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

Sujan Mamidi, Adam Healey, Pu Huang, Jane Grimwood, Jerry Jenkins, Kerrie Barry, Avinash Sreedasyam, Shengqiang Shu, John T. Lovell, Maximilian Feldman, Jinxia Wu, Yunqing Yu, Cindy Chen, Jenifer Johnson, Hitoshi Sakakibara, Takatoshi Kiba, Tetsuya Sakurai, Rachel Tavares, Dmitri A. Nusinow, Ivan BaxterJeremy Schmutz, Thomas P. Brutnell, Elizabeth A. Kellogg

Research output: Contribution to journalArticlepeer-review

77 Scopus citations


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 C4 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 of S. viridis and 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 validated Less Shattering1 (SvLes1) as a gene whose product controls seed shattering. In S. italica, this gene was rendered nonfunctional by a retrotransposon insertion in the domesticated loss-of-shattering allele SiLes1-TE (transposable element). This resource will enhance the utility of S. viridis for dissection of complex traits and biotechnological improvement of panicoid crops.

Original languageEnglish
Pages (from-to)1203-1210
Number of pages8
JournalNature Biotechnology
Issue number10
StatePublished - Oct 1 2020


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