skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Abstract

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 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 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.

Authors:
ORCiD logo; ; ; ORCiD logo; ORCiD logo; ; ORCiD logo; ORCiD logo; ; ; ; ; ; ; ; ORCiD logo; ORCiD logo; ; ; more »; ORCiD logo; ; ORCiD logo « less
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1670237
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:
Nature Publishing Group
Country of Publication:
United States
Language:
English

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. 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., and Kellogg, Elizabeth A. Mon . "A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci". United States. doi: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 = {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 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 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 = {2020},
month = {10}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1038/s41587-020-0681-2

Save / Share:

Works referenced in this record:

Reference Genome for the Highly Transformable Setaria viridis ME034V
journal, July 2020

  • Thielen, Peter M.; Pendleton, Amanda L.; Player, Robert A.
  • G3: Genes|Genomes|Genetics
  • DOI: 10.1534/g3.120.401345

Millets across Eurasia: chronology and context of early records of the genera Panicum and Setaria from archaeological sites in the Old World
journal, October 2008

  • Hunt, Harriet V.; Vander Linden, Marc; Liu, Xinyi
  • Vegetation History and Archaeobotany, Vol. 17, Issue S1
  • DOI: 10.1007/s00334-008-0187-1

Morphological, phylogenetic, and ecological diversity of the new model species Setaria viridis (Poaceae: Paniceae) and its close relatives
journal, March 2014

  • Layton, Daniel J.; Kellogg, Elizabeth A.
  • American Journal of Botany, Vol. 101, Issue 3
  • DOI: 10.3732/ajb.1300428

Genome-wide association study of leaf architecture in the maize nested association mapping population
journal, January 2011

  • Tian, Feng; Bradbury, Peter J.; Brown, Patrick J.
  • Nature Genetics, Vol. 43, Issue 2
  • DOI: 10.1038/ng.746

An SNP Caused Loss of Seed Shattering During Rice Domestication
journal, April 2006


Effects of abiotic stress on physiological plasticity and water use of Setaria viridis (L.)
journal, October 2016


A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica)
journal, June 2013

  • Jia, Guanqing; Huang, Xuehui; Zhi, Hui
  • Nature Genetics, Vol. 45, Issue 8
  • DOI: 10.1038/ng.2673

KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 2000

  • Kanehisa, Minoru; Goto, Susumu
  • Nucleic Acids Research, Vol. 28, Issue 1, p. 27-30
  • DOI: 10.1093/nar/28.1.27

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
journal, May 2013

  • Chin, Chen-Shan; Alexander, David H.; Marks, Patrick
  • Nature Methods, Vol. 10, Issue 6
  • DOI: 10.1038/nmeth.2474

Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL.
journal, September 1996

  • Gaut, B. S.; Morton, B. R.; McCaig, B. C.
  • Proceedings of the National Academy of Sciences, Vol. 93, Issue 19
  • DOI: 10.1073/pnas.93.19.10274

Setaria viridis : A Model for C 4 Photosynthesis
journal, August 2010

  • Brutnell, Thomas P.; Wang, Lin; Swartwood, Kerry
  • The Plant Cell, Vol. 22, Issue 8
  • DOI: 10.1105/tpc.110.075309

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic
journal, November 2014

  • Sonnhammer, Erik L. L.; Östlund, Gabriel
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1203

The maize gene liguleless2 encodes a basic leucine zipper protein involved in the establishment of the leaf blade-sheath boundary
journal, January 1998

  • Walsh, J.; Waters, C. A.; Freeling, M.
  • Genes & Development, Vol. 12, Issue 2
  • DOI: 10.1101/gad.12.2.208

Construction of RFLP-based maps of foxtail millet, Setaria italica (L.) P. Beauv.
journal, January 1998

  • Wang, Z. M.; Devos, K. M.; Liu, C. J.
  • Theoretical and Applied Genetics, Vol. 96, Issue 1
  • DOI: 10.1007/s001220050705

Rice Domestication by Reducing Shattering
journal, March 2006


Plant Development: Regulation by Protein Degradation
journal, August 2002


Genetic Control of Seed Shattering in Rice by the APETALA2 Transcription Factor SHATTERING ABORTION1
journal, March 2012


WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas: NEW CLIMATE SURFACES FOR GLOBAL LAND AREAS
journal, May 2017

  • Fick, Stephen E.; Hijmans, Robert J.
  • International Journal of Climatology, Vol. 37, Issue 12
  • DOI: 10.1002/joc.5086

The lignin toolbox of the model grass Setaria viridis
journal, June 2019

  • Ferreira, Sávio Siqueira; Simões, Marcella Siqueira; Carvalho, Gabriel Garon
  • Plant Molecular Biology, Vol. 101, Issue 3
  • DOI: 10.1007/s11103-019-00897-9

Components of Water Use Efficiency Have Unique Genetic Signatures in the Model C 4 Grass Setaria
journal, August 2018

  • Feldman, Max J.; Ellsworth, Patrick Z.; Fahlgren, Noah
  • Plant Physiology, Vol. 178, Issue 2
  • DOI: 10.1104/pp.18.00146

QTL Mapping Combined With Comparative Analyses Identified Candidate Genes for Reduced Shattering in Setaria italica
journal, July 2018

  • Odonkor, Sandra; Choi, Soyeon; Chakraborty, Debkanta
  • Frontiers in Plant Science, Vol. 9
  • DOI: 10.3389/fpls.2018.00918

