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Title: Sparse panicle1 is required for inflorescence development inSetaria viridis and maize

Abstract

Setaria viridis is a rapid-life-cycle model panicoid grass. Here, to identify genes that may contribute to inflorescence architecture and thus have the potential to influence grain yield in related crops such as maize, we conducted an N-nitroso-N-methylurea (NMU) mutagenesis of S. viridis and screened for visible inflorescence mutant phenotypes. Of the approximately 2,700 M2 families screened, we identified four recessive sparse panicle mutants (spp1-spp4) characterized by reduced and uneven branching of the inflorescence. To identify the gene underlying the sparse panicle1 (spp1) phenotype, we performed bulked segregant analysis and deep sequencing to fine map it to an approximately 1 Mb interval. Within this interval, we identified disruptive mutations in two genes. Complementation tests between spp1 and spp3 revealed they were allelic, and deep sequencing of spp3 identified an independent disruptive mutation in SvAUX1 (AUXIN1), one of the two genes in the ~1 Mb interval and the only gene disruption shared between spp1 and spp3. SvAUX1 was found to affect both inflorescence development and root gravitropism in S. viridis. A search for orthologous mutant alleles in maize confirmed a very similar role of ZmAUX1 in maize, which highlights the utility of S. viridis in accelerating functional genomic studies in maize.

Authors:
ORCiD logo [1];  [1];  [1];  [2];  [3];  [2];  [4];  [1];  [1]; ORCiD logo [1]
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  1. Donald Danforth Plant Science Center, St. Louis, MO (United States)
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); National Science Foundation (NSF)
OSTI Identifier:
1619076
Grant/Contract Number:  
AC02-05CH11231; SC0008769; IOS-1413824
Resource Type:
Accepted Manuscript
Journal Name:
Nature Plants (Online)
Additional Journal Information:
Journal Name: Nature Plants (Online); Journal Volume: 3; Journal Issue: 5; Journal ID: ISSN 2055-0278
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; plant development; plant genetics

Citation Formats

Huang, Pu, Jiang, Hui, Zhu, Chuanmei, Barry, Kerrie, Jenkins, Jerry, Sandor, Laura, Schmutz, Jeremy, Box, Mathew S., Kellogg, Elizabeth A., and Brutnell, Thomas P. Sparse panicle1 is required for inflorescence development inSetaria viridis and maize. United States: N. p., 2017. Web. doi:10.1038/nplants.2017.54.
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Huang, Pu, Jiang, Hui, Zhu, Chuanmei, Barry, Kerrie, Jenkins, Jerry, Sandor, Laura, Schmutz, Jeremy, Box, Mathew S., Kellogg, Elizabeth A., & Brutnell, Thomas P. Sparse panicle1 is required for inflorescence development inSetaria viridis and maize. United States. https://doi.org/10.1038/nplants.2017.54
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Huang, Pu, Jiang, Hui, Zhu, Chuanmei, Barry, Kerrie, Jenkins, Jerry, Sandor, Laura, Schmutz, Jeremy, Box, Mathew S., Kellogg, Elizabeth A., and Brutnell, Thomas P. Tue . "Sparse panicle1 is required for inflorescence development inSetaria viridis and maize". United States. https://doi.org/10.1038/nplants.2017.54. https://www.osti.gov/servlets/purl/1619076.
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@article{osti_1619076,
title = {Sparse panicle1 is required for inflorescence development inSetaria viridis and maize},
author = {Huang, Pu and Jiang, Hui and Zhu, Chuanmei and Barry, Kerrie and Jenkins, Jerry and Sandor, Laura and Schmutz, Jeremy and Box, Mathew S. and Kellogg, Elizabeth A. and Brutnell, Thomas P.},
abstractNote = {Setaria viridis is a rapid-life-cycle model panicoid grass. Here, to identify genes that may contribute to inflorescence architecture and thus have the potential to influence grain yield in related crops such as maize, we conducted an N-nitroso-N-methylurea (NMU) mutagenesis of S. viridis and screened for visible inflorescence mutant phenotypes. Of the approximately 2,700 M2 families screened, we identified four recessive sparse panicle mutants (spp1-spp4) characterized by reduced and uneven branching of the inflorescence. To identify the gene underlying the sparse panicle1 (spp1) phenotype, we performed bulked segregant analysis and deep sequencing to fine map it to an approximately 1 Mb interval. Within this interval, we identified disruptive mutations in two genes. Complementation tests between spp1 and spp3 revealed they were allelic, and deep sequencing of spp3 identified an independent disruptive mutation in SvAUX1 (AUXIN1), one of the two genes in the ~1 Mb interval and the only gene disruption shared between spp1 and spp3. SvAUX1 was found to affect both inflorescence development and root gravitropism in S. viridis. A search for orthologous mutant alleles in maize confirmed a very similar role of ZmAUX1 in maize, which highlights the utility of S. viridis in accelerating functional genomic studies in maize.},
doi = {10.1038/nplants.2017.54},
journal = {Nature Plants (Online)},
number = 5,
volume = 3,
place = {United States},
year = {Tue Apr 18 00:00:00 EDT 2017},
month = {Tue Apr 18 00:00:00 EDT 2017}
}
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https://doi.org/10.1038/nplants.2017.54
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Cited by: 44 works
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Figures / Tables:

