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Activity Summaries

Activity 111 Establishment: Terms of reference (TOR) and job descriptions have been developed for the MBP Management Team. A Platform Manager, Informatics Coordinator and one Service Manager are on board. A project web site and Wiki have been established . Contracts have been accepted by all partners, and funds disbursed for all activities. The formal project launch meeting was conducted 17th to 20th February 2010 in Hyderabad, India.TOR for the IBP Scientific and Management Advisory Committee (SiMAC) were developed and five Core Members appointed. Seven additional members agreed to serve on the Specialist Group. From its first meeting during the Launch Meeting, SiMac presented a favourable report.TORs for a User Committee (UC) were developed and the committee established with representatives for each use case crop. A User-Developer teleconference was held in January 2010 and the UC had its first face-to-face meeting during the Launch meeting, and a further teleconference in May 2010.A business plan was developed and reviewed by participants at the Launch Meeting, receiving favourable comments. However, due to the ongoing CGIAR reform process further development of the plan will be delayed until a clearer picture of the future CGIAR emerges. A communications strategy was defined in consultation with the Communications and Marketing advisor on SiMAC, and presented at the launch workshop. Feedback from the majority of the participants was that the name Molecular Breeding Platform needed to be revised. This was done consultatively, resulting in a name change to Integrated Breeding Platform. Logos were also designed. Several press releases and a public awareness brochure have been written. Full Report.

Activity 112 Portal: The Portal is at the advanced planning stage. Implementation was delayed by late recruitment of the Platform Manager and the need to plan the integration of several existing and new informatics components some of which have also been delayed. Full Report.

Activity 113 Helpdesks: Helpdesk protocols and procedures are under development.. However, it is functioning via email with the Platform Manager, Informatics Coordinator and PIs - with a formal launch scheduled for Month 18. Four Data Management Workshops have been conducted covering seven use cases and four more are planned over the next six months which will cover the remaining use cases. A Data Analysis Workshop was held, demonstrating analytical techniques to representatives of most use cases. Sessions explaining molecular breeding techniques were included in rice, sorghum, cassava, and wheat use case project meetings and will continue with legumes and wheat again over the next two months. A User Community Relations strategy is under development. An annual platform meeting bringing together users, service providers, and developers was held in Hyderabad, India, 17-20th February 2010, also serving as the project launch. Full Report.

Activity 114 Communities of Practice: Active communities of practices (CoP) that are discipline- and commodity-oriented are critical to the adoption and promotion of the tools and services to be accessed through the IBP, and for sustainability of the platform. However, this activity has had a slow start-up as it takes time to bring potential CoPs together and stimulate interactions. The development of IBP crop CoPs builds on lessons learnt from 2 CoPs that predate the IBP: Rice in Asia and Cassava in Africa. Resources allocated to this activity have been used to support the Cassava in Africa CoP as a pilot project to inspire and guide the establishment of CoPs within the IBP. The CoP is led by the National Root Crops Research Institute in Nigeria, and includes scientists from Ghana, Tanzania and Uganda as well as mentors from CIAT, Cornell University, EMBRAPA and IITA. The CoP promotes modern breeding in general and marker technologies in particular. During the launch meeting in Hyderabad a community of data managers, grouping leaders in that field from CGIAR centres and key NARS, was established. These data managers, who will be the future trainers of the informatics tools, met again in Zaragoza (May 31- June 4) to define the trait dictionaries for the different crops in the use cases and a suitable format for the electronic field books. Launch workshops for several of the use cases provided opportunity to initiate crop-specific CoPs, and select a CoP leader. The workshops contained a significant Data Management and Analysis component and representatives from the data management CoP have been engaged as well. Resources allocated to this activity will be critical to the establishment CoPs in the lifetime of the IBP project, supporting leadership, capacity building activities, a forum for communication and exchange, and participation in key events.

Activity 211 Germplasm Data: Current ICIS tools and databases were installed manually on computers of use-case Data Managers' at the IBP Informatics Workshop in February, It was established that the current ICIS installer is inadequate for IBP use-cases, and a new installer is being developed by CRIL. A series of presentations about entering pedigree data were given.For those who were ready, the Activity team helped them to start loading their pedigree data. Discussions were held with use case Breeders and their Data Managers about their needs and how they can apply ICIS. 91 bug fixes and 50 feature requests have been implemented, including a new check to the pedigree data section of the Data Validation Tool. A report on the use of bar-coding practices in breeding programs was prepared and presented at the Launch Meeting. Full Report .

