Identification of differentially expressed genes involved in seed protein content in soybean, Glycine max

Adaptation of Canadian soybean agriculture to changing climate conditions is important to producing an adequate crop yield with acceptable levels of seed protein and oil content. The Canadian Grain Commission has reported lower seed protein content from soybeans grown in western Canada compared to eastern Canada. Reduced interest in soybean production as a major part of Canadian agriculture means losing a key nitrogen fixing partner from the crop rotation. Ten soybean lines ranging in seed protein and oil content are growing in four locations across Canada. Transcriptome-wide differential expression analysis via RNA sequencing (RNA-seq) is being used to identify differences in expression of genes contributing to seed protein and oil content,and to investigate the effect of environmental variation on geographically-dependent gene expression (East vs West). To accomplish this, three groups of genes are being investigated; genes involved in seed protein and oil biosynthesis mechanisms, stress response genes, and genes that code for regulatory proteins capable of influencing expression of other genes. Tissue from each line has been collected over the last three years and subjected to RNA-seq to allow creation of a large, high-quality data set. Gene ontology, differential gene expression, differential transcript expression, differential exon usage, and new transcript discovery are the key bioinformatic tools in determining candidate genes. This research will support allele-specific marker developments for strategic molecular breeding. In addition, this project is generating a large RNA-seq data set useful for subsequent investigation of differential gene expression in other economically important pathways.