Theme 3: Crop information systems 

Rationale

GCP’s Theme 3 on Crop information systems supports the development of infrastructure to network and publish diverse databases and supported tools and standards for the integration and analysis of data from different sources and disciplines, particularly for molecular breeding in conjunction with the Integrated Breeding Platfrom (IBP).

Emphasis in GCP's 2010–2012 Medium-Term Plan (MTP) is on user support, both for the IBP and for the Research Initiatives. Outputs (MTP language for ‘projects’) are organised into four objectives covering: i) user support; ii) data curation and quality; iii) methodology development; and, vi) infrastructure.

Main achievements in 2010
Crop information databases, trait dictionaries and phenotyping templates have been initiated or improved for the eight crops and fourteen breeding projects associated with the IBP. Trait ontologies have been further developed for seven crops (wheat, rice, maize, sorghum, cowpeas, chickpeas, beans), and a cassava trait ontology has been initiated.

An analytical pipeline has been established for processing next generation sequencing (NGS) data from raw sequence reads to detected SNPs and haplotypes, thus providing a cost-effective and efficient method of developing genomic resources for less-studied crops. An enhanced query interface has been developed to the International Rice Information System (IRIS)  as part of the GCP informatics platform, demonstrating the utility and versatility of the platform technology for publishing information for any crop.