Genedata Selector™: Software for Molecular Breeding of Climate Ready Crops

Climate change and population growth will increase the global demand for sustainable crops to produce feed and food products, as well as biofuels and bio-based chemicals. Maximizing biomass is a key to the agricultural and biofuel industry’s success.

Molecular breeding of new feedstock crops resistant to abiotic stresses such as drought requires integration of diverse biological data including genotypes, phenotypes, and expression measurements. Due to constantly declining costs for next generation sequencing, genomic-based studies have become central in crop improvement programs and are an integral part of marker-assisted breeding (MAB). Genedata Selector™ supports MAB through integrated management and analysis of whole genome sequences, gene annotation, and associated phenotype information.

Genedata Selector™ is a comprehensive, integrated software system for managing and analyzing genome sequences along with phenotype information for optimization of crops. We show how the software can be used to annotate newly sequenced genomes and refine gene models. We used the software to compare crops across multiple strains to select those that have improved resistance to climate related stress factors. Mutations are linked to related information from different biological sources, including experimental transcriptomic, proteomic and metabolomic data and viewed in different biological contexts, for example regulatory networks.  We focus on variant transcription factors which regulate stress related target proteins in crops such as corn, maximizing crop yields under abiotic stress conditions including drought. Additionally, target genes of interest are linked to phenotypes and assay data, as well as patents.