I am engaged with answering plant biology questions in the aspect of genomics beginning with his graduate study. In the early 2000s, during my PhD study, the plant research community was extensively starting genome sequence projects of crops which genomes are larger and more complicated than the two sequenced plant genomes, Arabidopsis and rice, at that time and there was no exception for legume research community. To facilitate the progress of the soybean genome project, I addressed two fundamental issues: characterizing the mechanisms underlying genome expansion in the modern soybean genome, and investigating the fates of duplicated genes and the driving forces shaping duplicated genomic regions in the paleopolyploid soybean genome.

To expand my research spectrum from comparative genomics to functional genomics, during my postdoctoral study, I focused on addressing how a seed is formed using functional genomics approaches. To understand the role of epigenetics in seed development, I characterized the genome-wide DNA methylation patterns across seed development, including soybean and Arabidopsis seeds. Additionally, to elucidate the functions of specialized large suspensors (the tissue connecting the embryo proper and mother plant) versus small ones in different species, I utilized comparative transcriptome analysis across legume species (soybean bean, common bean and scarlet runner bean) and Arabidopsis. Collectively, these study experiences in comparative and functional genomics of crop and model species have paved the research dorection and laid the foundation for my current research.

The focus in my laboratory is to understand how a reproduction tissue/organ is formed. We investigate the genome-wide molecular processes controlling phase transitions, including seed development and fruit development, using genomic tools. The major questions addressed in our research are: (i) What are the epigenetic mechanisms that regulate gene expression to drive developmental programs? (ii) how are genes interconnected with each other and with the cognate regulatory sequences to form gene regulatory networks that promote seed developmental processes? (iii) how are gene loci organized in the genome to program developmental processes?

The second focus is to understand the role of epigenomic changes in response to environmental stress. The major questions are: (i) What are epigenome plasticity and stability in plant cells under stress? (ii) Which genes have their activities controlled by epigenetic changes in plant cells under stress?