• Comparative genomics and epigenomics in plant genome evolution

We seek to understand the function of transposable elements (TEs) in plant evolution, the differentiation and functional consequences of duplicated genes, and co-evolution of small RNAs and their targets, including the fates of microRNAs and protein coding genes, and the evolutionary patterns of small interfering RNAs and RNA-directed DNA methylation (RdDM) components.

Research idea: Co-evolution and regulation of small RNAs and their targets.

Project 1: Dissection of the evolutionary distance of the genes involved in small RNA silencing pathways. It is known that most of the RdDM targets are TEs, and TEs are evolved much faster than other DNA component. The working hypothesis here is that genes involved in RdDM (also known as transcriptional gene silencing (TGS) pathway have evolved faster than other genes. We have detected ~100 small RNA pathway genes in the maize and soybean reference genomes, respectively. Out of these 100 genes, ~60 are involved in TGS, and the left participate in post- transcriptional gene silencing (PTGS). Next step, we will compare their evolutionary distance between these genes and their flanking genes and randomly selected genes.

Project 2: Cross talks between different maize genomes. This project aims to detect small RNAs in one maize genome could trigger the silencing of their targets in another maize genome when they are merged together, and the silencing effects could be eliminated in the mutants which are responsible for small RNA biogenesis. In order to test this, we have generated RNASeq, small RNA and whole genome bisulfite sequencing data of two maize mutants in the F1 hybrid background (B73/Mo17;mop1/mop1 and B73/Mo17;lbl1/lbl1). We are currently analyzing the data. We will first try to detect a subset of loci in which mop1 or lbl1-dependent small RNAs produced by one genome influence DNA methylation and silencing of the other genome.

Research idea: Evolutionary differentiation of protein structures of the duplicated genes in maize and soybean. In our 2015 and 2017 Plant Cell papers, we demonstrated the evolutionary patterns of MicroRNA genes and protein encoding genes by comparing their nucleotide sequence divergence, and illustrated unbiased fractionation in soybean, and proposed a paleo-autopolyploid origin of soybean and provided insights into how autopolyploids may evolve distinctly from allopolyploids. However, little is known about protein structure differentiation of the duplicated genes. We are trying to determine how duplicated genes are differentiated in their protein structures.

  • Genetic and epigenetic regulation of meiotic recombination in maize

Research ideas: We are currently using classical genetics to work on an active transposon system, Mutator, and RdDM mutants to dissect epigenetic regulation and evolution of TEs in maize. We have focused on how RdDM pathway mutants affect meiotic recombination rates, Mutator transposon activity, double strand break repair, and the mechanisms underlying the evolution of plant imprinting.

Project 1: Genetic and epigenetic effects of transposable elements on meiotic recombination in maize. We aim to identify novel genetic and epigenetic factors that can influence meiotic recombination to better understand this fundamental process. Our central hypotheses are that removal of DNA methylation introduced by silenced transposons and/or the presence of active transposons without DNA methylation can alter the frequency of recombination. The overall objective of this project is to determine how TEs effect recombination, either due to double-strand breaks they introduce when they are active, or due to DNA methylation they bring to genes once they are epigentically silenced. This project is currently funded by NIH NIGMS.

Project 2: Genetic and epigenetic regulation of meiotic recombination between sexes in maize. My group has been using several maize lines including the 25 parental inbreds of the maize nested association mapping (NAM) population to compare recombination frequency during male and female meiosis. The NAM lines were selected because these fully sequenced lines maximize genetic diversity and thus are most likely to show variation between male and female recombination. The overall objectives of this project are to determine whether and how meiotic recombination differs between female and male meiosis in maize as well as to elucidate factors important for regulation and control of this biological process.

  • Genetic dissection of important agronomic traits in maize

Research ideas: We have been using high copy Mutator transposons and Ethyl methanesulfonate (EMS) as mutagens to screen knockout mutants which show deficiency of important agronomic traits in maize. We are eager to identify the candidate genes and dissect the function of the genes.