Meixia Zhao

Chun Liang

Assistant Professor

358 Pearson Hall
Genetics, Genomics and Bioinformatics Lab

Biographical Information

Our research laboratory uses a combination of computational and functional genomic, genetic and epigenetic approaches to study the mechanisms underlying genome evolution, epigenetic regulation of transposable elements (TEs), and the effects of TEs on meiotic recombination using maize and soybean as model systems. Ongoing research area includes:

  • Comparative genomics and epigenomics in plant genome evolution. We seek to understand the function of 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 encoding genes, and the evolutionary patterns of small interfering RNAs and RNA-directed DNA methylation (RdDM) components.
  • Genetic and epigenetic regulation of meiotic recombination in maize. We are currently using classical genetics and computational genomics to dissect genetic and epigenetic regulation of meiotic recombination in maize. We have focused on how RdDM pathway mutants affect the rates of meiotic recombination, and how and why sexes differ in meiotic recombination in maize using the parental lines of maize nested association mapping populations. We are also extending our maize epigenetic work to soybean to compare the conservation and differentiation of the RdDM pathway in these two important crops.
  • Genetic dissection of important agronomic traits in maize. 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.

Courses Taught

  • BIO/MBE 116: Biological Concepts: Structure, Function, Cellular and Molecular Biology
  • BIO/CSE/MBI 256: Introduction to Programming for the Life Sciences
  • BIO 710: Advanced Seminar: Genomics, Epigenomics, and Phonemics

Selected Publications

(See Google Scholar for the complete list, **undergraduate student; *graduate student; †Corresponding Author)

  • Zhao M., Ku J.C., Liu B.*, Yang D.*, Yin L.*, Ferrell T.J.**, Stoll C.E.**, Guo W.*, Zhang X., Wang D., Wang C.R., and Lisch D. 2021. The mop1 mutation affects the recombination landscape in maize. Proc Natl Acad Sci U S A 118: e2009475118. [PDF]
  • Liu B.*, Iwata-Otsubo A., Yang D.*, Baker R.L., Liang C., Jackson S.A., Liu S., Ma J., and Zhao M. 2021. Analysis of CACTA transposase genes unveils the mechanism of intron loss and distinct small RNA silencing pathways underlying divergent evolution of Brassica genomes. Plant J. 105: 34-48. [PDF]
  • Zhao M., Zhang B., Lisch D., and Ma J. 2017. Patterns and consequences of subgenome differentiation provide insights into the nature of paleopolyploidy in plants. Plant Cell 29: 2974-2994. [PDF]
  • Zhang D.#, Zhao M.#, Li S.#, Sun L., Wang W., Cai C., Dierking E., and Ma J. 2017. Plasticity and innovation of regulatory mechanisms underlying seed oil content mediated by duplicated genes in the palaeopolyploid soybean. Plant J. 90: 1120-1133. (#Equal contributors) [PDF]
  • Zhao M., Meyers B.C., Cai C., Xu W., and Ma J. 2015. Evolutionary patterns and co-evolutionary consequences of MIRNA genes and microRNA targets triggered by multiple mechanisms of genomic duplications in soybean. Plant Cell 27: 546-562. [PDF]
  • Zhao M., Cai C., Zhai J., Lin F., Li L., Shreve J., Thimmapuram J., Hughes T.J., Meyers B.C., and Ma J. 2015. Coordination of microRNAs, phasiRNAs, and NB-LRR genes in response to a plant pathogen: insights from analyses of a set of soybean Rps gene near-isogenic lines. Plant Gen., 10.3835/plantgenome2014.09.0044. [PDF]
  • Lin F.#, Zhao M.#, Baumann D.D., Ping J., Sun L., Liu Y., Zhang B., Tang Z., Hughes E., Doerge R.W., Hughes T.J., and Ma J. 2014. Molecular response to the pathogen Phytophthora sojae among ten soybean near isogenic lines revealed by comparative transcriptpmics. BMC Genomics 15: 18. (#Equal contributors) [PDF]
  • Zhao M., Du J., Lin F., Tong C., Yu J., Huang S., Wang X., Liu S., and Ma J. 2013. Shifts in evolutionary rate and intensity of purifying selection between two Brassica genomes revealed by analyses of orthologous transposons and relics of a whole genome triplication. Plant J. 76: 211-222. [PDF]
  • Zhao M., and Ma J. 2013. Co-evolution of plant LTR-retrotransposons and their host genomes. Protein & Cell 4: 493-501. [PDF]