Meixia Zhao

Chun Liang

Assistant Professor

360 Pearson Hall
Zhao Genetics and Genomics Lab

Biographical Information

Our research lab uses a combination of comparative and functional genomics, genetics and epigenetics approaches to study the mechanisms underlying structural and functional genomics changes within and between different plant species, with an emphasis on the determination of how transposable elements (TEs) and polyploidy contribute to plant evolution, and how TEs are epigenetically regulated in agronomically important crop species. Ongoing research area includes

  • Comparative genomics and epigenomics in plant 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 coding genes, and the evolution patterns of small interfering RNAs and RNA-directed DNA methylation (RdDM) components.
  • Epigenetic regulation in soybean and maize. 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. We would also like to extend 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

Selected Publications

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

  • Zhao M.†, Zhang B., Ma J. and Lisch D. 2018. Genome-wide estimation of evolutionary distance and phylogenetic analysis of homologous genes. Bio-protocol8: e3097. [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]
  • Zhao M., and Ma J. 2017. Transposable Elements. In: Nguyen H., Bhattacharyya M. (eds). The Soybean Genome. Compendium of Plant Genomes. Springer, Cham. p. 171-181. [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]
  • Zhao M., Zhang B., Liu S., and Ma J. 2013. Transposon expression and potential effect on gene regulation in the Brassica rapaand Brassica oleracea  Hereditas 35: 1014-1022. [PDF]
  • Yu J.#, Zhao M.#, Wang X., Tong C., Huang S., Tehrim S., Liu Y., Hua W., and Liu S. 2013. Bolbase: a comprehensive genomics database for Brassica oleracea. BMC Genomics 14: 664. (#Equal contributors) [PDF]