Z. Jeffrey Chen

Molecular Biosciences, Department of Integrative Biology

D. J. Sibley Centennial Professor in Plant Molecular Genetics

Genomic and Epigenetic Bases of Polyploidy and Hybrid Vigor

Phone: 512-475-9327

Office Location
NMS 3.122

Postal Address
100 E. 24th Street Stop A5000
Austin, TX 78712

B.S., Zhejiang University (1980-1984)
M.S., Nanjing Agricultural University (1985-1987)
Ph.D., Texas A&M University (1990-1993)
Postdoc, University of Minnesota (1993-1995)
NIH Postdoc, Washington University (1995-1999)

Jeff Chen joined the faculty at Texas A&M University in 1999. There, the late Norman E. Borlaug, father of the Green Revolution, had inspired him to promote plant genetics and biotechnology for improving lives of the humankind. In 2005, he joined the faculty at The University of Texas at Austin and is the holder of the D. J. Sibley Centennial Professor in Plant Molecular Genetics. Prof. Chen is a pioneer for defining genomic and epigenetic changes in plant hybrids and polyploids with an emphasis on associating gene expression variation with phenotypic traits using Arabidopsis, cotton, and corn as experimental systems. In 2011, Prof. Chen was elected as a fellow of American Association for the Advancement of Science (AAAS), Fulbright US-UK Scholar, and Fellow Commoner in Trinity College at University of Cambridge.

Research Summary:

The goal of our research program is to elucidate genetic and epigenetic mechanisms for polyploidy and heterosis and their impact on crop domestication and improvement. Polyploidy and heterosis are two fundamental biological phenomena that are critically important to agriculture and the environment because many crops, such as wheat, cotton and canola, are polyploids; others, like corn (maize) are grown as hybrids. Allopolyploid plants form by interspecific hybridization followed by genome doubling, while the heterozygosity and heterosis are permanently fixed, which provides genetic materials and bases for selection and adaptation in response to human intervention and climate change. We employ interdisciplinary approaches using genetic, genomic, and computational technologies, including CRISPR genome editing tools to address the molecular bases for biomass and seed size heterosis in Arabidopsis and corn hybrids and for fiber cell development in cotton.  A recent discovery links altered circadian rhythms via epigenetic regulation to growth vigor in Arabidopsis hybrids and allopolyploids as well as in maize hybrids. Although heterosis is commonly observed, some hybrids and allopolyploids cannot produce offspring, a phenomenon known as hybrid incompatibility. We predict that molecular interactions between genes and small RNAs that are functionally diverged in the respective hybridizing species cause hybrid incompatibilities; siRNA-directed DNA methylation mediates spatiotemporal regulation of seed development and the parent-of-origin effect on heterosis. In cotton allotetraploids, we investigate epigenetic mechanisms for fiber cell initiation and development and biased expression of homoeologous genes. Beyond plants, hybrid vigor and inbreeding depression are common in sexually reproducing organisms including humans. Moreover, many cancer cells are polyploids and aneuploids, and the mechanisms associated with balancing ploidy and gene expression may therefore eventually serve as tools for understanding cancer and human health.


Zhang, T., Hu, Y., Jiang, W., Fang, L., Guan, X., Chen, J., Zhang, J., Saski, C. A., Scheffler, B. E., Stelly, D. M., Hulse-Kemp, A. M., Wan, Q., Liu, B., Liu, C., Wang, S., Pan, M., Wang, Y., Wang, D., Ye, W., Chang, L., Zhang, W., Song, Q., Kirkbride, R. C., Chen, X., Dennis, E., Llewellyn, D. J., Peterson, D. G., Thaxton, P., Jones, D. C., Wang, Q., Xu, X., Zhang, H., Wu, H., Zhou, L., Mei, G., Chen, S., Tian, Y., Xiang, D., Li, X., Ding, J., Zuo, Q., Tao, L., Liu, Y., Li, J., Lin, Y., Hui, Y., Cao, Z., Cai, C., Zhu, X., Jiang, Z., Zhou, B., Guo, W., Li, R., and Chen, Z. J. (2015) Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement, Nature Biotechnology 33:531-537

Miller, M., Song, Q., Shi, X., Juenger, T. E., and Chen, Z. J. (2015) Natural variation in timing of stress-responsive gene expression predicts heterosis in intraspecific hybrids of Arabidopsis, Nature Communications 6:7453

Song, Q., Guan, X., and Chen, Z. J. (2015) Dynamic roles for small RNAs and DNA methylation during ovule and fiber development in allotetraploid cotton, PLoS Genetics 11(12):e1005724.

Ng, D. W-K., Miller, M., Yu, H. H., Huang, T-.Y., Kim, E-D., Lu, J., Xie, Q., McClung, C. R., and Chen, Z. J. (2014) A role for CHH methylation in the parent-of-origin effect on circadian rhythms and biomass heterosis in plant hybrids, Plant Cell 26:2430-2440

Chen, Z. J. (2013) Genomic and epigenetic insights into the molecular bases of heterosis, Nature Reviews Genetics 14:471-482

Lu, J., Zhang, C., Baulcombe, D. C., and Chen, Z. J. (2012) Maternal siRNAs as regulators of parental genome imbalance and gene expression in endosperm of Arabidopsis seeds, Proc. Natl. Acad. Sci. USA 109: 5529-5534

Shi, X., Ng, D. W-K., Zhang, C., Comai, L. Ye, W., and Chen, Z. J. (2013) Cis- and trans-regulatroy divergence between progenitor species determines gene expression novelty in Arabidopsisallopolyploids, Nature Communications 3:950

Ha, M., Ng, D. W.-K., Li, W.-H., and Chen, Z. J. (2011) Coordinated histone modifications are associated with gene expression variation within and between species, Genome Research 21: 590-598

Chen, Z. J. (2010) Molecular mechanisms of polyploidy and hybrid vigor, Trends in Plant Science 15: 57-71

Ha, M., Lu, J., Tian, L., Ramachandran, V., Kasschau, K. D., Chapman, E. J., Carrington, J. C., Chen, X., Li, W.-H., Wang, X., and Chen, Z. J. (2009) Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids, Proc. Natl. Acad. Sci. USA, 106: 17835-17840

Ni, Z., Kim, E., Ha, M., Lackey, E., Liu, J., Zhang, Y., Sun, Q., and Chen, Z. J. (2009) Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids, Nature 457: 327-331

Chen, Z. J. (2007) Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids, Annual Review in Plant Biology 58: 377-406

  • 1989-1990 Graduate Scholarship, K. C. Wong Foundation in Hong Kong
  • 1995-1997 Monsanto Postdoctoral Fellowship, The Monsanto Company
  • 1997-1999 National Institutes of Health (NIH) National Research Service Award
  • 2005-present D. J. Sibley Centennial Professorship Fellow in Plant Molecular Genetics
  • 2005-present Fellow of the Institute for Cellular and Molecular Biology
  • 2010-2011 Faculty Development Program Award
  • 2010-2011 Fulbright US-UK Scholar Award
  • Lent 2011 Visiting Fellow Commoner, Trinity College, University of Cambridge
  • 2011 Elected Fellow, American Association for the Advancement of Science (AAAS)