Methylation Changes in Soybean Early Maturation Seed Compartments Using Laser Capture Microdissection (LCM)

What methylation changes are occurring in different compartments of early maturation stage seed largely remains unknown. To uncover the possible role of DNA methylation in different compartments of early maturation stage seed, we characterized the methylome of two major compartments (abaxial parenchyma and adaxial parenchyma) in embryonic cotyledon, four major compartments (parenchyma, plumule, root tip, and vascular) in embryonic axis, and seed coat layers (parenchyma and palisade) using Illumina sequencing. The whole seed coat and embryonic cotyledons were captured using LCM to serve as controls. Overall design: Illumina sequencing of bisulfite-converted genomic DNA from cotyledon abaxial parenchyma (EM-COT-ABPY), cotyledon adaxial parenchyma (EM-COT-ADPY), seed coat parenchyma (EM-SC-PY), seed coat palisade (EM-SC-PA), axis parenchyma (EM-AX-PY), axis plumule (EM-AX-PL), axis root tip (EM-AX-RT), axis vascular (EM-AX-VS), whole seed coat (EM-SC), and whole embryonic cotyledons (EX-COT)