Table 1 Table 1: Populations for bulked segregant analysis
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Works referenced in this record:

The role of barren stalk1 in the architecture of maize
journal, December 2004

  • Gallavotti, Andrea; Zhao, Qiong; Kyozuka, Junko
  • Nature, Vol. 432, Issue 7017
  • DOI: 10.1038/nature03148

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

Induction and analysis of gibberellin sensitive mutants in Arabidopsis thaliana (L.) heynh.
journal, November 1980

  • Koornneef, M.; van der Veen, J. H.
  • Theoretical and Applied Genetics, Vol. 58, Issue 6
  • DOI: 10.1007/BF00265176

Sequence-indexed mutations in maize using the UniformMu transposon-tagging population
journal, January 2007

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
journal, July 2002

Nonsense-mediated mRNA decay: terminating erroneous gene expression
journal, June 2004

The Inheritance of Certain "Abnormalities" in Maize
journal, January 1912

Model grasses hold key to crop improvement
journal, May 2015

Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data.
journal, August 1989

  • Wolfe, K. H.; Gouy, M.; Yang, Y. W.
  • Proceedings of the National Academy of Sciences, Vol. 86, Issue 16
  • DOI: 10.1073/pnas.86.16.6201

Auxin influx carriers stabilize phyllotactic patterning
journal, March 2008

  • Bainbridge, K.; Guyomarc'h, S.; Bayer, E.
  • Genes & Development, Vol. 22, Issue 6
  • DOI: 10.1101/gad.462608

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

The Relationship between Auxin Transport and Maize Branching
journal, June 2008

  • Gallavotti, Andrea; Yang, Yan; Schmidt, Robert J.
  • Plant Physiology, Vol. 147, Issue 4
  • DOI: 10.1104/pp.108.121541

Genetic and physical interaction suggest that BARREN STALK1 is a target of BARREN INFLORESCENCE2 in maize inflorescence development
journal, September 2008

Barren inflorescence1 Functions in Organogenesis During Vegetative and Inflorescence Development in Maize
journal, May 2008

Basic local alignment search tool
journal, October 1990

  • Altschul, Stephen F.; Gish, Warren; Miller, Webb
  • Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
  • DOI: 10.1016/S0022-2836(05)80360-2

OsAUX1 controls lateral root initiation in rice ( O ryza sativa  L.) : OsAUX1 controlling lateral root initiation
journal, January 2015

  • Zhao, Heming; Ma, Tengfei; Wang, Xin
  • Plant, Cell & Environment, Vol. 38, Issue 11
  • DOI: 10.1111/pce.12467

Yield Trends Are Insufficient to Double Global Crop Production by 2050
journal, June 2013

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

Structure-Function Analysis of the Presumptive Arabidopsis Auxin Permease AUX1
journal, October 2004

  • Swarup, Ranjan; Kargul, Joanna; Marchant, Alan
  • The Plant Cell, Vol. 16, Issue 11
  • DOI: 10.1105/tpc.104.024737

Genes Identified by Visible Mutant Phenotypes Show Increased Bias toward One of Two Subgenomes of Maize
journal, March 2011

vanishing tassel2 Encodes a Grass-Specific Tryptophan Aminotransferase Required for Vegetative and Reproductive Development in Maize
journal, February 2011

  • Phillips, Kimberly A.; Skirpan, Andrea L.; Liu, Xing
  • The Plant Cell, Vol. 23, Issue 2
  • DOI: 10.1105/tpc.110.075267

