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Title: Genome‐wide association and genomic prediction for biomass yield in a genetically diverse Miscanthus sinensis germplasm panel phenotyped at five locations in Asia and North America

Authors:
ORCiD logo [1];  [2];  [2];  [3];  [4];  [5];  [6];  [7];  [8]; ORCiD logo [1];  [9]; ORCiD logo [2];  [7];  [7];  [10]; ORCiD logo [1];  [1]
  1. Department of Crop Sciences University of Illinois, Urbana‐Champaign Urbana Illinois
  2. Field Science Center for Northern Biosphere Hokkaido University Sapporo Japan
  3. Department of Soil and Crop Sciences Colorado State University Fort Collins Colorado
  4. Department of Applied Bioscience Konkuk University Seoul South Korea
  5. Department of Biochemistry University of Nebraska‐Lincoln Lincoln Nebraska
  6. Bio Architecture Lab Berkeley California
  7. Department of Applied Plant Sciences Kangwon National University Chuncheon, Gangwon South Korea
  8. Department of Agronomy Zhejiang University Hangzhou China
  9. HuaZhi Biotechnology Institute Changsha China
  10. College of Plant Science and Technology Huazhong Agricultural University Wuhan China
Publication Date:
Research Org.:
Univ. of Illinois, Urbana-Champaign, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1512519
Alternate Identifier(s):
OSTI ID: 1510514; OSTI ID: 1512520
Grant/Contract Number:  
[SC0006634 DE-SC0018420; SC0018420]
Resource Type:
Published Article
Journal Name:
Global Change Biology. Bioenergy
Additional Journal Information:
[Journal Name: Global Change Biology. Bioenergy]; Journal ID: ISSN 1757-1693
Publisher:
Wiley-Blackwell
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Miscanthus sinensis; Miscanthus ×giganteus; genomic selection; genome‐wide association studies; RAD‐seq; biomass yield; field trials

Citation Formats

Clark, Lindsay V., Dwiyanti, Maria S., Anzoua, Kossonou G., Brummer, Joe E., Ghimire, Bimal Kumar, Głowacka, Katarzyna, Hall, Megan, Heo, Kweon, Jin, Xiaoli, Lipka, Alexander E., Peng, Junhua, Yamada, Toshihiko, Yoo, Ji Hye, Yu, Chang Yeon, Zhao, Hua, Long, Stephen P., and Sacks, Erik J. Genome‐wide association and genomic prediction for biomass yield in a genetically diverse Miscanthus sinensis germplasm panel phenotyped at five locations in Asia and North America. United Kingdom: N. p., 2019. Web. doi:10.1111/gcbb.12620.
Clark, Lindsay V., Dwiyanti, Maria S., Anzoua, Kossonou G., Brummer, Joe E., Ghimire, Bimal Kumar, Głowacka, Katarzyna, Hall, Megan, Heo, Kweon, Jin, Xiaoli, Lipka, Alexander E., Peng, Junhua, Yamada, Toshihiko, Yoo, Ji Hye, Yu, Chang Yeon, Zhao, Hua, Long, Stephen P., & Sacks, Erik J. Genome‐wide association and genomic prediction for biomass yield in a genetically diverse Miscanthus sinensis germplasm panel phenotyped at five locations in Asia and North America. United Kingdom. doi:10.1111/gcbb.12620.
Clark, Lindsay V., Dwiyanti, Maria S., Anzoua, Kossonou G., Brummer, Joe E., Ghimire, Bimal Kumar, Głowacka, Katarzyna, Hall, Megan, Heo, Kweon, Jin, Xiaoli, Lipka, Alexander E., Peng, Junhua, Yamada, Toshihiko, Yoo, Ji Hye, Yu, Chang Yeon, Zhao, Hua, Long, Stephen P., and Sacks, Erik J. Mon . "Genome‐wide association and genomic prediction for biomass yield in a genetically diverse Miscanthus sinensis germplasm panel phenotyped at five locations in Asia and North America". United Kingdom. doi:10.1111/gcbb.12620.
@article{osti_1512519,
title = {Genome‐wide association and genomic prediction for biomass yield in a genetically diverse Miscanthus sinensis germplasm panel phenotyped at five locations in Asia and North America},
author = {Clark, Lindsay V. and Dwiyanti, Maria S. and Anzoua, Kossonou G. and Brummer, Joe E. and Ghimire, Bimal Kumar and Głowacka, Katarzyna and Hall, Megan and Heo, Kweon and Jin, Xiaoli and Lipka, Alexander E. and Peng, Junhua and Yamada, Toshihiko and Yoo, Ji Hye and Yu, Chang Yeon and Zhao, Hua and Long, Stephen P. and Sacks, Erik J.},
abstractNote = {},
doi = {10.1111/gcbb.12620},
journal = {Global Change Biology. Bioenergy},
number = ,
volume = ,
place = {United Kingdom},
year = {2019},
month = {5}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1111/gcbb.12620

