Our lab is currently focused on two separate research areas: light-regulated de-etiolation and stomatal opening responses and Arabidopsis seed development.

Red/far-red light-absorbing phytochromes and blue/UV-A light-absorbing cryptochromes regulate seedling de-etiolation. Cryptochromes together with blue/UV-A light-absorbing phototropins also regulate stomatal aperture in a natural environment. The signal transduction cascades that link the perception of light to the de-etiolation and stomatal opening responses are still largely unknown, and hypersensitive to red and blue (hrb) mutants are of particular interest. The hrb mutants were initially isolated for their short hypocotyl phenotype under red and blue light. The hrb mutants are also more resistant to dehydration and show reduced water loss and blue light-regulated stomatal aperture. We have cloned HRB1 and HRB2 gene and mapped hrb3 to chromosomes 4. HRB1 encodes a nuclear ZZ-type zinc finger protein. We are exploring the actions and interactions of HRBs with others in the light-mediated signaling pathways, and identifying genes encoding HRB3. Our studies may open new possibilities to engineer plants to survive desiccation since the stomatal pores are situated in the leaf epidermis to allow CO2 uptake and the loss of water through transpiration. Periodic drought is one of the major environmental factors that limit biomass production and crop yield in a changing global climate. The stomatal aperture is also regulated by other environmental cues in addition to blue light. Given that hrb plants still respond to ABA, a well-known drought signal, these plants should enjoy the advantages of both constitutive and induced protection under water-limiting conditions.

Double fertilization in angiosperms leads to the formation of a diploid embryo and a triploid endosperm. Seed development in Arabidopsis then undergoes an initial phase of active endosperm proliferation followed by a second phase in which embryo grows at the expense of the endosperm. In many dicots, the embryo grows to full size and the mature seed contains only a single layer of endosperm cells. As the mature seed size is largely attained during the initial phase, the seed size is coordinately determined by the growth of the maternal ovule, endosperm, and embryo. The mechanisms underlying this control are still not well understood, yet seeds form the bulk of the diet of human population. SHB1 is a positive regulator of Arabidopsis endosperm proliferation and SHB1 gain-of-function increases seed size. SHB1 directly regulates the expression of MINI3 and IKU2, a WRKY transcription factor gene and an LRR receptor kinase gene. Mutation in either MINI3 or IKU2 retards endosperm development and reduces seed size. SHB1 is localized to the nucleus but is not a DNA binding protein. We are currently searching for proteins that recruit SHB1 to the MINI3 and IKU2 loci and the partners that SHB1 works with to activate endosperm proliferation. Seed size is the yield trait that traditional breeding has had the most limited success in improving effectively. Seed development in major seed crops such as soybean and canola follows a very similar path as Arabidopsis. Enhancing the potential for large seed sizes represents one of the most promising and less explored avenues for significant increases in agricultural yields.

Sun, Q., Wang, S., Xu, G., Kang, X., Zhang, M, and Ni, M. (2019). SHB1 and CCA1 interaction desensitizes light responses and enhances thermomorphogenesis. Nature Communications https://doi.org/10.1038/s41467-019-11071-6.

Kang, X., Xu, G., Lee, B., Chen, C., Zhang, H., Kuang, R., and Ni, M. (2018). HRB2 and BBX21 interaction modulates Arabidopsis ABI5 locus and stomatal aperture. Plant Cell Environ. doi: 10.1111/pce.13336.

Zhang, H., Cheng, F., Xiao, Y., Kang, X., Wang, X., Kuang, R., and Ni, M. (2017). Global analysis of canola genes targeted by SHORT HYPOCOTYL UNDER BLUE 1 during endosperm and embryo development. Plant Journal doi: 10.1111/tpj.13542.

Xiao, Y., Sun, Q., Kang, X., Chen, C., and Ni, M. (2016). SHORT HYPOCOTYL UNDER BLUE1 or HAIKU2 mixexpression alters canola and Arabidopsis seed development. New Phytol. 209: 636-49. doi: 10.1111/nph.13632

Raschke, A., Ibañez, C., Ullrich, K.K., Anwer, M.U., Becker, S., Glöckner, A., Trenner, J., Denk, K., Saal, B., Sun, X., Ni, M., Davis, S.J., Delker, C., Quint, M. (2015). Natural variants of ELF3 affect thermomorphogenesis by transcriptionally modulating PIF4-dependent auxin response genes. BMC Plant Biol doi: 10.1186/s12870-015-0566-6.

Kang, X., Li, W., Zhou, Y., and Ni, M. (2013). A WRKY transcription factor recruits SYG1-like protein SHB1 to activate gene expression and seed cavity enlargement. PLoS Genetics. 9(3): e1003347.

Sun, X., Kang, X., and Ni, M. (2012). Hypersensitive to Red and Blue 1 and its modification by Protein Phosphatase 7 are implicated in the control of Arabidopsis stomatal aperture. PLoS Genetics 8(5): e1002674.

Sun X., and Ni M. (2011). HYPOSENSITIVE TO LIGHT, an alpha/beta fold protein, acts downstream of HY5 to regulate Arabidopsis seedling de-etiolation. Molecular Plant 4, 116-126.

Zhou Y., and Ni, M. (2010). SHB1 truncations and mutations alter its association with a signaling protein complex. Plant Cell 22, 703-715.

Zhou Y., and Ni, M. (2009). SHB1 plays dual roles in photoperiodic and autonomous flowering. Developmental Biology 331, 50-57.

Zhou Y., Zhang, X., Kang, X., Zhao, X., Zhang, X., and Ni, M. (2009). SHORT HYPOCOTYL UNDER BLUE1 associates with MINISEED3 and HAIKU2 promoters in vivo to control Arabidopsis seed development. Plant Cell 21, 106-117.

Kang, X., Zhou, Y., Sun, X., and Ni, M. (2007). HYPERSENSITIVE TO RED AND BLUE 1 and its C-terminal regulatory function control FLOWERING LOCUS T expression. Plant Journal 52, 937-948.

Chen, M., and Ni, M. (2006). RED AND FAR-RED INSENSITIVE 2, a RING-domain zinc-finger protein, negatively regulates CONSTANS expression and photoperiodic flowering. Plant Journal 46, 823-833.

Kang, X., and Ni, M. (2006). Arabidopsis SHORT HYPOCOTYL UNDER BLUE 1 contains SPX and EXS domains and acts in cryptochrome signaling. Plant Cell 18, 921-934.

Chen, M., and Ni, M. (2006). RED AND FAR-RED INSENSITIVE 2, a RING-domain zinc-finger protein, mediates phytochrome-controlled seedling de-etiolation responses. Plant Physiology 140, 457-465.

Kang, X., Chong, J., and Ni, M. (2005). HYPERSENSITIVE TO RED AND BLUE 1, a ZZ-type zinc finger protein, regulates phytochrome B-mediated red and cryptochrome-mediated blue light responses. Plant Cell 17, 822-835.

Ni, M., Tepperman, J., and Quail, P.H. (1999). Binding of phytochrome B to its nuclear signaling partner PIF3 is reversibly induced by light. Nature 400, 781-784.

Ni, M., Tepperman, J., and Quail, P.H. (1998). PIF3, a phytochrome interacting factor necessary for photoinduced signal transduction, is a basic helix-loop-helix protein. Cell 95, 657-667.

Ni, M., Dehesh, K., Tepperman, J., and Quail, P.H. (1996). GT-2: In vivo transcriptional activation activity and definition of twin novel DNA-binding domains with reciprocal target-site selectivity. Plant Cell 8, 1041-1059.