Epigenetic Variation in Legume Crops

Epigenetic variation, that is non-sequence-based variation, has been of great interest in plant and animal research in the last few years. Little has been done to explore epigenetic variation in the context of plant improvement. Using soybean, we are exploring the level of epigenetic variation in soybean breeding germ plasm from across many US breeding programs. Using sodium bisulfite DNA sequencing, Methyl C sequencing, we have sequenced more than 100 soybean accessions including landmark cultivars from the past 80 years of improvement in the US, parents of the public NAM (nested association mapping) population, landraces and undomesticated soybean. Using these data, including RNA-seq and small RNAs, we determined differentially methylated regions (DMR) for all three methylation contexts (CG, CHG and CHH). These DMRs were then analyzed for their genomic context: exonic, UTRs, upstream, downstream, and intergenic or repeat (e.g. transposable elements).  I will discuss these data in context of DMR variation (inherited and de novo) within and between varieties, landraces and wild soybean as well as their potential contribution to breeding/selection over the past 80 years and their contribution to variation.