Highly Efficient Discovery of Novel Genes in the Complex Perennial Populus Using GWAS and Coexpression Analyses in KBase

QTL cloning for the discovery of genes underlying polygenic traits has historically been cumbersome in long-lived perennial plants like Populus. Linkage disequilibrium-based association mapping has been proposed as a cloning tool, and recent advances in high-throughput genotyping and whole-genome resequencing enable marker saturation to levels sufficient for association mapping with no a priori candidate gene selection. Here we illustrate how we have successfully leverage advanced computing resources in the DOE  Systems Biology Knowledgebase (KBase) to perform GWAS analysis of complex traits in Populus with single-gene resolution. We have analyzed hundreds of phenotypes ranging from secondary metabolites, growth, callus formation, phenology, disease resistance, crown architecture, and cell wall chemistry using a panel of 8.2 million high quality SNPs and indels. Additionally the KBase coexpression network platform enabled us to identify a major transcriptional regulator of the phenylpropanoid, flavonoid and tryptophan pathways not previously reported.