Activity 212 Phenotypic Data: The parser development was integrated into the Maize fieldbook, and is undergoing testing. The CIMMYT Fieldlog was chosen as the preferred handheld application. It was integrated with the ICIS Workbook, with a macro programmed to convert the ICIS Workbook template to two CSV files used by the Fieldlog, and then put the data from the CSV files back to the ICIS Workbook. The HP iPAQ 110 and Dell Axim x51v were evaluated for use with the Fieldlog, and the HP was selected because of the ready availability of units and post-purchase support. The Ontology schema was reviewed and its integration with the ICIS schema designed. The Data Mining tool was modified and generalized to integrate well with the central IWIS3 database. Full Report .

Activity 213 Genotypic Data:Various modifications were implemented on the Laboratory Information Management System (LIMS) based on workflow requirements, including: allowing users to upload DNA plates; modifying the Run Plate workflow to allow pooling of samples; and uploading Nanodrop Spectrophotometer output files. Improved functionality and reporting was implemented, including: allowing the use of markers from related crop species; implementation of access levels for improved security and standardization of protocols within the laboratory; reporting normalized Plate data and DNA Pooled Plates; and reporting Normalization data based on the number of samples. Bug fixing and improving user-friendliness included: implementation of list boxes as opposed to suggestion lists for fields with many values; improving performance while assigning marker/s to a plate; the quantification module improved to retrieve the concentration values properly; and screen resolution was improved. Full Report .

Activity 221 Statistical and Genetic Analysis Methodology: A guide for analyzing individual breeding trials was developed and user documentation produced. Software has been written to facilitate the analysis of single trials using standard and advanced spatial models, and a tutorial produced together with an example data set. The development of first generation GenStat procedures and documentation for phenotypic (single trial and GxE analyses), and for genotypic analysis (genetic diversity, QTL, QTLxE, and LD mapping) has produced a wide range of powerful advanced methods for analysing breeding data sets. Documentation of the procedures and example data sets and exercises have been produced to facilitate the adoption of the technology. The methods are available within one software package, saving the breeders the inconvenience of using multiple software tools to perform different analyses. A user-friendly interface eliminates the need to understand command language. Full Report .

Activity 222 Cross prediction and Selection Methodology: An existing program has been improved for application to different marker selection schemes. The enhanced program, OptiMAS, has new algorithms to compute probabilities of allele transmission in different mating systems, while reducing computation times and enabling greater flexibility and adaptability of the program to different marker-assisted selection schemes and mating designs. The flexibility has been enhanced to manage variable numbers of founders, overlapping generations and allow for residual heterozygosity among founders. Initial development of decision support tools for breeding include a tool to select the subset of informative markers best adapted to follow the favourable parental alleles (based on haplotypes) throughout generations of selection. A graphical interface has been developed to complement line code, visualize results, help the selection of individuals and design intermating. The first versions of these tools have been tested on a 4 parental design and on a more complex design derived from 13 parental lines, with favourable results. Full Report .

Activity 223 Simulation Tools: Key enhancements have been incorporated into the QuGene user interface including high-speed import/export of QuGene data formats with those of common QTL analysis software and genotype browsing tools that are to be used in the IBP; the cluster capability for QuGene has been implemented to allow automated runs of QuGene utilising installations of Condor or Microsoft HPC server. Current versions of QuLine, QuHybrid and QuMars are all enabled in QuGeneUI. They can generate breeding workflows from each of the application modules based on breeding program descriptions, and use ZGRviewer to interactively display breeding workflows. Integration with FlapJack will enable read and write to and from FlapJack for the Gene-Environment System, allowing direct building of QuGeneUI from GenStatQTL analysis. An updated version of QuHybrid has been incorporated into the user interface. A new seed propagation type "Testcross" has been implemented in QuHybrid, allowing selection to be conducted using the performance of a testcross. A new generation advance method "Superbulk" has been implemented in QuHybrid, that allows mixing of all selected individuals in all families into one population, thereby decomposing the family structure. A new QuMARS application module to properly simulate the three stages involved in a MARS breeding programme has been developed. Simulations have been developed for three case studies (sorghum MARs, rice backcross, wheat cross prediction). The Activity Team is working towards full documentation of the breeding programs of the GCP use cases, to enable preliminary simulations during the next 12 months. Full Report .

NB: A complete overhaul of the strategy and management of Objective 2.3 Information network, decision support tools and a workflow management system is under discussion due to unanticipated technical and administrative complexities leading to failure to meet some milestones. For the full report on progress thus far on the integrated activities under this objective and lessons learnt click here .

Activity 231 Middleware Infrastructure: General project review of the GCP domain model was completed. Changes were incorporated into a 2.0 release of the GCP domain models and associated Java libraries. A review of GCP Java API ("Pantheonbase") was completed, and a 3.0 release GCP/IBP-compliant API developed and specified for writable data sources. More than 20 middle layer simple and complex use cases were implemented with the data sources for retrieving data based on different filter and output requirements. Caching systems inside the database and on the Java object layer were added to data sources to promote system performance. IBP development team members were trained on GCP/IBP compliant technologies. Full Report .

