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Z. Jeffrey Chen

Molecular Biosciences, Department of Integrative Biology

D. J. Sibley Centennial Professorship in Plant Molecular Genetics

Genomic and Epigenetic Bases of Polyploidy and Hybrid Vigor


Phone: 512-475-9327

Office Location
NMS 3.122

Postal Address
AUSTIN, TX 78712

Zengjian Jeffrey Chen is the D. J. Sibley Centennial Professor of Plant Molecular Genetics at University of Texas at Austin. Chen received his B.S. at Zhejiang Agricultural University (now Zhejiang University), M.S. at Nanjing Agricultural University, and Ph.D. in Genetics at Texas A&M University. Following a postdoctoral position at University of Minnesota and as a National Institutes of Health (NIH) Postdoctoral Fellow at Washington University in St. Louis, he joined the faculty at Texas A&M in 1999, where he was promoted to the rank of Associate Professor with tenure. In 2005, he moved to The University of Texas at Austin, holding the D. J. Sibley Centennial Professorship in Plant Molecular Genetics, and was promoted to Full Professor in 2008 in the Section of Molecular Cell and Developmental Biology (now Department of Molecular Biosciences) and Adjunct Professor in the Department of Integrative Biology. Sicne 2011, Prof. Chen is also an Adjunct Professor (summmer part-time) at Nanjing Agricultural University. Chen is an elected fellow of American Association for the Advancement of Science (AAAS) (2011) and has received NIH National Research Service Award (1997-1999), Fulbright US-UK Scholar Award (2011), and Cotton Biotechnology Award (2016). Chen is known for his pioneering work on defining genomic and epigenetic changes in plant hybrids and polyploids with an emphasis on linking gene expression variation with phenotypic traits using Arabidopsis, cotton and corn as experimental systems.

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 eventually serve as tools for understanding cancer and human health.

Selected Publications (Out of 120+)

Song, Q., Ando, A., Jiang, N., Ikeda, Y., Chen, Z. J. (2020) Single-cell analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes. Genome Biology 21:178.

Chen, Z. J., Sreedasyam, A., Ando, A., Song, Q., De Santiago, L. M., Hulse-Kemp, A. M., Ding, M., Ye, W., Kirkbride, R. C., Jenkins, J., Plott, C., Lovell, J., Lin, Y.-M., Vaughn, R., Liu, B., Wen, L., Simpson, S., Scheffler, B. E., Saski, C. A., Grover, C. E., Hu, G., Conover, J., Carlson, J. W., Shu, S., Boston, L. B., Williams, M., Peterson, D. G., McGee, K., Jones, D. C., Wendel, J. F., Stelly, D. M., Grimwood, J., Schmutz, J. (2020) Genomic diversifications of five allopolyploid Gossypium species and their impact on cotton improvement. Nature Genetics 52:525–533.

Song, Q., Huang, T. Y., Chen, H. H., Mass, P., Ha, M., Chen, Z. J. (2019) Diurnal regulation of SDG2 and JMJ14 by circadian clock oscillators orchestrates histone modification rhythms in ArabidopsisGenome Biology 20:170.

Kirkbride, R. C., Lu, J., Zhang, C., C., Mosher, R. A., Baulcombe, D. C., Chen, Z. J. (2019) Maternal small RNAs mediate spatial and temporal regulation of gene expression and seed development in ArabidopsisProc. Natl. Acad. Sci. USA 116:2761-2766.

Song, Q., Ando, A., Xu, D., Fang, L., Zhang, T., Huq, E., Qiao, H., Deng, X. W., Chen, Z. J. (2018) Diurnal down-regulation of ethylene biosynthesis mediates biomass heterosis. Proc. Natl. Acad. Sci. USA 115:5606-5611.

Song, Q., Zhang, T., Stelly, D. M., Chen, Z. J. (2017) Epigenomic and functional analyses reveal roles for epialleles in the loss of photoperiod sensitivity during domestication of allotetraploid cottons. Genome Biology 18:99.

Ko, D. K., Rohozinski, D., Song. Q., Taylor, S. H., Thomas E. Juenger, T. E., Harmon, F. G., Chen, Z. J. (2016) Temporal shift of circadian-mediated gene expression and carbon fixation contributes to biomass heterosis in maize hybrids. PLoS Genetics 12(7): e1006197.  

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.

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.

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 Arabidopsis allopolyploids. Nature Communications 3:950.

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.

Wang, J., Tian, L., Lee, H.-S., Wei, N. E., Jiang, H., Watson, B., Madlung, A., Osborn, T. C., Doerge, R. W., Comai, L., Chen, Z. J. (2006) Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 172:507-517.

  • 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
  • 2005-2007 D. J. Sibley Centennial Professorship Fellow
  • 2008-present D. J. Sibley Centennial Professor in Plant Molecular Genetics
  • 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)
  • 2016 Cotton Biotechnology Award

327G Genomics