Genetic and epigenetic bases for adaptation to mega-environments in soybean

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Crop improvement relies on continued use of genetic variation in plants and a lack of variation may impede further progress from plant breeding. Genetic variation can be found in breeding populations but also in gene banks or in nature across many regions of the world such as centres of origin or diversity for crop plants. However, only a fraction of existing variation in many crop plants has been used by plant breeders mainly due to an inherent lack of adaptation of exotic sources to target breeding environments. Soybean is a crop in which 90% of the genetic variation in North American soybeans is derived from as few as 35 ancestors. In contrast, vast amount of genetic variation exists in China as the centre of origin for soybean and may be available for use by plant breeders. In our previous NSERC Discovery grants we have identified a number of universal and ME specific Quantitative Trait Loci (QTL[U] and QTL[SP]) for yield and agronomic traits of which some were unique. Alleles for high yield have been often contributed by the PI (exotic) parent in each respective ME demonstrating the potential for introgressing new positive alleles from exotic germplasm. Both minor and major QTL alleles were contributed by the Chinese parent in the Canadian ME, the majority of them being QTL[U] across all three ME: Canada, northern U.S. and China. In addition, QTL[U] explained a greater amount of variation and were distributed across fewer linkage groups than the QTL[SP]. Universal QTL also exhibited fewer interactions and of smaller magnitude than the specific ones. Eighty-six percent of QTL[U] were associated with other agronomic or seed quality traits but acted as either QTL[U] or QTL[SP] for the yield related traits (Palomeque et al. 2009a and 2009b). We want to explore the underlying reasons for differential QTL expression that affect plant adaptation across different environments. DNA methylation is known to cause epigenetic changes that result in altered gene expression. Differential gene or QTL expression may be one of the reasons for difficulties in identifying exotic sources as potential parents for hybridization with adapted cultivars because their true genetic potential may be impacted (or masked) by epigenetic factors. In order to increase the use of plant germplasm from China to further improve soybeans in Canada, we will study the role of DNA methylation in the genomic regions that have been associated with seed yield as the ultimate measure of plants' adaptation to a new environment. An improved understanding of the role that DNA methylation plays in the expression of QTL for yield across different mega- and macro-environments will allow for the development of strategies for enhanced used of exotic germplasm. This in turn may lead to an increase in genetic gain from selection for seed yield in plant breeding populations and accelerate progress from and economic impacts of plant breeders' efforts. A continuous increase in seed yield of crops such as soybean will address the need for producing adequate food supplies for an increasing human population around the world.