Activity 232 Visualisation: A prototype of the Information System for MAB (ISMAB) has been developed for the Marker-assisted backcrossing workflow. It includes a Molecular Breeding Design Tool (MBDT) to assist breeders in selecting parental germplasm based on phenotypic data, check availability of and view genotyping data for recipients and donors, and allow users to choose markers and design crosses. It also includes the Molecular Selection Tool (MOSEL) that facilitates the selection of the most promising lines; filtering, sorting and scrolling graphical genotypes for proximity to target and parental lines; and choosing lines and crossing schemes for further development. Full Report

Activity 233 Configurable Workflow System: Design document and use case specification repository for IBP workflow system has been established and populated with initial design requirements from end users. The appropriate informatics tools for implementation in the CWS to support the application of markers were identified through intensive discussion with breeders. These tools were identified as fundamental: molecular design tool for parental selection, a cross predictor tool for cross selection, a marker-assisted backcrossing optimizer, a marker-assisted gene pyramiding designer, and simulation tools for designing marker-assisted recurrent selection, including genomic selection. Emerging statistical methods for gene mapping were reviewed to identify the tools required to implement these methods and evaluate whether such tools should be integrated in the CWS. A few R packages that have a good graphic user interface and can be used to conduct basic statistical analysis of plant breeding data were compared. The CropStat software was chosen and is being converted into an R package, and will then become part of the of the configurable workflow system. R packages for QTL mapping (linkage and association mapping) have been studied, but none has a desirable graphical user interface, hence it was decided that a user-friendly interface be developed for the R/QTL and GenAbel packages that will then become part of the configurable workflow system. Full Report .

Activity 311 Genetic Resource Support Service: A paper entitled Accessing genetic diversity for crop improvement was published in the April 2010 issue of the journal Current Opinion in Plant Biology (COPB 13:1-7), describing the utility of core reference sets of crop genetic resources. New genotyping has been completed for banana/plantain (Musa), bringing to ten the number of complete validation data sets - finger millet, sorghum, groundnut, pigeon pea, chickpea, barley, maize, wheat, coconut, and now Musa. Quality assessment of the datasets has been completed for six of the species (Barley, Coconut, Finger millet, Groundnut, Musa and Pigeon pea). Comparison has been completed for Barley, Chickpea, Coconut, Finger millet, Groundnut, Musa, Pigeon pea and Sorghum . Analyses are progressing for Common Bean, Cowpea, Lentil and Yam, while Maize and wheat are ready for quality assessment. Seed has been regenerated for Chickpea and Sorghum. For the other crops, requests for detailed information and contingent planning for regeneration are to be synchronised with the actions taken to solve the problems highlighted in the data quality reports. Full Report .

Activity 312 Marker Services: Nine potential marker services providers were identified and evaluated. Agreements were subsequently concluded with BecA (Kenya), KBioscience (UK), and DNA Landmark (Canada).Working documents previously successfully used for the Genotyping Support Service were adapted for use with the Marker Services. Thirteen service requests were fulfilled - covering cowpea, maize, potato, groundnut, faba bean and peach. Requests came from Bolivia, Burkina Faso, Hungary, Mexico, Senegal and USA. Marker types used for the services were 7 for SNPs and 6 for SSR. Service providers utilized were: DNA Landmarks, ICRISAT and KBioscience. Two of the clients were use cases of the IBP while the balance were National Programs. Full Report .

Activity 313 Trait and Metabolite Services: Preliminary discussions took place with a few collaborators to identify potential trait and metabolite service providers. An effort has commenced to catalogue the needs of potential service users. This activity will be pursued with greater vigour in the second project year - particularly following the hiring of a full-time Breeding Services Manager, scheduled for the last quarter of 2010. Full Report .

Activity 321 Breeding Plan Development: Generic breeding workflow outlines have been developed for MAS projects and MABC projects. A Project appraisal and cost-benefit analysis tool to support decision-making is to be implemented in the second year of the project, in part based on the recently completed breeding project simulation tools developed under Activity 2.2.

