Identification of differentially-expressed genes involved in seed protein content in soybean

Soybean (Glycine max), a well-known legume for its protein-rich seeds (40% protein content), is the fourth largest crop by production area in Canada and has become a remarkable part of the Canadian agriculture due to its wide use for food, feed, and fuel. Although advancements in plant breeding have allowed the development of newer cultivars of soybean that are grown in Eastern Canada, growing soybean in the Western and Northern parts of Canada has presented farmers with a number of issues such as a lower protein content and delayed times of flowering and maturity. Thus, there is a need to develop advanced varieties of soybean that are not only tailored for the different environments of the Western and Northern parts of Canada where they are exposed to longer photoperiods and colder temperatures, but that will also meet the global soybean seed composition standards. Much has been done to understand the way specific environmental stresses such as drought and salt can affect gene expression in soybean, however, the role of environment in Western Canada and in regulating gene expression involved in seed protein content have yet to be systematically investigated. Using advanced molecular biology techniques such as Next Generation Sequencing (NGS) at a whole transcriptome level will enable us to identify differentially-expressed genes that are associated with a lower seed protein content in soybean cultivars grown in Western Canada compared to Eastern Canada. In order to address this issue, ten different varieties of soybean, with a range of seed protein content, have been grown in three different locations across Canada (Morden, Brandon, and Ottawa). RNA sequencing has been performed at an average of ~18-25 million base reads-depth for each of the 90 samples to increase the chance of detecting genes with lower expression frequency (higher transcriptome-wide coverage). Our preliminary data analysis (i.e. expression analysis, gene ontology analysis) have identified a list of genes (include isoforms) expressed differently in Western Canada involved in seed protein content, seed oil content and response to abiotic stresses. Further follow-up experiments including co-expression network analysis, QTL mining for the candidate genes etc., are underway to shed more light into differential expression of the selected candidate genes. Identification and characterization of genes involved in seed protein content especially influenced by environmental variations (i.e. Eastern vs Western Canada) will lead us to allele-specific marker development for marker-assisted selection and also identification of alleles that will best enhance soybean breeding programs for seed protein content in specific locations, targeting Western Canada.