Title: “Systems genetics in crop breeding: applying an eQTL bioinformatics pipeline in Galaxy to the grey leaf spot-maize pathosystem”



Systems genetics is the integration of trait phenotype, genotype, and global cellular data (e.g. transcript, protein or metabolite) to dissect complex traits. Understanding quantitative resistance and susceptibility of crops to pathogens is a worthy goal of systems genetics.  Our research is focused on grey leaf spot (GLS) disease of maize caused by Cercospora spp. fungi.  GLS is a threat to maize production in Africa and most maize producing regions globally.  We took a systems genetics approach to the problem by combining phenotyping (GLS disease scoring), genotyping (genetic mapping) and transcriptomics (Agilent whole genome microarrays) of a maize population segregating for GLS susceptibility.  We carried out (i) expression QTL analyses and (ii) weighted gene co-expression network analysis. Data integration allowed us to explore the genetic basis for coordinated expression responses to GLS disease in susceptible maize plants. A customized bioinformatics pipeline for eQTL analysis was developed in the Galaxy platform. The pipeline is applicable to systems genetics analysis of complex traits using  transcriptome data (microarrays or RNAseq) from segregating populations of other crop species.