Stephen Patrick Moose


Dr. Moose discovers genes that influence corn and related bioenergy grasses’ response to nitrogen supply. He develops new approaches to increase crop yields with lower input costs and help mitigate environmental issues associated with nitrogen fertilizer. His work reveals how genes cooperate to control plant traits important to both productivity and nutritional quality.

Primary Disciplines


  • B.S.: Biology, Case Western Reserve University — 1990
  • Ph.D.: Genetics & Crop Science (co-major), North Carolina State University — 1995

Research Interests

  • The structure and function of the Miscanthus genome. Complete genome sequences exist for the annual crops maize and sorghum, but are lacking for the related perennials Miscanthus and Saccharum (sugarcane, energy cane).  With the support of the Energy Biosciences Institute, I have led a research group to develop genomic resources for Miscanthus.  We have determined the content and activity of transposon repeat sequences in Miscanthus (Swaminathan et al., 2010), which also established Sorghum as a valuable reference genome for both Miscanthus and Saccharum (Wang et al., 2010).  We constructed a complete genetic map for Miscanthus sinensis (Swaminathan et al., 2012), where it was discovered that the Miscanthus genome arose via a recent whole genome duplication of a Sorghum-like genome.  We also recently reported an analysis of the majority of expressed genes within Miscanthus (Barling et al., 2013), including those that function in the rhizome tissue important for perenniality.  Our group is now focused on producing an assembled genome sequence for Miscanthus sinenis.
  • The regulatory impacts of small RNAs on plant growth and development.  Small RNAs play important roles in regulating plant development, stress response, viral immunity and maintaining genome integrity.  Most studies of small RNAs have focused on microRNAs that regulate protein coding genes, such as our discovery that microRNA172 is a key regulator of shoot maturation in maize, by downregulating the maize Glossy15 gene that maintains vegetative development (Lauter et al., 2005).  However, most plant small RNAs are derived from transposons, “jumping genes” that are present in many interspersed copies that form the majority of plant genomes.  We have recently used deep sequencing methods to monitor variation in the activities of transposon-derived small RNAs and how they impact hybrid vigor, the greater growth and stress tolerance of progeny produced from crosses of genetic diverse parents (Barber et al., 2012 and Li et al., 2012).
  • Discovery of genes controlling N utilization.  High crop yields depend on sufficiently levels of available soil nitrogen (N), which in modern intensive agricultural systems is provided by N fertilizer.  Corn and other cereals typically use only one-third to one-half of applied N fertilizer, leading to higher energy use and input costs to the farmer, as well as increased greenhouse gas emissions and nitrate levels in water supplies due to N losses.  Improving N use efficiency in corn would thus offer significant economic and environmental benefits to agriculture.  Prior agronomic studies have established that increasing the amount of biomass produced per unit of plant N, or N utilization,  offers the greatest potential for genetic improvement of nitrogen use efficiency in maize (Moose and Below, 2008).  We have documented phenotypic variation for N utilization in diverse maize populations (e.g. Uribelarrea et al., 2007; White et al., 2012; Ayodeji et al., 2012) that have also been the focus of functional genomics studies in our lab and others.  Important to these studies are the Illinois Protein Strains, created by more than century of selection for changes in grain protein concentration and N utilization (Lucas and Moose, 2012).  Recent work has identified a number of genes that regulate N utilization in maize hybrids, and further testing of these genes is in progress.  We are also beginning to extend our learnings from maize to sorghum, an emerging annual bioenergy crop.  Furthermore, because perennial grasses require less N for maximal biomass production, we are studying Miscanthus (see below) to learn how it achieves higher N utilization, with the potential to apply those findings to cereals like maize.
  • My research group applies functional genomics approaches to characterize genes that modulate productivity and sustainability in maize and related crop species: sorghum, Miscanthus, and sugarcane.  Each of these closely related grasses within the Andropogoneae tribe perform highly productive C4 photosynthesis and are important global sources of food, feed, bioenergy, and renewable biochemicals.  They also share a high degree of similarity in their genome and complementary advantages in the study of economically important traits.  Maize is a primary focus because of its advanced tools for relating genes to phenotypes.

