A functional genomics approach for the identification of a candidate gene for maturity locus in soybean

Soybean 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 are crucial. The E8 maturity locus was previously identified in our lab using classical breeding practices and a genome-wide SSR marker analysis, revealing a large, high confidence region. This region has been investigated by a functional genomics approach using a bioinformatics tool called Soybean-PIPE (Protein-Protein Interaction Prediction Engine) which predicts genome wide protein-protein interactions. To filter the ~1000 genes of the E8 region, each gene was ordered based on how many of its interacting partners (genes) were involved in development and flowering, shortlisting the candidate region down to ~25 genes. A likely candidate Glyma.04G124300, is annotated with FAR-RED ELONGATED HYPOCOTYLS 3 (FHY3) and FAR-RED-IMPAIRED RESPONSE 1 (FAR1) functions. These proteins are known to have multifaceted roles in light signaling and various physiological and developmental processes. Sequencing contrasting lines for E8 and e8 revealed a number of single nucleotide polymorphisms (SNPs) and insertion and deletion (INDELs), altogether suggesting that Glyma.04G124300 is the likely candidate gene for maturity locus E8.