Pathway Modeling for Citrus Variation

Cost reduction in sequencing technologies has made feasible the massive sequencing of plant and animal accessions to study genomic variations associated to breed identification, production or adaptation traits.  Genome sequencing and comparison to a reference genome makes it possible to identify nucleotide variations (SNVs, indels, deletions, etc) characteristics of a particular individual or variety. Such analyses typically result in thousands of variants with respect to the template genome and interpretative analysis of this genomic variation poses a great challenge.  A suitable approach to the understanding of the relationship of genome variants with the phenotype is their analysis in the context of metabolic or signally pathways relevant to the properties of the species of interest. However, most pathway information and tools have been developed for model organisms and utilization of such resources for non model species is not trivial. Within the CITRUSEQ project, we have sequenced more than 100 different citrus varieties and are developing bioinformatics tools to manage, analyze and understand the genomic basis of citrus diversity. In this scenario, we have addressed the analysis of citrus variation in the context of pathway data.  We have used reference organism databases such as Aracyc to map citrus genes to existing plant specific pathways and use the Aracyc pathway modeling tools to complete and extend pathway models for the Citrus genus. Visualization tools are being developed to display and explore cultivar variation in the context of pathway information. We believe this is a powerful tool for variety characterization and breeding.