Chapters in Books

  • Moose, S.P. and F. E. Below (2008) Biotechnology approaches to improving maize nitrogen use efficiency, book chapter in Molecular Genetic Approaches to Maize Improvement, A.L. Kriz and B. A. Larkins (eds.) Springer-Verlag. Biotechnology_Approaches_to_Improving_Maize_N_Use_Efficiency.pdf
  • Lucas, C.J., Zhao, H., Schneerman, M. and Moose, S.P. (2012) Genomic changes in response to 110 cycles of selection for seed protein and oil concentration in maize. Book chapter in Seed Genomics. P. Becraft ed., Wiley. Lucas_et_al_Seed_Genomics_chapter.pdf

Selected Articles in Journals

  • Fontes, E.B.P, Chank, B.B., Wrobel, R.L., Moose, S.P., O’Brian, G.R., Wurtzel, E.T., and R.S. Boston (1991). Characterization of an immunoglobulin binding protein homolog in the maize floury-2 endosperm mutant. The Plant Cell 3: 483-496.
  • Moose, S. P. and P. H. Sisco (1994). Glossy15 controls the epidermal juvenile-to-adult phase transition in maize. The Plant Cell 6: 1343-1355.
  • Moose, S. P. and P.H. Sisco (1996). Glossy15, an APETALA2-like gene from maize that regulates leaf epidermal cell identity. Genes and Development 10: 3018-3027.
  • Vicente-Carbajosa, J., Moose, S. P., Parson, R.L., and R. J. Schmidt (1997). A maize zinc-finger protein binds the prolamin box in zein gene promoters and interacts with the basic leucine zipper transcriptional activator Opaque2. Proc. Natl. Acad. Sci. USA 94: 7685-7690.
  • Salvador, R., Moose, S. Chassy, B. and Hodge, K. (2002) Magnanimous Iowans – a case study in bioethics, in Life Science Ethics, G.L. Comstock, ed. Iowa State Press.
  • Xu, F.-X., Laguda, E., Moose, S.P., and Riechers, D. (2002) Tandemly duplicated safener-induced glutathione S-transferase genes from Triticum tauschii contribute to genome- and organ-specific expression in hexaploid wheat. Plant Physiology 130: 362-373.
  • Naidu, S.L., Al-Shoabi, K.A., Raines, C.A., Moose, S.P., and Long, S.P. (2003) Cold-tolerant C4 photosynthesis in Miscanthus x giganteus. Plant Physiology 132: 1688-1697.
  • Guo, H. and Moose, S.P. (2003) Conserved noncoding sequences among cultivated cereal genomes identify candidate regulatory sequence elements and patterns of promoter evolution. Plant Cell 15: 1143-1158.
  • Below, F.E., Seebauer, J.R, Uribelerrea, M., Schneerman, M.C. and Moose, S.P. (2004) Accompanying changes in crop physiology from long-term selection for grain protein in maize. Plant Breeding Reviews 24(1): 133-151.
  • Moose, S.P., Lauter, N.L., and Carlson, S.R. (2004). The maize macrohairless1 locus specifically promotes leaf blade macrohair initiation and responds to factors regulating leaf identity. Genetics 166: 1451-1461.
  • Uribelarrea, M., Below, F.E. and Moose, S.P. (2004). Grain composition and productivity of maize hybrids derived from the Illinois Protein Strains in response to variable nitrogen supply. Crop Science 44: 1593-1600.
  • Moose, S.P., Rocheford, T.R. and Dudley, J.W. (2004). Maize selection turns 100: a 21st century genomics tool. Trends in Plant Science 9: 358-364. doi:10.1016/j.tplants.2004.05.005
  • Hwang, Y.S., Ciceri, P., Parsons, R., Moose, S.P., Schmidt, R.J. and Huang, N. (2004) The maize O2 and PBF proteins act additively to promote transcription of storage protein gene promoters in rice endosperm cells. Plant and Cell Physiology 45: 1509-1518.
  • Seebauer, J., Moose, S.P., Fabbri, B., Crossland, L. and Below, F.E. (2004) Amino acid metabolism in young maize earshoots: implications for assimilate movement and nitrogen signaling. Plant Physiol. 136: 4326-4334
  • Lauter, N., Kampani, A., Carlson, S., Goebel, M. and Moose, S.P. (2005) microRNA172 downregulates glossy15 to promote vegetative phase change in maize. Proc. Natl. Acad. Sci 102: 9412-9417.