An Expanded Maize Gene Expression Atlas based on RNA Sequencing and its Use to Explore Root Development
journal, January 2016

CIRCADIAN CLOCK-ASSOCIATED 1 and LATE ELONGATED HYPOCOTYL regulate expression of the C-REPEAT BINDING FACTOR (CBF) pathway in Arabidopsis
journal, April 2011

  • Dong, M. A.; Farre, E. M.; Thomashow, M. F.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 17
  • DOI: 10.1073/pnas.1103741108

The auxin transporter, OsAUX1, is involved in primary root and root hair elongation and in Cd stress responses in rice ( Oryza sativa L.)
journal, July 2015

  • Yu, ChenLiang; Sun, ChenDong; Shen, Chenjia
  • The Plant Journal, Vol. 83, Issue 5
  • DOI: 10.1111/tpj.12929

BARREN INFLORESCENCE2 Interaction with ZmPIN1a Suggests a Role in Auxin Transport During Maize Inflorescence Development
journal, January 2009

  • Skirpan, Andrea; Culler, Angela Hendrickson; Gallavotti, Andrea
  • Plant and Cell Physiology, Vol. 50, Issue 3
  • DOI: 10.1093/pcp/pcp006

Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations.
journal, November 1991

  • Michelmore, R. W.; Paran, I.; Kesseli, R. V.
  • Proceedings of the National Academy of Sciences, Vol. 88, Issue 21
  • DOI: 10.1073/pnas.88.21.9828

MutMap accelerates breeding of a salt-tolerant rice cultivar
journal, March 2015

  • Takagi, Hiroki; Tamiru, Muluneh; Abe, Akira
  • Nature Biotechnology, Vol. 33, Issue 5
  • DOI: 10.1038/nbt.3188

sparse inflorescence1 encodes a monocot-specific YUCCA-like gene required for vegetative and reproductive development in maize
journal, September 2008

  • Gallavotti, A.; Barazesh, S.; Malcomber, S.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 39
  • DOI: 10.1073/pnas.0805596105

A genetic playground for enhancing grain number in cereals
journal, February 2012

Patterns of Inflorescence Development of Three Prairie Grasses (Andropogoneae, Poaceae)
journal, November 2014

  • Hodge, John G.; Kellogg, Elizabeth A.
  • International Journal of Plant Sciences, Vol. 175, Issue 9
  • DOI: 10.1086/677652

Protter: interactive protein feature visualization and integration with experimental proteomic data
journal, October 2013

Validating Internal Control Genes for the Accurate Normalization of qPCR Expression Analysis of the Novel Model Plant Setaria viridis
journal, August 2015

High-Affinity Auxin Transport by the AUX1 Influx Carrier Protein
journal, June 2006

Arabidopsis as a Genetic Tool
journal, December 1975

Brachypodium distachyon and Setaria viridis : Model Genetic Systems for the Grasses
journal, April 2015

Arabidopsis AUX1 Gene: A Permease-Like Regulator of Root Gravitropism
journal, August 1996

Floral displays: genetic control of grass inflorescences
journal, February 2007

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    Works referencing / citing this record:

    Climate-smart crops with enhanced photosynthesis
    journal, May 2018

    • Jansson, Christer; Vogel, John; Hazen, Samuel
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    • DOI: 10.1093/jxb/ery213

    Epistasis Detection and Modeling for Genomic Selection in Cowpea (Vigna unguiculata L. Walp.)
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    Correction to: Fine mapping and identification of the fuzzless gene GaFzl in DPL972 (Gossypium arboreum)
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    Setaria Comes of Age: Meeting Report on the Second International Setaria Genetics Conference
    journal, September 2017

    Optimization of Phenotyping Assays for the Model Monocot Setaria viridis
    journal, December 2017

    • Acharya, Biswa R.; Roy Choudhury, Swarup; Estelle, Aiden B.
    • Frontiers in Plant Science, Vol. 8
    • DOI: 10.3389/fpls.2017.02172

    Domestication and Improvement in the Model C4 Grass, Setaria
    journal, May 2018

    • Hu, Hao; Mauro-Herrera, Margarita; Doust, Andrew N.
    • Frontiers in Plant Science, Vol. 9
    • DOI: 10.3389/fpls.2018.00719

    Generation and Characterization of a Foxtail Millet (Setaria italica) Mutant Library
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    Developmental Roles of AUX1/LAX Auxin Influx Carriers in Plants
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