Activity 322 Information Management: Information management software and training materials have been developed/adapted and made available for download. Three training courses/workshops for Data Managers have been held: Hyderabad, India, in February; Sorghum use case, in Eldoret, Kenya, in May at which the central International Sorghum Information System (ISGIS) was established containing the traits from the Crop Ontology , and a data management workshop for Use Case Data Managers and Crop Lead Centers in Zaragoza, Spain, in June. An on-site support visit was made to ICRISAT to upgrade their International Chickpea Information System (ICHiS). ISIGIS was installed in the computers of 10 attendees during the Sorghum CI Data Management Workshop, and at Zaragoza ICIS was installed or updated in 15 computers of attendees representing different use cases. Databases for beans, cassava, yam and soybean were upgraded to ICIS Schema 5.5. The upgraded central database for beans (IPHIS) was installed for CIAT, who will manage the beans central database. Similarly upgraded databases for cassava, cowpea, yam and soybean were set-up for IITA. Fieldlog, an application for handheld devices for recording plot data, was installed in ten devices, which were distributed to collaborators from the Cassava, Chickpea, Cowpea, Rice, Sorghum and Wheat use cases. Helpdesk support has been provided to users through email. An IBP staff position for a Data Manager/ Training Specialist has been advertised and is expected to be filled shortly, which will greatly enhance the Help Desk function. Full Report .

Activity 323 Data Curation: Training materials for data curation have been developed/adapted and made available for download. The Informatics Workshops/Training Courses cited for Activity 3.2.2 above included significant elements of Data Curation. Regular meetings have been held with the wheat informatics team at CIMMYT for review and update of IWIS3. Technical support for Data Curation has been provided to various users via eMail and WebEx. The staff position cited in Activity 3.2.2 above will also help enhance user support for data curation. Full Report .

Activity 324 Design and Analysis: Training tutorials have been developed for the different aspects of the QTL mapping methodology. The guides, include: a) Practical single trait QTL Mapping which focuses on the search for QTLs for a single trait in a single experiment (environment), and illustrates the approach using a barley data set; b) Practical Multi-Environment QTL Mapping which scales up the QTL analysis to multiple environments. The guide illustrates how to fit and compare different models to identify the best model for the specific data set,and uses maize drought stress trials in as the example; and c) Practical Linkage Disequilibrium Mapping covers the mixed models for LD mapping developed in Activity 2.2.1. This guide illustrates all available methods with a practical example in barley. A training workshop for statisticians and quantitative geneticists from different use cases and crop lead centres was held in Zaragoza, Spain in June to present the material developed in this activity, and create a network to amplify the scope and products of this activity. The demand for Helpdesk support was modest. Specific queries were addressed by the activity group, mainly from researchers in Africa. Support was given to Activity 3.2.6 Genotype Support Services in reviewing proposals for the service. Full Report .

Activity 325 Phenotyping Support Service: Thirty-four potential field phenotyping sites in Africa, twenty-four in Asia, eight in South America, and one in North America, have been identified. Progress was made in site characterization. Plans are in place to improve site infrastructure by funding specific projects in areas such as weather stations, irrigation, heat or rain shelters, fences, and land clearing and. Two workshops are proposed forlater this year, one in French in Mali and another in English in Ghana, to train African field station managers. A publication on the innovative drought characterisation tool used in the assessment of the sites is being prepared for submission to Computers and Electronics in Agriculture after internal GCP review. A phenotyping manual prepared with detailed contributions from various crop and trait experts awaits publication. Full Report .

Activity 326 Genotyping Support Service: The 3rd call for Genotyping Support Service proposals opened in October 2009 and closed in January 2010. Sixty-two applications were received from 19 different developing countries, covering Cassava, Chickpea, Cowpea, Groundnut, Maize, Millet, Musa, common bean, Rice, Sorghum, Sweet potato and Wheat. A panel of GCP and external experts reviewed the proposals of which 56 fulfilled the minimum requirements, and grantees will be announced in the near future. Identification and contracting of appropriate service providers was done simultaneously with the selection for Activity 3.1.2 Marker Services, already reported. During the reporting period, five work orders were concluded from the previous GSS call- sorghum (Ethiopia), cassava (Thailand), potato (Bolivia), maize (Bolivia) and barley (Peru), and seven work orders were committed- cassava (Ghana and Nigeria), coconut (Sri Lanka), common bean (Bulgaria), maize (Hungary and India), and Musa (Ecuador). Four jobs are in the pipeline, while another 11 cases are awaiting availability of the required new markers. As soon as a critical mass of beneficiaries is achieved, a data analysis and interpretation workshop will be arranged for the grantees. Full Report .

Activity 327 IP and Policy Helpdesk: The GCP Executive Board mandated the establishment of a programme-wide IP Advisory Committee. The Committee comprises eminent IP professionals drawn from various institutions and organisations. A virtual IP Help Desk has been established And populated with preliminary resource materials including frequently asked questions. Additional IP Policy and Training materials for GCP are under development by Bioversity. Demand for helpline services has been limited. Queries have been referred to relevant experts and responses preserved in the Frequently Asked Questions portion.

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