2009 Annual Research Meeting

Dates: 20–23 September 2009

Venue: Laico L’Amitié Bamako Hotel, Bamako, Mali

The Annual Research Meeting (ARM) is an excellent forum for scientists in GCP projects to meet with their project teams and other GCP scientists, share their research results and jointly plan for the upcoming year. The 2009 event took place in Bamako, Mali, from 20-23 September 2009. Participation was by invitation only, and PIs of all ongoing projects were expected to attend.

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Agendas
The agenda included the following sessions:

GCP platforms
Challenge Initiatives
Bioinformatics and crop information
Genomics & gene discovery
Capacity-building and enabling delivery

In addition to these main plenary sessions, there were also four parallel sessions across two days, covering the following topics:

Cereals research–Diversity
Legumes research and development

Cereal research–Breeding
Clonally-propagated crops     

These structured sessions were also complemented by more informal group meetings, consisting of both brainstorming and panel discussions.

Full agenda details are available below:

Main ARM agenda
Parallel sessions agenda

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Presentations
View 2009 ARM presentations

Poster session
Poster abstracts booklet
Poster PDFs
Poster winners

All ARM participants were invited to present a poster on GCP work, or on work related to GCP’s mission for non-GCP scientists.

Posters were grouped by the four themes listed further below. The idea was for communication and fun whilst sharing information. The scope of the posters was to be exciting results from GCP projects, or non-GCP work which is however related to GCP’s mission. Striking concepts and methodologies were also welcome.

The four poster themes were:

Theme 1: Exploiting allelic diversity
Theme 2: Genomic resources and  gene/pathway discovery
Theme 3: Marker development and breeding applications
Theme 4: Support services and enabling delivery (incorporating training and capacity-building)

In line with the previous ARM poster sessions, presenters were faced with the challenge of engaging the audience and employing the necessary powers of persuasion to 'sell' their respective posters as the best of the bunch - and all in  Powerpoint-barred presentations of 60 seconds or less! Besides a ticking clock, poster presenters were also restricted to using only one old-fashioned transparency as a means of presentation support material - but besides time and material limitations, presenters were encouraged to let their imagination, creativity, and all-important sense of humour roam free!  

As in previous years, the poster presentations were followed by poster viewing sessions, in which our ARM audience were asked to cast votes for their favourite posters within each of the four themes. GCP is pleased to announce the following as the four winning posters:

Theme 1: Exploiting allelic diversity (2 winners)
Poster 1.6: Generating new wheat germplasm with enhanced drought/heat tolerance using AB genomes
 - Presenter: Satish Chandra Misra
 - Authors: Satish Chandra Misra*, Maria Zaharieva, S Dreisigacker, J Crossa, T Payne, RR Hanchinal, MY Mujahid, R Trethowan and Tetali Sujata (*Agharkar Research Institute (ARI), Pune, Maharashtra, India; e-mail: satishmisra@yahoo.com)

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Poster 1.7: The genontyping validation of GCP reference sets
 - Presenter: Sarah McGrath
 - Author: Sarah McGrath, Agropolis–CIRAD, UMR DAP, TA A-96/03, Avenue Agropolis, 34398 Montpellier Cedex 5, France; e-mail:
sarah-katherine.mcgrath@cirad.fr)

Theme 2: Genomic resources and gene/pathway discovery (2 winners)
Poster 2.5: Phenotyping tools to select for adaptive traits in drought environments
 - Presenter: Francis Ogbonnaya
 - Authors: Francis C Ogbonnaya*, Fernanda Dreccer, Osman Abdalla, Tony Condon, Hassan Ouabbou, Sripada M Udupa, Solomon Gelacha, Matthew Reynolds and David Bonnett (*International Center for Agricultural Research in the Dry Areas (ICARDA), Aleppo, Syria; e-mail: F.Ogbonnaya@cgiar.org).

Poster 2.15: Diversity and distribution of single feature polymorphisms in food crop legumes
 - Presenter: Doug Cook
 - Authors: R Varma Penmetsa*, Andrew D Farmer, Noelia Carrasquilla-Garcia, Birinchi K Sarma, Subhojit Datt a, Sally L Vail, Bert Vandenberg, Jimmy Woodward, Gregory D May, George E Bruening, Rajeev K Varshney and Douglas R Cook (*Department of Plant Pathology, University of California–Davis, CA, USA)

Theme 3: Marker development and breeding applications
Poster 3.9: Evaluation of cassava F1 genotypes and progenitors resistant to Cassava Mosaic Disease (CMD) for the putative presence of the CDM2 resistant gene using molecular markers
 - Presenter: Elizabeth Parkes
 - Authors: Elizabeth Parkes*, Bright Boakye Peprah, Edem Lotsu, Priscilla Boateng, Ruth Thompson and Marian Dorcas Quain (*Crops Research Institute, P. O. Box 3785, Kumasi, Ghana)

Theme 4: Support services and enabling delivery
Poster 4.15: Interactive Resource Centre and Helpdesk – now on Facebook!
 - Presenter: Theresa Fulton
 -Author: Theresa Fulton (Institute for Genomic Diversity, Cornell University, 130C Biotechnology Building, Ithaca, NY 14853, USA, Phone: 1-607-255-4323, Fax: 1-607-254-6379; Tf12@cornell.edu)

And the special prize goes to...
In addition to the Theme winners outlined above, the GCP judges were also so impressed by the wit, ingenuity and all-round entertainment factor evoked by some of our poster presenters that a series of special awards were also granted. The details of these random subjective awards from the 60-second presentation session are given below, though not in order of merit, or any order whatsoever! And no metrics have been applied either.