  • Uribelarrea, M., Moose, S.P., and Below, F.E. (2007) Divergent selection for grain protein affects nitrogen use efficiency in maize hybrids. Field Crops Res. 100: 82-90, Uribelarrea_et_al_divergent_selection_and_N_use.pdf
  • Moose, S.P. and Mumm, R.H. (2008) Molecular breeding as the foundation for 21st century plant improvement. Plant Physiology 147: 969-977.
  • Wang, D., Portis, A.R., Moose, S.P. and Long, S.P. (2008) Cool C4 photosynthesis – Pyruvate Pi Dikinase expression and activity corresponds to the exceptional cold tolerance of carbon assimilation in Miscanthus x giganteus. Plant Physiology 148: 557-567.
  • Lauter, N., Moscou, M.J., Habiger, J., and Moose, S.P. (2008) Quantitative genetic dissection of shoot architecture traits in maize: towards a functional genomics approach. The Plant Genome 1: 99-110.
  • Swaminathan, K., Alabady, M., Varala, K., De Paoli, E., Ho, I., Rokhsar, D., Ming, R., Green, P.J., Meyers, B.C., Moose, S.P., and Hudson, M. (2010) Surveying the structure and expression of genomic repetitive elements from Miscanthus x giganteus. Genome Biology 11: R12,
  • Wang, J., Roe, B., Macmil, S., Yu, Q., Murray, J.E., Tang, H., Chen, C., Najar, F., Wiley, G., Bowers, J., Van Sluys, M.-A., Rokhsar, D.S., Hudson, M.E., Moose, S.P., Paterson, A.H. and Ming, R. (2010) Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes. BMC Genomics 11: 261
  • White, W.G., Moose, S.P. and Below, F.E. (2012) The sugar, biomass and biofuel potential of temperate by tropical maize hybrids. Global Change Biology Bioenergy 4: 1-13. White_12_GCB_Bioenergy_Energy_Maize_EtOH_potential.pdf
  • Swaminathan, K., Chae, W.B., Mitros, T., Varala, K., Xie, L., Barling, A., Glowacka, K., Hall, M., Jezowski, S., Ming, R., Hudson, M., Juvik, J., Moose, S.P. and Rokhsar, D.S. (2012)  Deep sequencing identifies markers for a framework genetic map and reveals recent allotetraploidy in Miscanthus. BMC Genomics 13: 142.
  • Barber, W.T., Zhang, W., Win, H., Varala, K.K., Dorweiler, J.E., Hudson, M.E. and Moose, S.P. (2012) Repeat associated small RNAs vary among parents and following hybridization in maize. Proceedings National Academy of Sciences (USA) 109: 10444-10449.
  • Li, Y., Varala, K., Moose, S.P. and Hudson, M.E. (2012) The inheritance pattern of 24nt siRNA clusters in Arabidopsis hybrids is influenced by proximity to transposable elements. PLoS One 7: e47043.
  • Dwiyant, M.S., Rudolph, A., Swaminathan, K., Nishiwaki, A., Shimono, Y., Kuwbara, S., Matuura, H., Nadir, M., Moose, S., Stewart, J.R., Yamada, T. (2012)  Genetic analysis of putative triploid Miscanthus hybrids and tetraploid M. sacchariflorus collected from sympatric populations of Kushima, Japan.  BioEnergy Research, DOI 10.1007/s12155-012-9274-3, published online October 26, 2012. 2013_Dwiyanti_et_al_BioEnergy_Res.pdf
  • Ayodeji, A., Menkir, A., Moose, S.P., Adetimirin, V., Olaniyan, A. (2013) Genetic variation for nitrogen use efficiency among a selection of tropical maize hybrids differing in grain yield. Journal of Crop Improvement 27: 31-52.
  • Venkata, B.P., Lauter, N., Li, X., Chapple, C., Krupke, C., Johal, G. and Moose, S.P. (2013) Corn rootworm1- A novel maize mutant highly susceptible to foliar damage by the western corn rootworm beetle.  PLoS One 8: e71296.
  • Barling, A., Swaminathan, K., Mitros, T., James, B.T., Morris, J., Ngamboma, O., Hall, M.P., Kirkpatrick, J., Alabady, M., Varala, K., Hudson, M., Rokhsar, D.S., Moose, S.P. (2013)  A comprehensive expression study of the Miscanthus genus reveals changes in the transcriptome associated the rejuvenation of spring rhizomes.  BMC Genomics 14: 864 DOI: 10.1186/1471-2164-14-864,