A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci
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.
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- Publication Date:
- Research Org.:
- Donald Danforth Plant Science Center, St. Louis, MO (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1670237
- Alternate Identifier(s):
- OSTI ID: 1701739; OSTI ID: 1833824
- Grant/Contract Number:
- AC02-05CH11231; SC0008769
- Resource Type:
- Published Article
- Journal Name:
- Nature Biotechnology
- Additional Journal Information:
- Journal Name: Nature Biotechnology Journal Volume: 38 Journal Issue: 10; Journal ID: ISSN 1087-0156
- Publisher:
- Springer Nature
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Mamidi, Sujan, Healey, Adam, Huang, Pu, Grimwood, Jane, Jenkins, Jerry, Barry, Kerrie, Sreedasyam, Avinash, Shu, Shengqiang, Lovell, John T., Feldman, Maximilian, Wu, Jinxia, Yu, Yunqing, Chen, Cindy, Johnson, Jenifer, Sakakibara, Hitoshi, Kiba, Takatoshi, Sakurai, Tetsuya, Tavares, Rachel, Nusinow, Dmitri A., Baxter, Ivan, Schmutz, Jeremy, Brutnell, Thomas P., and Kellogg, Elizabeth A. A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci. United States: N. p., 2020.
Web. doi:10.1038/s41587-020-0681-2.
Mamidi, Sujan, Healey, Adam, Huang, Pu, Grimwood, Jane, Jenkins, Jerry, Barry, Kerrie, Sreedasyam, Avinash, Shu, Shengqiang, Lovell, John T., Feldman, Maximilian, Wu, Jinxia, Yu, Yunqing, Chen, Cindy, Johnson, Jenifer, Sakakibara, Hitoshi, Kiba, Takatoshi, Sakurai, Tetsuya, Tavares, Rachel, Nusinow, Dmitri A., Baxter, Ivan, Schmutz, Jeremy, Brutnell, Thomas P., & Kellogg, Elizabeth A. A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci. United States. https://doi.org/10.1038/s41587-020-0681-2
Mamidi, Sujan, Healey, Adam, Huang, Pu, Grimwood, Jane, Jenkins, Jerry, Barry, Kerrie, Sreedasyam, Avinash, Shu, Shengqiang, Lovell, John T., Feldman, Maximilian, Wu, Jinxia, Yu, Yunqing, Chen, Cindy, Johnson, Jenifer, Sakakibara, Hitoshi, Kiba, Takatoshi, Sakurai, Tetsuya, Tavares, Rachel, Nusinow, Dmitri A., Baxter, Ivan, Schmutz, Jeremy, Brutnell, Thomas P., and Kellogg, Elizabeth A. Mon .
"A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci". United States. https://doi.org/10.1038/s41587-020-0681-2.
@article{osti_1670237,
title = {A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci},
author = {Mamidi, Sujan and Healey, Adam and Huang, Pu and Grimwood, Jane and Jenkins, Jerry and Barry, Kerrie and Sreedasyam, Avinash and Shu, Shengqiang and Lovell, John T. and Feldman, Maximilian and Wu, Jinxia and Yu, Yunqing and Chen, Cindy and Johnson, Jenifer and Sakakibara, Hitoshi and Kiba, Takatoshi and Sakurai, Tetsuya and Tavares, Rachel and Nusinow, Dmitri A. and Baxter, Ivan and Schmutz, Jeremy and Brutnell, Thomas P. and Kellogg, Elizabeth A.},
abstractNote = {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.},
doi = {10.1038/s41587-020-0681-2},
journal = {Nature Biotechnology},
number = 10,
volume = 38,
place = {United States},
year = {Mon Oct 05 00:00:00 EDT 2020},
month = {Mon Oct 05 00:00:00 EDT 2020}
}
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