Thomas Brutnell, Ph.D.

Solving the world’s food, feed and biofuels challenges requires multiple approaches and a diversity of skills.  At the Danforth Center, scientists collaborate to develop new technologies, new model systems and new analytical approaches to tackle these problems.  This intellectual excitement is perhaps only equaled by the promise of achieving our goals for food and energy security.

Setaria as a model system:                                                              
Setaria viridis is a C4 Panicoid grass with many favorable attributes for a model C4 genetic system including short stature, rapid lifecycle, high seed production and simple growth requirement (link to article). We are currently developing numerous resources to accelerate the adoption of this model plant.
Setaria Resources:
   Setaria viridis v1.1 (Green foxtail) - link to phytozome10.3
   Setaria italica Genomve v2.1 -
link to phytozome10.1
   Setaria viridis Genome Resources - link to BLAST database
   Setaria for biofuels - link to foxmillet
   Protocol for Growing Setaria - download here
   Wet moss treatment method for breaking seed dormancy - download here
   How to perform crosses in Setaria - link to jove video
   Setaria Recombinant Inbred Line Development - link to USDA GRIN
                    For more information, please contact Hui Jiang (
Maize Resources:
     Genome-wide mutagenesis of Maize using Ac/Ds transposons - a collection of sequence-tagged Ds
insertions in W22-derived inbred lines, for reverse genetics in maize.  
to AcDs tagging site
Brachypodium Resources:
       Brachypodium distachyon  is  an excellent  model organism for studying temperate grasses. In order to facilitate reverse genetics, we have created an EMS-mutagenized Bd21-3 TILLING population of ~ 5000 M2 families.  TILLING (Targeting Induced DanforthRobotFig2%20Brachypodium_3329_60Local Lesions IN Genomes) is an efficient technique to identify mutations in genes of interest through PCR-based screens of mutagenized populations.  By integrating TILLING methods with Illumina sequencing of target gene amplicons, we have developed a High throughput protocol and informatics pipeline for efficiently identifying single base pair mutations among pools of mutant individuals.  To date, we have screened for 67 SNPs in 6 target genes and 55 SNPs were confirmed as positive through Sanger sequencing thus providing a high efficiency of 82% on average.  Currently, we are optimizing our method to minimize per gene cost. 
     If you are interested in obtaining mutants from this TILLING population, we would be happy to provide it for a service fee (to cover the cost). Please submit a request to Ying Rong (
Molecular Tools:
Custom Illumina RNAseq Library Protocol -
download here
     Southern Blotting Protocol - download here
     TaqMan protocol for Copy Number Variation (CNV) - download here 
Work in the Brutnell Lab is supported by the Bill & Melinda Gates Foundation, the U.S. Department of Energy and the National Science Foundation. Information on specific grants can be found here.