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1. The Creativity Award: Theresa Fulton, for Poster 4.4: The GCP phenotyping template wizard
A creative and refreshing blend of poetry and science.

2. The Double-Double Award: Trushar Shah and Guy Davenport, for Poster 4.7: Extension of the GCP stress gene catalogue using the maize genome sequence information
A new approach and time economy, miraculously cramming two presenters into 60 seconds and doubling their verbal output through dialogue.

3. The Green Award (no puns intended!): Elisabeth van Strien for Poster 4.12: Support to GCP scientists regarding issues related to bioinformatics and data handling.
For environmental-friendliness and candour by recycling slide from last ARM…and having the courage and frankness to own up to it!

4. The Dangerous Driving Award (with a light touch!): Abishek Rathore for Poster 4.11: Further development and support for use if iMAS by NARS and the other user communities
Award for extremely high-speed verbal delivery and therefore the greatest number of words ever spoken in 60 seconds in the history of the ARM. But please note: no measures were taken on how many words the audience heard clearly at that speed, much less retained.

5. The Humour Award (with a ‘heavy’ light touch!): Jean-Christophe Glaszmann for Poster 1.4: A whole genome scan of cultivated sorghum (Sorghum bicolor L Moench): evolving diversity in the light of different marker systems.
An extremely high entertainment factor in just 60 seconds – wrong order of poster number, slide placed on projector with paper blocking the slide, slide upside down, daring to attempt to argue with the poster presentation moderator – one intimidating Theo Van Hintum. Hmmmmh! …after science, JC can definitely seriously consider circus clown as his next career move. No award for the title of the poster though!

6. The Drama Award: Elizabeth Parkes for Poster 3.9: Evaluation of cassava F1 genotypes and progenitors resistant to Cassava Mosaic Disease (CMD) for the putative presence of the CMD2 resistant gene using molecular markers.
Successfully packing a one-woman skit into 60 seconds.

7. The Enthusiasm and Sparkle Award: Ruth Thompson for Poster 3.7: Marker-assisted and farmer-participatory breeding for the development of farmer-preferred cassava lines resistant to pests and disease
Needs no further explanation if you remember her presentation and infectious enthusiasm. As a young breeder, we hope she will start and sustain a positive pandemic.


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Field trip
Tuesday 22nd September was a designated field trip day. The options available to participants were:

Option 1
• Visit Sanankoroba, Marako and Dialakoroba villages; sites include IER sorghum and maize experimentation, first guinea race sorghum hybrid seed production in farmers’ fields and maize seed production with one of the first private companies in Mali.
• Lunch at the Campement “Woloni”, on the shore of the lake.
• In Selingue, a perimeter for irrigated rice was visited, including a walk along the lake.
• Visit led by Abdoulaye Diallo (sorghum breeder) and Ntji Coulibaly (Head of Maize Programme, IER).
• Max distance to site (ie. Distance of the furthest of the three villages from Bamako): 150km
 
Option 2
• Visit the villages around Siby; focus was on farmers’ experimentation with sorghum varieties and legume crops (including groundnut, cowpea and soybean);  this trip also included a visit to a farmer seed producers cooperative.
• Picnic lunch at a natural arch
• Visit led by Dr Eva Weltzien (sorghum breeder, ICRISAT), Dr Sidi Bekaye Coulibaly (sorghum breeder, IER–Cinzana), and Mamadou Coulibaly (Association des Organizations Paysannes Professionelles [AOPP]).
• Max distance to site (ie. Distance of the furthest of the villages from Bamako): 80km
 
Option 3
• Visit to the IER Sotuba research station, near Bamako; focus was on sorghum breeding research, including CP-funded projects. The AGRA-funded experimentation with maize, cowpea, rice, millet and sorghum was included.
• Possibility of visiting the ICRISAT/IER GIS laboratory.
• Picnic lunch in the garden of the national museum, and guided tour of the museum afterwards.
• Visit led by Dr. Niaba Teme (geneticist) and Abocar Toure (sorghum breeder).
• Approx. distance to site: 7km

Option 4
• Visit to the ICRISAT research station at Samanko, near Bamako; focus was on groundnut breeding, aflatoxin management and sorghum breeding research for the Sudanian zone, including GCP-funded experimentation.
• The visit included an overview of AVRDC experimentation with vegetables in Mali, and ICRAF’s collection of Zizyphus, and Moringa ssp.
• Picnic lunch at Samanko research station, followed by a visit to the Bamako Handcrafts market.
• Visit led by Dr. Fred Rattunde (sorghum breeder) and Dr. Bonny Ntare (groundnut breeder).
• Approx. distance to site: 20km

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Side events: GCP Project Day, 24th September
Thursday 24th September was set aside for project PIs to hold project meetings, workshops or demonstrations.

