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

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

doi:10.1038/s41587-020-0681-2

Abstract

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.

Highlights

We provided a high-quality genome of S. viridis, a model C4 plant and a wild progenitor of domesticated foxtail millet (S. italica)
Multiple sources of evidence support that S. viridis has an ancestral range in Eurasia[19], was introduced to the United States via multiple routes and subsequently dispersed within the United States
The resequenced accessions described here provide a rich source of variants (SNP, PAV and SV) that reflect the population structure of the species in the United States

Summary

Methods

The reference line A10.1 is a descendant of the line used by Wang et al.[41] in early restriction fragment length polymorphism maps. The original line was found to be heterozygous, and, A10.1 was propagated via single-seed descent by Andrew Doust (Oklahoma State University; personal communication). It is thought to have originated in Canada. The other reference, ME034 ( known as ME034v), was collected by Matt Estep (Appalachian State University) in southern Canada as part of a diversity panel[19] included among the diversity lines sequenced here; its genome has been assembled recently[37]. Transformation is more efficient for ME034 than for A10.137, and, the latter is being used widely for functional genetic studies

Results

Discussion

Conclusion