A Comprehensive Survey of Epigenomic Variation on a Population Scale in Legumes

Epigenomics is an intensely investigated area, not just because it expands our abilities to understand and explain observed phenotypic variations, but also because of its reversible nature it can be used to alter and manipulate economically important processes in crop plants. Legumes, such as soybean (Glycine max) and common bean (Phaseolus vulgaris) are major crop species that provides our daily food and oils, occupying an unreplaceable position in the nutrition pyramid. In this study, we surveyed legume epigenomic variations on a population scale with multiple data types, including methylomes (MethylC-seq), transcriptomes (RNA-seq), and small-RNAs (Small RNA-seq) in soybean, common bean and Medicago truncatula. In this study, we are aiming to 1) identify natural epigenomic variations and investigate how much of them are driven by genetic variation, 2) expand our understanding of the intimate symbiotic relationships between soil bacteria (rhizobia) and legumes and to explore potential epigenomic mechanisms behind each legume species and compare the differences between them, 3) compare and contrast the epigenomic variations between the two major types of nodules, determinate (soybean and common bean) vs. indeterminate (Medicago) nodules, 4) determine the role of genes targeted for gene silencing by RdDM (RNA-directed DNA methylation) and if they may serve a functional role in particular developmental processes or stress responses such as rapid response to infection, 5) determine the conservation of gene body methylation and RdDM targeting methylation within and between legumes.