat hogens Existing control strategies are not sufficient � Resist ance not always in commercially viable cult ivars � Pressure t o reduce use of “ nematicides” Nemagenics

Interactions with the host Nematodes have complex interactions with plants - biotrophy Nemagenics

Interactions with the host Nematodes induce complex feeding sites in plants Syncytium (Cyst nematodes) / Giant cell (Root-knot nematodes) � Enlarged � Highly met abolically act ive � Mult inucleat e � Cell wall ingrowt hs adj oining vascular tissue � Nemat odes depend on feeding sit e for all nut rient s required t o develop t o adult st age Nematode feeding site (NFS) induction involves profound changes in plant gene expression � Genes have been charact erised � Source of promot ers for t ransgenic solut ions Nemagenics

Interactions with the host – st at e of t he art Nematode secreted proteins are key to this process Produced in gland cells � 2 subvent ral � 1 dorsal Secreted into the plant via the stylet Nemagenics

Interactions with the host – st at e of t he art Enormous progress has been made in identifying and characterising nematode secreted proteins A range of genes have been identified � Plant cell wall degrading enzymes � Candidat e defence prot eins � Prot eins involved in feeding sit e induct ion Systems for functional analysis have been developed � Nemat ode gene knockout s: RNAi � Het erologous expression in plant s Nemagenics

Almost all major breakthroughs in this area have been made by EU groups during RTD programmes First animal pectate lyase & expansin � Nat ure , 427, 30; Nat ure, 406, 36-37 RNAi of nematode pathogenicity genes � MPMI , 18, 621-625; MPMI, 18, 615-620 NFS and meristem formation share regulatory steps � EMBO Journal , 17, 6799-6811 dsRNA Importance of cytoskelton & cell cycle progression in NFS development � Plant Cell , 11, 793-807; Plant Cell, 16, 2529-2540 Expression of dsRNA in plants leads to resistance EU groups demonstrably ahead of competitors in US & Japan � Crit ical role for support from EU Control � Example of how Lisbon goals can be achieved Nemagenics

The need for a new COST Action Genomics has completely changed the way in which biological problems are addressed Genomics � St udy of all t he genes in a species A new approach to tackling biological problems � Priorit y lies wit h defining funct ion of genes � Abilit y t o include all genes when seeking genes associat ed wit h t rait s of int erest � Ident ificat ion of concert ed changes in gene expression � Role of “ dry science” - bioinformat ics Genomics is increasingly accessible to biologists � Cost s decreasing � Number of species analysed increasing Nemagenics

The need for a new COST Action Genomics information is becoming available for many important crops and nematodes Genomes � Crops – Tomat o, Pot at o, Rice � Plant nemat odes – M. hapla, M. incognit a, H. glycines, (G. pallida) � Animal parasit ic & free living nemat odes ESTs � Almost all maj or crop and nemat ode species Tools � Microarrays � Comparat ive genomics soft ware � Funct ional genomics Major challenge is the integration of activities to ensure effective exploitation of information Nemagenics

The need for a new COST Action – Work programme 3 main work areas proposed: WG1: Functional genomics of plant parasitic nematodes WG2: Comparative genomics of nematodes WG3: Functional genomics of plant responses Nemagenics

The need for a new COST Action – Work programme WG1: Functional genomics of plant parasitic nematodes Development and application of tools for functional analysis of nematode genes � RNAi � Cell biology � Transcript ome monit oring Outputs: � Validat ed met hodology & t ools � Funct ionally charact erised pat hogenicit y genes � Target s for cont rol Nemagenics

The need for a new COST Action – Work programme WG2: Comparative genomics of nematodes Genome annotation Comparative genomics � Different plant parasit ic nemat odes � Plant parasit ic, animal parasit ic & free living nemat odes � Plant parasit ic nemat odes & ot her plant pat hogens Exploitation of model systems � Nemat ode ( C. elegans ) and plant ( Arabidopsis ) Outputs � Genome sequences in a format accessible t o communit y t hat needs t o exploit t hem � Genes specific t o plant parasit ic nemat odes, parasit ic nemat odes, plant pat hogens Nemagenics

The need for a new COST Action – Work programme WG3: Functional genomics of the plant response Susceptible response � microarrays � TILLING Plant resistance � R genes & R gene evolut ion � Defence response pat hways Identification of nematode Avr genes Outputs � Key genes import ant for NFS format ion � markers for R genes � Funct ional screens based on Avr genes Nemagenics

The need for a new COST Action – Key Activities How will a new COST Action help? Links between groups are needed more than ever before � New informat ion means co-ordinat ion of act ivit ies vit al � Previously est ablished net works in danger of falling apart for lack of funds Short term exchange visits � New skills need t o be shared t o opt imise progress and exploit opport unit ies � Training of next generat ion of scient ist s � Int eract ions & exchanges bet ween scient ist s working at bench Meetings/Workshops � Exchange of informat ion � Co-ordinat ion of act ivit ies � Building new collaborat ions � Links bet ween academia & indust ry Dissemination to end-users Nemagenics

The need for a new COST Action – Pract ical out put s (I) A new COST Action will lead to significant practical benefits Improved methods of nematode control are a priority for many growers � Pot ent ial wit hdrawal of aldicarb from EU � Environment al harm of nemat icides � Consumer pressure for no residues Information to underpin new and durable GM strategies � RNAi mediat ed st rat egies � Nemat ode or pat hogen specific t arget s Information to guide development of new nematicides � Enzyme pat hways � Nemat ode specific t arget s Nemagenics

The need for a new COST Action – Pract ical out put s (II) A new COST Action will lead to significant practical benefits Better understanding of interactions between nematodes and natural enemies � Biological cont rol � Improved underst anding of nemat ode defences against pat hogens Understanding of interactions of nematodes with plant R genes � Underpin select ion of durable R genes � Ident ificat ion of resist ance breaking populations Unanticipated benefits arise from genomics projects � e.g Erwinia as an opport unist pat hogen � Abilit y t o exploit t hese opport unit ies Nemagenics

The need for a new COST Action - summary Benefits to Europe The proposed COST Action will: � Contribute to the EU science base and add value to planned investments in the field � Provide training & education for young scientists in an emerging field � Provide knowledge that underpins development & profitability for world-leading companies in this area (based in the EU) � As shown by int erest from several companies in part icipat ing � Build on investment made through RTD programmes � Build links that will allow participating scientists to exploit genome sequences from around the world Nemagenics

A new COST Action: Has the backing of a substantial group of dynamic, successful & enthusiastic scientists keen to participate � ~ 200 research act ive scient ist s (t o dat e!) Nemagenics