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 helps 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


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

Research Interests

  • 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.
  • 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.
  • 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).
  • 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.

Chapters in Books

Selected Articles in Journals