Generation Challenge Programme

Day One, Tuesday, 16th September

Plenay session I: GCP perspectives

Programme perspectives (J-M Ribaut)

Subprogramme 1 (JC Glaszmann)

Subprogramme 2 (RK Varshney)

Subprogramme 3 (P Monneveux)

Subprogramme 4 (G McLaren)

Subprogramme 5 (C de Vicente)

Stakeholder perspectives

The history and the role of BIOTEC (Thailand) as a hub for scientific development in the region (M Tanticharoen, BIOTEC)

The Community of Practice concept applied to rice production in the Mekong Region—the Cambodia component (O Makara, CARDI, Cambodia)

Linking public–private seed sectors in India: a model for GCP? (D Joshi, Barwale Foundation)

The challenges of product delivery (Indonesia) (M Bustaman, ICABIOGRAD)

Parallel Subprogramme Sessions

Subprogramme 1

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Introduction (JC Glaszmann)

Data quality, Data resolution (Theo van Hintum, WUR)

Reference data validation (Jean-François Rami, Agropolis−CIRAD)

Advanced genotyping in rice (Ken McNally, IRRI)

Resequencing in ADOC (Dominique This, Agropolis−CIRAD)

Diversity at AlTol gene in sorghum (Jurandir Magalhaes, EMBRAPA)

Further mining diversity (Ken McNally in the absence of Ruaraidh Sackville Hamilton, IRRI)

Haplotype management (Claire Billot/Gautier Sarah, Agropolis−CIRAD)

Sampling markers and germplasm (Fred van Eeuwijk, WUR)

Lessons learned in various projects (Hari Upadhyaya et al, ICRISAT)

Subprogramme 2

Subtheme 1: Genomic resources and genome infrastructure

Agenda/Intro (RK Varshney)

DArT for generating genomic resources in less characterised species (Andrzej Killian, DArT Pty Ltd, Australia)

Development of genomic and genetic resource in sweet potato – GCP Wave I project (Roland Schafleitner, CIP, Peru)

Development of genomic resources in pigeonpea - linking of Indian Pigeonpea Genomics Initiative with Wave II commissioned project and TLII (Nagendra Singh, NRCPB, India)

Subtheme 2: Comparative genomics

Comparative genomics in legumes- SP2/SP3 project links with TLI and GLIP (David Bertioli, UCB, Brazil)

Orthologous genomics tools - Phylogenomics, GreenPhyl and GOST– SP4 support tool (Matthieu Conte, IRRI, Philippines)

Subtheme 3: Gene discovery

Comparative analysis of gene expression profiles across crops- maize/rice (Ramil Mauleon, IRRI, Philippines)

Subtheme 4: Marker/gene/ pathway validation

Staygreen QTLs in sorghum- links with new project to be started under Challenge Initiative (Andrew Borrell, DPI, Australia)

Reverse genetics in rice for gene validation (Andy Pereira, VBI, USA)

Subprogramme 3

Topic 1: Promoting the use of molecular markers in the South, expected impact and constraints

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Example of groundnut (Daniel Fonceka, ISRA Senegal)

Example of cowpea (Jean-Baptiste Tignegre, INERA Burkina-Faso)

Topic 2: Validation projects: Constraints to development and implementation (Abdel Ismael, IRRI)

Topic 3: Building a phenotyping network, focusing on users needs (Glen Hyman, CIAT)

Topic 4 (jointly with SP5): Crop platforms: Opinions from users

   Example of rice in Asia (Dinesh Joshi, Barwale Foundation, India)

   Example of rice in Africa (Mathias Lorieux, CIAT & Marie-Noelle Ndjiondjop, WARDA)

Subprogramme 5

1) Capacity Building à la Carte

Enhancing capacity of ICABIOGRAD in phenotyping and molecular analysis to develop elite rice lines suitable to Indonesian uplands (Masdiar Bustaman, ICABIOGRAD)

2) Communities of Practice

Marker-Assisted Selection of Rice in the Mekong Basin (Theerayut Toonjinda, RGDU, Thailand)

A Cassava Breeding Community of Practice in Africa for Accelerated Production and Dissemination of Farmer-Preferred Cassav Varieties Resistant to Pests and Diseases (Emmanuel Okogbenin, CIAT/NRCRI)

3) Genotyping Support Service

Looking for new sources of drought tolerance in maize by combining introduced varieties with local germplasm (James Gethi, KARI, Kenya)

The experience of providing genotyping services to breeders through the GSS (S Senthilvel, ICRISAT)

Day Two, Wednesday, 17th September

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Plenary session I: Impact pathways