A Map of Recent Positive Selection in the Human Genome
journal, March 2006


Efficient multivariate linear mixed model algorithms for genome-wide association studies
journal, February 2014


Setaria viridis as a model for translational genetic studies of jasmonic acid-related insect defenses in Zea mays
journal, February 2020


Brassinosteroids Modulate Meristem Fate and Differentiation of Unique Inflorescence Morphology in Setaria viridis
journal, December 2017

  • Yang, Jiani; Thames, Shuiyi; Best, Norman B.
  • The Plant Cell, Vol. 30, Issue 1
  • DOI: 10.1105/tpc.17.00816

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing
journal, February 2012


PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels
journal, April 2015


Second-generation PLINK: rising to the challenge of larger and richer datasets
journal, February 2015


RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
journal, January 2014


adegenet 1.3-1: new tools for the analysis of genome-wide SNP data
journal, September 2011


Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
journal, April 2006


Anatomy and ultrastructure of embryonic leaves of the C4 species Setaria viridis
journal, February 2018

  • Junqueira, Nicia E. G.; Ortiz-Silva, Bianca; Leal-Costa, Marcos Vinícius
  • Annals of Botany, Vol. 121, Issue 6
  • DOI: 10.1093/aob/mcx217

Genome-Wide Analysis of Syntenic Gene Deletion in the Grasses
journal, January 2012

  • Schnable, James C.; Freeling, Michael; Lyons, Eric
  • Genome Biology and Evolution, Vol. 4, Issue 3
  • DOI: 10.1093/gbe/evs009

Deletion in a gene associated with grain size increased yields during rice domestication
journal, July 2008

  • Shomura, Ayahiko; Izawa, Takeshi; Ebana, Kaworu
  • Nature Genetics, Vol. 40, Issue 8
  • DOI: 10.1038/ng.169

Heritability and Functional Importance of the Setaria viridis Bacterial Seed Microbiome
journal, January 2020


MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
journal, September 2017

  • Xiao, Chuan-Le; Chen, Ying; Xie, Shang-Qian
  • Nature Methods, Vol. 14, Issue 11
  • DOI: 10.1038/nmeth.4432

Genetic dissection of seed shattering, agronomic, and color traits in American wildrice (Zizania palustris var. interior L.) with a comparative map
journal, November 2002


fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets
journal, April 2014


Genotype Imputation with Millions of Reference Samples
journal, January 2016

  • Browning, Brian L.; Browning, Sharon R.
  • The American Journal of Human Genetics, Vol. 98, Issue 1
  • DOI: 10.1016/j.ajhg.2015.11.020

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
journal, July 2010


Sparse panicle1 is required for inflorescence development in Setaria viridis and maize
journal, April 2017


hapbin: An Efficient Program for Performing Haplotype-Based Scans for Positive Selection in Large Genomic Datasets: Fig. 1.
journal, August 2015

  • Maclean, Colin A.; Chue Hong, Neil P.; Prendergast, James G. D.
  • Molecular Biology and Evolution, Vol. 32, Issue 11
  • DOI: 10.1093/molbev/msv172

Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure
journal, December 2017

  • Gordon, Sean P.; Contreras-Moreira, Bruno; Woods, Daniel P.
  • Nature Communications, Vol. 8, Issue 1
  • DOI: 10.1038/s41467-017-02292-8

Parallel domestication of the Shattering1 genes in cereals
journal, May 2012

  • Lin, Zhongwei; Li, Xianran; Shannon, Laura M.
  • Nature Genetics, Vol. 44, Issue 6
  • DOI: 10.1038/ng.2281

The genomic landscape of molecular responses to natural drought stress in Panicum hallii
journal, December 2018


Divergent gene expression networks underlie morphological diversity of abscission zones in grasses
journal, August 2019

  • Yu, Yunqing; Hu, Hao; Doust, Andrew N.
  • New Phytologist, Vol. 225, Issue 4
  • DOI: 10.1111/nph.16087

Reference genome sequence of the model plant Setaria
journal, May 2012

  • Bennetzen, Jeffrey L.; Schmutz, Jeremy; Wang, Hao
  • Nature Biotechnology, Vol. 30, Issue 6
  • DOI: 10.1038/nbt.2196

Accurate detection of complex structural variations using single-molecule sequencing
journal, April 2018


Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
journal, October 2003


Gepard: a rapid and sensitive tool for creating dotplots on genome scale
journal, February 2007


Population genetics of Setaria viridis , a new model system
journal, September 2014

  • Huang, Pu; Feldman, Maximilian; Schroder, Stephan
  • Molecular Ecology, Vol. 23, Issue 20
  • DOI: 10.1111/mec.12907

A Multipurpose Toolkit to Enable Advanced Genome Engineering in Plants
journal, May 2017

  • Čermák, Tomáš; Curtin, Shaun J.; Gil-Humanes, Javier
  • The Plant Cell, Vol. 29, Issue 6
  • DOI: 10.1105/tpc.16.00922

Abscission zone development in Setaria viridis and its domesticated relative, Setaria italica
journal, June 2016

  • Hodge, John G.; Kellogg, Elizabeth A.
  • American Journal of Botany, Vol. 103, Issue 6
  • DOI: 10.3732/ajb.1500499

Methods for Performing Crosses in <em>Setaria viridis</em>, a New Model System for the Grasses
journal, January 2013

  • Jiang, Hui; Barbier, Hugues; Brutnell, Thomas
  • Journal of Visualized Experiments, Issue 80
  • DOI: 10.3791/50527

Generating samples under a Wright-Fisher neutral model of genetic variation
journal, February 2002