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Works referenced in this record:

Genomic prediction in CIMMYT maize and wheat breeding programs
journal, April 2013


Mixed linear model approach adapted for genome-wide association studies
journal, March 2010

  • Zhang, Zhiwu; Ersoz, Elhan; Lai, Chao-Qiang
  • Nature Genetics, Vol. 42, Issue 4
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G ST and its relatives do not measure differentiation
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Efficient Methods to Compute Genomic Predictions
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Marker-Trait Association for Biomass Yield of Potential Bio-fuel Feedstock Miscanthus sinensis from Southwest China
journal, June 2016


Winter hardiness of Miscanthus (I): Overwintering ability and yield of new Miscanthus × giganteus genotypes in Illinois and Arkansas
journal, January 2019

  • Dong, Hongxu; Green, Steven V.; Nishiwaki, Aya
  • GCB Bioenergy, Vol. 11, Issue 5
  • DOI: 10.1111/gcbb.12588

Methyl-CpG-binding domain proteins in plants: interpreters of DNA methylation
journal, February 2007


Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol
journal, January 2013


Genomic Selection for Predicting Head Blight Resistance in a Wheat Breeding Program
journal, January 2015


A footprint of past climate change on the diversity and population structure of Miscanthus sinensis
journal, June 2014

  • Clark, Lindsay V.; Brummer, Joe E.; Głowacka, Katarzyna
  • Annals of Botany, Vol. 114, Issue 1
  • DOI: 10.1093/aob/mcu084

The impact of population structure on genomic prediction in stratified populations
journal, January 2014

  • Guo, Zhigang; Tucker, Dominic M.; Basten, Christopher J.
  • Theoretical and Applied Genetics, Vol. 127, Issue 3
  • DOI: 10.1007/s00122-013-2255-x

The WUS homeobox-containing (WOX) protein family
journal, January 2009


Enhancing genomic prediction with genome-wide association studies in multiparental maize populations
journal, February 2017


GAPIT: genome association and prediction integrated tool
journal, July 2012


Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP
journal, January 2011


AtMBD9: a protein with a methyl-CpG-binding domain regulates flowering time and shoot branching in Arabidopsis
journal, April 2006


Genetic mapping of biomass yield in three interconnected Miscanthus populations
journal, August 2017

  • Dong, Hongxu; Liu, Siyao; Clark, Lindsay V.
  • GCB Bioenergy, Vol. 10, Issue 3
  • DOI: 10.1111/gcbb.12472

Population structure correction for genomic selection through eigenvector covariates
journal, December 2017

  • Azevedo, Camila Ferreira; Resende, Marcos Deon Vilela de; Silva, Fabyano Fonseca e.
  • Crop Breeding and Applied Biotechnology, Vol. 17, Issue 4
  • DOI: 10.1590/1984-70332017v17n4a53

Miscanthus for Renewable Energy Generation: European Union Experience and Projections for Illinois
journal, October 2004


Fitting Linear Mixed-Effects Models Using lme4
journal, January 2015

  • Bates, Douglas; Mächler, Martin; Bolker, Ben
  • Journal of Statistical Software, Vol. 67, Issue 1
  • DOI: 10.18637/jss.v067.i01

Accelerating the Switchgrass (Panicum virgatum L.) Breeding Cycle Using Genomic Selection Approaches
journal, November 2014


A Review on Miscanthus Biomass Production and Composition for Bioenergy Use: Genotypic and Environmental Variability and Implications for Breeding
journal, September 2014


Genomic Selection in Wheat Breeding using Genotyping-by-Sequencing
journal, January 2012


Characterizing a Germplasm Collection for Yield, Yield Components, and Genotype × Environment Interactions
journal, January 2015


Genetic relationships between spring emergence, canopy phenology, and biomass yield increase the accuracy of genomic prediction in Miscanthus
journal, October 2017

  • Davey, Christopher L.; Robson, Paul; Hawkins, Sarah
  • Journal of Experimental Botany, Vol. 68, Issue 18
  • DOI: 10.1093/jxb/erx339

