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Research and Funding

 Currently Funded

The ROOTS Project

The ROOTS Project is an ARPA-E funded project (and a branch of the larger ARPA-E project called SUBTERRA) that aims to develop high throughput phenotyping techniques, increase our understanding of the genetics of complex traits in maize, and investigate the genetics of carbon sequestration in maize roots.  A multi-year field experiment was carried out using a maize diversity panel to assess their response to drought conditions.   We collected an assortment of phenotypic data in order to investigate the effects of drought on maize.  What we are most interested in, however, is the behavior of the root system and how it responds to drought conditions.  We are interested in the root systems because they contain large amounts of carbon and because the root systems remain in the soil even after the maize is harvested.  These factors could play a major role in combating atmospheric carbon emission recovery and ultimately sequestration.  To study the root systems, we implemented large scale Root Pulling Force events in which we collected data for the force required to remove the plant from the ground.  The extracted root systems are then processed further and many more phenotypes are collected.  By identifying and understanding phenotypes of interest that can improve carbon sequestration, we hope to provide the world with the knowledge it needs in order to begin using plants to combat atmospheric carbon accumulation.


Although Dr. John McKay and his team lead the efforts in the ROOTS Project, the larger SUBTERRA Project consists of collaborators around the country that are all working on different issues pertaining to climate change mitigation efforts.  You can find out more about the SUBTERRA project by following this link:


Extending Functional Understanding from Arabidopsis to Brassica Genomes

As the first plant genome to be sequenced, the Arabidopsis thaliana genome is a reference for plant comparative genomics. An emerging question in agriculture is the degree to which breeding will be informed by results from the model plant Arabidopsis. A logical starting point for this endeavor is in the Brassica oilseed crops. Comparisons of the two genomes show large regions of synteny, where segments of Arabidopsis chromosomes are present, often in triplicate, in the diploid Brassica species genomes. Recent work comparing genomes across the family Brassicaceae reconstructs eight ancestral chromosomes that rearranged into the current chromosome numbers found in the family. This evolutionary perspective shows that much of the difference between the Arabidopsis and Brassica genomes is due to rearrangements in the Arabidopsis lineage that occurred after the split from Brassica approximately 20 million years ago.

We are working to identify genomic regions in the Brassica species that are homologous to all twelve already identified drought avoidance QTL in Arabidopsis. We are focusing on the easiest approach, finding homologous regions in the diploid species Brassica rapa, which is currently being sequenced. The B. rapa genome is found not only in B. rapa, but also in the allotetraploid species Brassica napus (a major oilseed crop). To date, syntenic regions or blocks of the Arabidopsis genome have been identified for over 90% of the B. napus linkage map. The screening for homologous regions will be done using eight varieties of B. rapa, as well as spring and winter varieties of B. napus. Homozygous lines will be germinated in the greenhouse and transplanted into a field experiment at the CSU-USDA site in Akron, OH. Later, these plants will also be grown in controlled environment chambers. Effects of QTL on yield and physiological genotypes such as carbon isotope ratio will be determined using simple statistical contrasts between the two homozygous classes within a given cross.

Enhancing Education and Research Capacity in Plant Breeding for Drought Tolerance

PI: Patrick F. Byrne, Colorado State University
Co-PI’s: John McKay, Colorado State University
Stephen Baenziger, University of Nebraska-Lincoln
Bjorn Martin, Oklahoma State University
Collaborator: Scott Haley, Colorado State University

Information about this training program, which is funded by a grant from the USDA-CSREES (Cooperative State Research, Education, & Extension Service) can be found at

Identification of Genes That Control Biomass Production Using Rice as a Model System

Principal Investigators:
Daniel Bush, Colorado State University
Hei Leung, International Rice Research Institute, Manila, Philippines
John McKay, Colorado State University
Jan E. Leach, Colorado State University


Developing a sustainable biofuels program that makes significant contributions to the national energy budget requires unprecedented inputs of biomass for energy conversion. These crops must provide a net energy gain, be environmentally friendly, economically competitive, non-competitive with food supply, and be producible in large quantities. Historically, focus on biofuel plants has been on those which placed more carbon in the harvested grain than on the rest of the plant in order to increase crop yield. The new “energy crops,” however, must be vigorous growers that yield maximum dry biomass per acre. This can be acheived by maximizing growth of vegetative tissues largely composed of cell walls, since the available free energy in multicellular plants is found in the cell walls of vegetative issues. The consensus among biofuel researchers is that perennial grasses will be one of the “new energy” crops developed for biomass production.

Our goal is to provide the applied biomass research community and industry with information to allow exploitation of the genes and pathways relevant to biomass accumulation in grasses. Our specific objectives include:

Objective 1: Identify genes involved in biomass accumulation. Using genetic populations for rice lines that exhibit extremes in biomass accumulation, we will (a) map QTL using a phenotyping/genotyping approach, (b) confirm the QTL location and phenotyping effect, and (c) screen a deletion mutant collection to identify large deleted regions corresponding to biomass accumulation.