The following workshops were held:

1. The Ontology Network meeting (Coordinator: Rosemary Shrestha)
a.) Brief introduction to the Crop Ontology and its development
b.) Demonstration of The Ontology Browser
c.) Demonstration of the application of crop ontology: show the actual application of ontology for searching data and comparative studies across crop species.

2.  Data management clinic (Coordinator: Elisabeth van Strien)
a.) Presentation and discussion on ‘Uploading data on the Central Registry’
b.) Presentation and discussion on ‘The Phenotyping Wizard’
c.) Helpdesk and practice sessions on preparing data and uploading data to the Central Registry.

This workshop incorporated a Data management clinic session in the afternoon, which include personalised assistance in project registering, data set uploading and searching the CR and in ontology.

3. A half-day training course on using simulation in breeding projects (Coordinator: Jiankang Wang)
Introduction of the principles of breeding simulation (0.5 hr, Jiankang Wang); the genetics and breeding simulation tools and their applications in optimizing breeding strategies and improving breeding efficiency (1 hr, Jiankang Wang); use of the QU-GENE graphical user interfaces to design and complete simulation experiments, analyse and visualise the results (1.5 hrs, Scott Chapman)

4. Design and analysis of marker-trait association studies (Coordinator: Marcos Malosetti)
Presenters: Marcos Malosetti & Fred van Eeuwijk
As part of the GCP commissioned project Design and analysis of marker-trait association studies (G4007.09), Marcos and Fred presented guidelines and methodology for design and analysis of LD studies. Items up for discussion included:
a.) Data quality protocols for genotypic and phenotypic data
b.) Studying diversity, identifying population structure, and estimating genetic relations
c.) Studying LD decay and designing experiments for use in marker-trait association studies
d.) Mixed model methodology for marker-trait association studies
e.) Software and support available to GCP community with respect to marker-trait association studies

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5. Chickpea Challenge Initiative meeting (Coordinator: Pooran Gaur)
The aim of this workshop was to discuss a workplan for the Chickpea Challenge Initiative, following the schedule below:

 - Updates on Chickpea CI activities (Pooran Gaur)
 - Genetic and physical mapping in chickpea (Rajeev Varshney)
 - Current status of SNP discovery in chickpea (Doug Cook)
 - Updates from NARS, Kenya (Paul Kimurto)
 - Updates from NARS, India (M Yasin)
 - Discuss and refine workplan for chickpea CI

6. Rice Challenge Initiative meeting (Coordinator: MN Ndjiondjop)
Objectives and outputs
To identify donors and populations that could be used for MARS, and commission small activities necessary to ensure the MARS populations will be available on time
 
Rationale
The Rice CI team needs an opportunity to identify as a group the donors of MARS populations and to develop coherent and effective list of donors and populations, agreed on the timeline of their availability to achieve overall goals of the Challenge Initiatives.

Activities
a.) Choice of donor parents by breeders
a. Establish a list of potential donors bases on their agronomic performance, acceptability by farmers, information on drought tolerance
b. Establish a list of F2 and F3 populations already developed by breeders and other scientists for breeding for rainfed lowland rice.
c. Establish a prioritised list of crosses
b.) Seed multiplication
c.) Discuss and establish a detailed timeline of the availability of the populations
d.) PLS add any other points that need to be discuss

7. Sorghum Challenge Initiative meeting

8. Assessment of the breeding value of superior haplotypes for AltSB, a major Al tolerance gene in sorghum: linking upstream genomics to acid soil breeding in Niger and Mali (ALTFIELD) (Coordinator: Robert Schaffert)
 - Current status of project (Embrapa Maize and Sorghum, INRAN, ICRISAT–Mali and ICRISAT–Niger)
 - Financial status and report
 - Technical status and report project strategy workplan for Year 2 and Year 3 (Embrapa Maize and Sorghum, INRAN, ICRISAT, Mali and ICRISAT Niger)
 - Development of phenotyping sites for tolerance to al toxicity
 - Status of germplasm exchange
 - Special instructions for increasing germplasm marker assisted selection GCP Genotyping Services

8. SGRP, GCP and the long-term management of genetic resources and associated information in the CGIAR (Coordinator: D Williams)
Speakers:
a.) David Williams: Introduction and prospects
b.) Jean Christophe Glaszmann: Advances in the development of the GCP reference sets
c.) Ruaraidh Sackville-Hamilton: Experiences with curation and distribution of the GCP reference sets
d.) Hari Upadhyaya: The role of CG Centres as hosts of GCP products
e.) Elizabeth Arnaud: Accession-level information management
f.) David Williams: The way forward and general discussion

For more information and outcomes of the workshops held, please contact the relevant coordinator(s) directly.

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