A bioinformatics approach (PIPE) in functional genomics of soybean and soybean-cross species interactome

Soybean (Glycine max) is one of the largest sources of vegetable oil and protein in the world, and also an important legume crop to the Canadian economy. In order to expand soybean further north and west in Canada, the identification and characterization of genes involved in time of flowering and maturity as well as genes conferring resistance to the Soybean Cyst Nematode (Heterodera glycines) are crucial. The genes underlying many QTLs for time of flowering and maturity and for resistance to SCN are yet to be identified.
Protein-Protein Interactions (PPIs) are essential molecular interactions that define the biology of a cell, its development and its responses to various stimuli. Theoretically, if a gene interacts with groups of genes involved in one specific pathway, that gene might also be involved in that specific pathway (i.e. “guilt by association”). The soybean Protein-protein Interaction Prediction Engine (Soybean-PIPE) is a computational tool capable of predicting genome-wide PPI in soybean.
The latest version of PIPE (v.4) was used to predict the soybean and soybean-SCN comprehensive interactomes (genome-wide). As an example, the E8 maturity locus which was previously identified in our lab using classical breeding practices and a genome-wide SSR marker analysis, revealing a large region on chromosome 4 has been investigated by PIPE. Soybean-PIPE gene ontology, loss of function analysis, DNA sequencing, and expression analysis etc. were used in combination to identify the potential candidate gene for this maturity locus.
Identification of candidate genes for economically important loci may have a far-reaching agricultural and economic impact for diverse goals including marker assisted selection.