• Rice improvement in Africa (A Ghesquière, Agropolis−LGDP/IRD) Rice improvement in Africa (M-N Ndjondnjop, WARDA)
• Sorghum improvement for acid soil (J Magalhães, EMBRAPA); Sorghum improvement for acid soil (R Schaffert, EMBRAPA)
• Rice improvement for soil problems (S Heuer, IRRI); Rice improvement for soil problems (M Thomson, IRRI)
• Stress tolerance improvement in cassava (Part 1: E Okogbenin, CIAT/NRCRI; Part 2: M Feguson, IITA; Part 3: A Alves, EMBRAPA)

Plenary session II: Gene discovery

• Targeted discovery of superior disease QTL alleles in maize and rice genomes (R Nelson, Cornell University)
• CEREALIMMUNITY’ (J-B Morel, Agropolis−CIRAD)
• Identifying genes responsible for failure—rice and wheat (R Seraj, IRRI)
• Common genetic basis for tissue growth rate (C Welcker, Agropolis−INRA)
• Transcriptome analysis of rice NIL (S Kikuchi, NIAS)

Day Three, Thursday, 18th September

Plenary session I: Marker development and breeding applications

•  Unlocking the genetic diversity in peanut's wild relatives with genomic and genetic tools (D Bertioli, UCB, Brazil)
• Drought-tolerant rice cultivars for North China and South/Southeast Asia by highly efficient pyramiding of QTLs from diverse origins (Z-K Li, CAAS)
• Maize association mapping (T Setter, Cornell University)
• Linkage disequilibrium mapping of downy mildew resistance in elite maize inbred lines in Thailand (C Phumichai, BIOTEC)
• Marker-assisted selection for sweet potato virus disease (SPVD) resistance in sweet potato germplasm and breeding populations (W Grüneberg, CIP)
• Genetic dissection of drought-adaptive mechanisms in bread and durum wheat (D Mullan, CIMMYT)
• Integrating marker-assisted selection into the conventional breeding procedure for improvement of wheat (Triticum aestivum L) in the drought-prone areas of Northern China (R Jing)
• Detecting and fine-mapping QTLs with major effects on rice yield under drought stress for deployment via marker-aided breeding (A Kumar, IRRI)

Plenary session II: World Cafe (click on hyperlink for discussion summary minutes)

Day Four, Friday, 19th September

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Plenary session I: Reference collections

• GCP Crops Genotyping: The concept (JC Glaszmann)
• Reference set characterisation: A case study (H Upadhyaya)
• Statistical rules for defining characteristic genotype and marker sets (F van Eeuwijk)
• Germplasm qualiy data management, theory and practice (J-F Rami)
• Phenotyping of a reference sample: the case of maize (J Gethi, M Zaharieva)

Plenary session II: Genomic resources

• ADIC (D This)
• SNP discovery, validation and mapping in groundnut (S Knapp)
• Genomic resources in cowpeas (T Close)
• Development of genomic resources for molecular breeding of drought tolerance in cassava (P Rabinowicz)

Plenary session III: Tropical Legumes I

• Groundnuts (V Vadez)
• Developing SNP-based modern cowpea breeding for resistance to key biotic and abiotic stresses (J Ehlers)
• Improved common bean productivity for drought-prone environments in Eastern and Southern Africa (M Blair)
• Chickpeas (RK Varshney)
• Cross-species resources for comparative genomics in tropical crop legumes (D Cook)

Plenary session IV: Molecular Breeding Platform

• Overall concept (G McLaren)
• Modelling approach to support plant phenotyping (D Luquet, R Gomide)
• Modelling tools to support molecular approach (S Chapman)
• Genotyping Support Service (H Gómez)
• Statistical Support Helpdesk (M Malosetti)

Day Five, Saturday, 20th September

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Minutes from Brainstorming session II: Molecular Breeding Platform (MBP)

1. Experimental design, data management and analysis for molecular breeding projects (Fred van Eeuwijk)

2. Decision support tools for molecular breeding (Scott Chapman)

3. Sharing crop information and required access to public data resources (Thomas Metz)

4. Marker service laboratories – access, turnaround, costs and quality (Humberto Gomez)

5. Phenotyping services – environments, grain and nutrition quality, metabolomics (Vincent Vadez)

Plenary session I: Support services and enabling delivery

• Carr. México - Texcoco km 36.5, a 5 min del Centro, a 1 km de la Universidad Autónoma de Chapingo, pasando la Pepsi de San Bernardino
• McClintock Crop Bioinformatics Course (R Bruskiewich)
• GCP Phenotyping Platform (P Monneveux)
• Upgrading the quality and utility of GCP phenotyping data (R Koebner)
• A farming systems approach to targeting and impact assessment (G Hyman)
• Ex ante impact analysis of marker-assisted selection technologies supported by GCP (G Norton)