A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci

Wild and weedy relatives of domesticated crops harbor genetic variants that can advance agricultural biotechnology. Here we provide a genome resource for the wild plant green millet (Setaria viridis), a model species for studies of C(4)grasses, and use the resource to probe domestication genes in the close crop relative foxtail millet (Setaria italica). We produced a platinum-quality genome assembly ofS. viridisand de novo assemblies for 598 wild accessions and exploited these assemblies to identify loci underlying three traits: response to climate, a 'loss of shattering' trait that permits mechanical harvest and leaf angle, a predictor of yield in many grass crops. With CRISPR-Cas9 genome editing, we validatedLess Shattering1(SvLes1) as a gene whose product controls seed shattering. InS. italica, this gene was rendered nonfunctional by a retrotransposon insertion in the domesticated loss-of-shattering alleleSiLes1-TE(transposable element). This resource will enhance the utility ofS. viridisfor dissection of complex traits and biotechnological improvement of panicoid crops. Sequencing wild relatives of millet identifies genes that regulate yield and harvesting traits.