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Hong Ma

Hong Ma

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Professor of Biology

Huck Distinguished Research Professor of Plant Molecular Biology

328B Mueller Lab
University Park, PA 16802
Phone: (814) 865-5343
Lab Address: 419 Mueller Lab


  1. Ph.D., Massachusetts Institute of Technology, 1988
  2. B.A., Temple University, 1983

Postdoc Training

  1. California Institute of Technology, 1988-1990

Honors and Awards

  1. Elected Fellow of AAAS, 2011
  2. Distinguished Professor in Biology, 2008
  3. Faculty Scholars Medal in Life and Health Sciences, 2005
  4. The John Simon Guggenheim Fellowship 2004-2005
  5. American Cancer Society Junior Faculty Research Award 1994-1997

Research Interests

Molecular Genetics of Plant Reproductive Development; Molecular Evolution and Phylogenetics of Angiosperms and Other Eukaryotes

I have a long standing interest in the molecular basis of plant reproductive development and evolutionary biology, using molecular genetic, cell biological, genomic and bioinformatic approaches.

In the area of functional studies of genes important for plant reproductive development, we focus on molecular basis of meiotic homologous recombination and chromosome condensation and segregation, gene networks controlling anther and pollen development, and regulatory elements ensuring reproductive development in response to environmental changes, such as light, drought and heat. A recent study revealed a negative interaction between TOE proteins and CO, a crucial mediator of long-day promotion of flowering in Arabidopsis; other discoveries include an essential role of MMD1, a PHD finger protein in ensuring normal meiotic chromosome condensation, and the function of DYT1 in regulating a complex network for anther somatic cell development and function.

A second focus in our lab is molecular evolution of reproductive genes and their homologs, as well as other regulatory gene families, such as those of epigenetic regulators, such as histone methylases and demethylases, as well as RNA polymerases, which are important for small RNA biogenesis. We also have a program on the systematic investigation of angiosperm phylogenies using nuclear genes, largely obtained using transcriptomics, including the phylogenies of major angiosperm lineages and large families such as Brassicaceae, Asteraceae, and Rosaceae. We also are interested in understanding the phylogenies of other eukaryotic groups, such as the early divergences of eukaryotic supergroups. These phylogenies can then provide a framework for addressing other evolutionary questions, such as molecular clock estimates of divergence times, shifts of rate of diversification, and ancestral character reconstruction of morphological and other features. 

Selected Publications

Xiang, Y.#, Huang, C.-H.#, Hu, Y., Wen, J., Li, S., Yi, T., Chen, H., Xiang, J.*, Ma, H.* 2017. Evolution of Rosaceae fruit types based on nuclear phylogeny in the context of geological times and genome duplication. Mol. Biol. Evol. 34: 262-281. Doi:10.1093/molbev/msw242 (#equal contribution)

Huang, C.-H., Zhang, C., Liu, M., Hu, Y., Gao, T., Qi, J.*, Ma, H.* 2016. Multiple polyploidization events across Asteraceae with two next events in the early history revealed by nuclear phylogenomics. Mol. Biol. Evol. 33: 2820-2835.

Ren, R., Sun, Y., Zhao, Y., Geiser, D., Ma, H.*, Zhou, X.* 2016. Phylogenetic resolution of deep eukaryotic and fungal relationships using highly conserved low-copy nuclear genes.  Genome Biol. Evol. 8: 2683-2701.

Wang, J., Niu, B., Zhang, S., Huang, J., Ye, J., Dai, H., Wang, H., Dong, A., Makaroff, C., Cao, X., Ma, H.*, Wang Y.* 2016. Arabidopsis MMD1/DUET ensures the progression of male meiotic chromosome condensation and directly regulating the expression of condensin gene CAP-D3. Plant Cell. 28: 1894-1909. doi:10.1105/tpc.16.00040

Cui, J., You, C., Zhu, E., Huang, Q., Ma, H.*, Chang, F.* 2016. Feedback regulation of DYT1 by interactions with downstream bHLH factors promotes DYT1 nuclear locations and anther development. Plant Cell. 28: 1078-1093.

Huang, C.-H., Sun, R., Hu, Y., Zeng, L., Zhang, N., Cai, L., Zhang, Q., Edger, P., Al-Shehbaz, I., Marcus, Pires, C., Tan, D.-Y., Ma, H.* 2016. Resolution of Brassicaceae phylogeny using nuclear genes uncovers nested radiations and supports convergent morphological evolution. Mol. Biol. Evol. 33: 394-412. doi: 10.1093/molbev/msv226.

Zhang, B., Wang, L., Zeng, L., Zhang, C., Ma, H.* 2015. Arabidopsis TOE proteins convey photoperiodic signal to antagonize CONSTANS and regulate flowering time. Genes & Dev. 29: 975-987.

Huang, J., Cheng, Z., Wang, C., Hong, Y., Su, H., Wang, J., Copenhaver, G. P., Ma, H.* Wang, Y.* 2015. Formation of interference-sensitive of meiotic crossovers requires sufficient leading strand elongation. Proc. Natl. Acad. Sci. USA. 112: 12534-12539.

Niu, B., Wang, L., Zhang, L., Ren, D., Ma, H.*, Wang, Y.* 2015. The Arabidopsis CDC20.1 gene is required for normal meiotic spindle assembly and chromosome segregation. Plant Cell. 27: 3367-3382.

Qian, S., Wang, Y., Ma, H.*, Zhang, L.* 2015. Expansion and functional divergence of the JmjC gene family: significance of duplications in ancestral angiosperms and vertebrates. Plant Physiol. 168: 1321-1337.

Qi, J., Chen, Y., Copenhaver, G.P., Ma, H.* 2014. Detection of genomic variations and DNA polymorphisms and impact on analysis of meiotic recombination and genetic mapping. Proc. Natl. Acad. Sci. USA. 111: 10007-10012.

Zeng, L., Zhang, Q., Sun, R., Kong, H., Zhang, N.*, Ma, H.* 2014. Resolving deep angiosperm phylogenetic relationships using conserved nuclear genes. Nat Comm. 5: 4956.

Ma, H.* 2013. A battle between genomes in plant male fertility. Nat. Genet. 45: 472-473.