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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 C₄grasses, 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.