A functional genomics approach (PIPE, Protein-protein Interaction Prediction Engine) to identify new early maturity alleles in soybean for Western Canada

As fundamental steps in successful seed production, the flowering time and maturity pathways play crucial roles in industrial agriculture including soybean production. The development of short season (early flowering and maturity) soybeans for Canadian and northern regions requires effective use of early maturity genes. Nine maturity loci have been reported in soybean, however the molecular basis of some of them are not yet clear. The list of novel factors affecting these pathways in soybean, and in model plants like Arabidopsis, continues to grow suggesting the presence of other novel players which are yet to be discovered. To this end, we have used three different approaches; classical plant breeding, molecular biology, and bioinformatics (functional genomics) to identify novel genes involved in flowering and maturity pathways in soybean.
Using plant breeding approaches followed by applied molecular biology techniques (analysis of SSR and SNP haplotypes), we have identified a new maturity locus tentatively called “E10” which has not previously been reported. E10E10 represents late flowering, alternatively e10e10 represents early flowering.
Protein-Protein Interactions (PPIs) are essential molecular interactions that define the biology of a cell, its development and responses to various stimuli. Theoretically (guilt by association), if a gene interacts with groups of genes involved in one specific pathway, that gene might also be involved in that specific pathway. Our knowledge of global PPI networks in complex organisms such as human and plants is restricted by technical limitations of current methods. Here we have used a bioinformatics tool called PIPE, Protein-Protein Interaction Prediction Engine, to predict the first comprehensive protein-protein interaction network for soybean. We are using it to help us to identify, short list and/or reconfirm the involvement of selected candidate genes in various projects including the breeding program for early flowering soybeans.