Objective 2: Dissect the QTL using an integrated analysis. First, we will use an expedited approach to generating near isogenic lines containing each QTL. Second, we will integrate genome-wide data to refine the QTL regions including (a) association mapping, (b) expression profiling, (c) mutant analysis, (d) fine scale mapping, and (e) comprehensive sequencing of the QTL region.

Objective 3: Validate the significance of candidate genes or pathways in biomass accumulation by using RNAi, reverse genetic resources (insertion and deletion mutants) and overexpression coupled to a comprehensive analysis or morophology and physiology.

Objective 4: Integrate expression and mapping data into gene browser/database to allow easy navigation and use of the data.

To approach these objectives, we are using rice as a model system because of the powerful genetic and genomic resources available for rice. In addition, rice has all of the genes necessary for high biomass productivity. We seek to identify those genes to expedite improvement of productivity in candidate biomass plants (switchgrass, Miscanthus, etc.).

Adaptation and Range Expansion in Barbed Goatgrass:

Aegilops triuncialis (Barbed Goatgrass) is an annual grass that was introduced from its native range in Eurasia, into California in 1924. In the past 30 years this species has become a problematic invasive in California. The invasive species is a federal and state-listed noxious weed due to its poor palatability for livestock, and is a recognized threat to western rangelands and native habitats. It is especially worrisome because of its ability to invade serpentine soil communities, which are very high in endemism and relatively free of exotic invasives. Aegilops triuncialis has been intensively studied because of its close relationship with cultivated wheat, Triticum aestivum, allowing the infrastructure and resources of wheat genomics to be applied to genetic questions in goatgrass invasions. We are studying the post-introduction evolutionary dynamics of this invasive species as well as the genetics of range expansion in severely bottlenecked populations of A. triuncialis in multiple sites in California. We have proposed that:

1) Maternal environmental effects (cross-generational phenotypic plasticity) are an important type of adaptive plasticity facilitating the persistence and initial spread of this invasive species.

2) Mutation accumulation in quantitative traits is an important source of genetic variation for adaptive change in selfing plant invaders that experience extreme bottlenecks.

Maternal environmental effects were studied in three serpentine sites where subpopulations were grown in “edge” and “core” habitats in order to answer questions relating to the interaction between maternal and offspring genotypes and environments.

To study the accumulation of mutation in A. triuncialis, we first identified populations founded by a single homozygous haplotype in order to test the hypothesis that populations derived from a single introduction event can be viewed as replicates within a mutation accumulation experiment. Because of the extreme bottlenecks that may often occur in biological invasions, this could provide a unique opportunity to examine how the basic evolutionary process of mutation can contribute to invasiveness.

Estimating the Frequency and Impact of Transgene Introgression from Wheat to Jointed Goatgrass

Principal Investigators:
John McKay (Evolutionary Genetics)
Patrick Byrne(Molecular-Quantitative Genetics)
Phillip Westra (Weed Control Systems and Herbicide Metabolisms)
Nora Lapitan (Plant Molecular Genetics and Cytogenetics)
Aegilops cylindrica (jointed goatgrass) competes directly with wheat production, decreasing yields and profitability to wheat farmers in the U.S. An increased interest in developing more effective weed control has resulted. Currently, an effective strategy is using an herbicide resistant transgenic variety of wheat, and controlling the jointed goatgrass with herbicide. The concern of this project is in the development of transgenic wheat and the movement of transgenes from wheat to Ae. cylindrica. Ae. cylindrica and wheat share a common ancestor, Ae. tauschii, and therefore both contain a common D genome. Hybridization between Triticum aestivum L (hard red winter wheat) and Ae. cylindrica has been documented and in Eastern Colorado a mean hybridization rate of 0.1% and a maximum hybridization rate of 1.6% has been determined (Gaines et al. 2008). Subsequent backcrosses of the F1 hybrid to Ae. cylindrica would provide a mechanism of gene introgression from wheat to Ae. cylindrica. Development of transgenic wheat, including herbicide resistance and drought tolerance, could transfer the advantageous transgenes into Ae. cylindrica making the weed more competitive and more difficult to manage.


1- a) Estimate the rate of backcross between F1 hybrids (Triticum aestivum x Aegilops cylindrica) with Ae. cylindrica as the pollen donor.

b) Determine the fertility and chromosome composition of the BC1 and further backcross generations.

2- Determine sequences specific to each Aegilops diploid genome to use to track the transfer of wheat DNA to the Ae. cylindrica genome.

3- Use 30 Western U.S. populations to compare phenotypic traits in Ae. cylindrica, especially drought tolerance.

4- a) Sample the genetic diversity of jointed Ae. cylindrica in U.S. and Eurasian populations to study the introduction history and lineage of Ae. cylindrica.

b) Compare determined phenotypic diversity to genetic diversity.

Funded by USDA grant 2007-33120-16481

Other Interests

  • Genomics of Allopolyploid Speciation
  • Adaptation and Conservation
  • Genetics of Cannabinoid Synthesis
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