Sequence-Enabled Genetics in Setaria viridis: A Model System for the Grasses

To accelerate the adoption of Setaria viridis (S. viridis) as a model system, genetic resources and tools are being developed that exploit high throughput sequencing technologies. To create mutant populations for forward and reverse genetics, we have conducted an NMU-mutagenesis and, to date, have generated and characterized approximately 3000 NMU mutant families, from which a TILLING population is being developed. A total of 55 mutant individuals are being sequenced at ~30x by JGI-DOE to empirically determine mutation frequency. We observed majority of the mutations are transitions, and the average non-synonymous mutation frequency was approximately 50 disruptive mutations per individual. A panicle mutant has been crossed with S. viridis accessions to fine map the gene using Bulk Segregant Analysis (BSA) followed by deep sequencing. We have also initiated the construction of six recombinant inbred populations generated by crossing diverse S. viridis accessions with A10.1. We have assembled a diverse germplasm collection of 390 S.viridis accessions with contributions from many collaborators. These accessions are being resequenced at JGI-DOE to establish a panel for population genetic analysis and genome wide association studies (GWAS). We demonstrated that phenotypes of interest can be mapped to fine resolution with a thorough characterization of the standing variations in a subset of this panel.  A subset of these 390 lines has been characterized for phenotypic traits and have been propagated for seed distribution at the USDA GRIN (http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?430573 ).