Integrated Genome-Scale Analysis Identifies Novel Genes and Networks Underlying Senescence in Maize

Sekhon, Rajandeep S.; Saski, Christopher; Kumar, Rohit; Flinn, Barry S.; Luo, Feng; Beissinger, Timothy M.; Ackerman, Arlyn J.; Breitzman, Matthew W.; Bridges, William C.; de Leon, Natalia; Kaeppler, Shawn M.

doi:10.1105/tpc.18.00930

Title: Integrated Genome-Scale Analysis Identifies Novel Genes and Networks Underlying Senescence in Maize

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Abstract

Premature senescence in annual crops reduces yield, while delayed senescence, termed stay-green, imposes positive and negative impacts on yield and nutrition quality. Despite its importance, scant information is available on the genetic architecture of senescence in maize (Zea mays) and other cereals. We combined a systematic characterization of natural diversity for senescence in maize and coexpression networks derived from transcriptome analysis of normally senescing and stay-green lines. Sixty-four candidate genes were identified by genome-wide association study (GWAS), and 14 of these genes are supported by additional evidence for involvement in senescence-related processes including proteolysis, sugar transport and signaling, and sink activity. Eight of the GWAS candidates, independently supported by a coexpression network underlying stay-green, include a trehalose-6-phosphate synthase, a NAC transcription factor, and two xylan biosynthetic enzymes. Source–sink communication and the activity of cell walls as a secondary sink emerge as key determinants of stay-green. Mutant analysis supports the role of a candidate encoding Cys protease in stay-green in Arabidopsis (Arabidopsis thaliana), and analysis of natural alleles suggests a similar role in maize. This study provides a foundation for enhanced understanding and manipulation of senescence for increasing carbon yield, nutritional quality, and stress tolerance of maize and other cereals.

Authors:

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Department of Genetics and Biochemistry, Clemson University, 314 Biosystems Research Complex, 105 Collings Street, Clemson, South Carolina 29634
Department of Plant and Environmental Sciences, Clemson University, 306B Biosystems Research Complex, 105 Collings Street, Clemson, South Carolina 29634
School of Computing, Clemson University, 210 McAdams Hall, Clemson, South Carolina 29634
Center for Integrated Breeding Research, University of Göttingen, D-37075 Göttingen, Germany
Department of Agronomy, University of Wisconsin, 1575 Linden Drive, Madison, Wisconsin 53706
Department of Mathematical Sciences, Clemson University, O-117 Martin Hall, Clemson, South Carolina 29634

Publication Date:: Tue Jun 25 00:00:00 EDT 2019

Research Org.:: Univ. of Wisconsin, Madison, WI (United States)

Sponsoring Org.:: USDOE Office of Science (SC)

OSTI Identifier:: 1529634

Alternate Identifier(s):: OSTI ID: 1609241

Grant/Contract Number:: FC02-07ER64494

Resource Type:: Published Article

Journal Name:: The Plant Cell

Additional Journal Information:: Journal Name: The Plant Cell Journal Volume: 31 Journal Issue: 9; Journal ID: ISSN 1040-4651

Publisher:: American Society of Plant Biologists

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; Biochemistry & Molecular Biology; Plant Sciences; Cell Biology

Citation Formats


                    Sekhon, Rajandeep S., Saski, Christopher, Kumar, Rohit, Flinn, Barry S., Luo, Feng, Beissinger, Timothy M., Ackerman, Arlyn J., Breitzman, Matthew W., Bridges, William C., de Leon, Natalia, and Kaeppler, Shawn M. Integrated Genome-Scale Analysis Identifies Novel Genes and Networks Underlying Senescence in Maize.  United States: N. p., 2019. 
Web.  doi:10.1105/tpc.18.00930.

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                    Sekhon, Rajandeep S., Saski, Christopher, Kumar, Rohit, Flinn, Barry S., Luo, Feng, Beissinger, Timothy M., Ackerman, Arlyn J., Breitzman, Matthew W., Bridges, William C., de Leon, Natalia, & Kaeppler, Shawn M. Integrated Genome-Scale Analysis Identifies Novel Genes and Networks Underlying Senescence in Maize.  United States.  https://doi.org/10.1105/tpc.18.00930

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                    Sekhon, Rajandeep S., Saski, Christopher, Kumar, Rohit, Flinn, Barry S., Luo, Feng, Beissinger, Timothy M., Ackerman, Arlyn J., Breitzman, Matthew W., Bridges, William C., de Leon, Natalia, and Kaeppler, Shawn M. Tue .  
"Integrated Genome-Scale Analysis Identifies Novel Genes and Networks Underlying Senescence in Maize".  United States.  https://doi.org/10.1105/tpc.18.00930.

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@article{osti_1529634,

  title        = {Integrated Genome-Scale Analysis Identifies Novel Genes and Networks Underlying Senescence in Maize},

  author       = {Sekhon, Rajandeep S. and Saski, Christopher and Kumar, Rohit and Flinn, Barry S. and Luo, Feng and Beissinger, Timothy M. and Ackerman, Arlyn J. and Breitzman, Matthew W. and Bridges, William C. and de Leon, Natalia and Kaeppler, Shawn M.},

  abstractNote = {Premature senescence in annual crops reduces yield, while delayed senescence, termed stay-green, imposes positive and negative impacts on yield and nutrition quality. Despite its importance, scant information is available on the genetic architecture of senescence in maize (Zea mays) and other cereals. We combined a systematic characterization of natural diversity for senescence in maize and coexpression networks derived from transcriptome analysis of normally senescing and stay-green lines. Sixty-four candidate genes were identified by genome-wide association study (GWAS), and 14 of these genes are supported by additional evidence for involvement in senescence-related processes including proteolysis, sugar transport and signaling, and sink activity. Eight of the GWAS candidates, independently supported by a coexpression network underlying stay-green, include a trehalose-6-phosphate synthase, a NAC transcription factor, and two xylan biosynthetic enzymes. Source–sink communication and the activity of cell walls as a secondary sink emerge as key determinants of stay-green. Mutant analysis supports the role of a candidate encoding Cys protease in stay-green in Arabidopsis (Arabidopsis thaliana), and analysis of natural alleles suggests a similar role in maize. This study provides a foundation for enhanced understanding and manipulation of senescence for increasing carbon yield, nutritional quality, and stress tolerance of maize and other cereals.},

  doi          = {10.1105/tpc.18.00930},

  journal      = {The Plant Cell},

  number       = 9,

  volume       = 31,

  place        = {United States},

  year         = {Tue Jun 25 00:00:00 EDT 2019},

  month        = {Tue Jun 25 00:00:00 EDT 2019}

}

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