Auxin response factors
journal, October 2007


Genomic prediction accuracy for switchgrass traits related to bioenergy within differentiated populations
journal, July 2018

  • Fiedler, Jason D.; Lanzatella, Christina; Edmé, Serge J.
  • BMC Plant Biology, Vol. 18, Issue 1
  • DOI: 10.1186/s12870-018-1360-z

Genetic variation in Miscanthus × giganteus and the importance of estimating genetic distance thresholds for differentiating clones
journal, June 2014

  • Głowacka, Katarzyna; Clark, Lindsay V.; Adhikari, Shivani
  • GCB Bioenergy, Vol. 7, Issue 2
  • DOI: 10.1111/gcbb.12166

Crop genome-wide association study: a harvest of biological relevance
journal, December 2018

  • Liu, Hai-Jun; Yan, Jianbing
  • The Plant Journal, Vol. 97, Issue 1
  • DOI: 10.1111/tpj.14139

Mapping the genome of Miscanthus sinensis for QTL associated with biomass productivity
journal, June 2014

  • Gifford, Justin M.; Chae, Won Byoung; Swaminathan, Kankshita
  • GCB Bioenergy, Vol. 7, Issue 4
  • DOI: 10.1111/gcbb.12201

Bottlenecks for genome-edited crops on the road from lab to farm
journal, October 2018


Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar
journal, October 2018

  • Clifton-Brown, John; Harfouche, Antoine; Casler, Michael D.
  • GCB Bioenergy, Vol. 11, Issue 1
  • DOI: 10.1111/gcbb.12566

Performance of 15 Genotypes at Five Sites in Europe
journal, January 2001


Association Analysis of Historical Bread Wheat Germplasm Using Additive Genetic Covariance of Relatives and Population Structure
journal, October 2007


Fast gapped-read alignment with Bowtie 2
journal, March 2012

  • Langmead, Ben; Salzberg, Steven L.
  • Nature Methods, Vol. 9, Issue 4
  • DOI: 10.1038/nmeth.1923

Biomass yield in a genetically diverse Miscanthus sinensis germplasm panel evaluated at five locations revealed individuals with exceptional potential
journal, March 2019

  • Clark, Lindsay V.; Dwiyanti, Maria S.; Anzoua, Kossonou G.
  • GCB Bioenergy, Vol. 11, Issue 10
  • DOI: 10.1111/gcbb.12606

Genomic index selection provides a pragmatic framework for setting and refining multi-objective breeding targets in Miscanthus
journal, October 2018

  • Slavov, Gancho T.; Davey, Christopher L.; Bosch, Maurice
  • Annals of Botany, Vol. 124, Issue 4
  • DOI: 10.1093/aob/mcy187

Genetic structure of Miscanthus sinensis and Miscanthus sacchariflorus in Japan indicates a gradient of bidirectional but asymmetric introgression
journal, January 2015

  • Clark, Lindsay V.; Stewart, J. Ryan; Nishiwaki, Aya
  • Journal of Experimental Botany, Vol. 66, Issue 14
  • DOI: 10.1093/jxb/eru511

An Analysis of Transformations
journal, July 1964


Accuracy of Genomic Selection Methods in a Standard Data Set of Loblolly Pine ( Pinus taeda L.)
journal, January 2012


Genomic and metabolic prediction of complex heterotic traits in hybrid maize
journal, January 2012

  • Riedelsheimer, Christian; Czedik-Eysenberg, Angelika; Grieder, Christoph
  • Nature Genetics, Vol. 44, Issue 2
  • DOI: 10.1038/ng.1033

Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement
journal, February 2016


A unified mixed-model method for association mapping that accounts for multiple levels of relatedness
journal, December 2005

  • Yu, Jianming; Pressoir, Gael; Briggs, William H.
  • Nature Genetics, Vol. 38, Issue 2
  • DOI: 10.1038/ng1702

A review of the genetic study of the energy crop Miscanthus
journal, July 2011


Genetics of Tillering in Rice and Barley
journal, January 2014


A Foundation for Provitamin A Biofortification of Maize: Genome-Wide Association and Genomic Prediction Models of Carotenoid Levels
journal, September 2014


Genetic Diversity and Population Structure of Miscanthus sinensis Germplasm in China
journal, October 2013


Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia
journal, July 2016

  • Clark, Lindsay V.; Dzyubenko, Elena; Dzyubenko, Nikolay
  • Annals of Botany, Vol. 118, Issue 5
  • DOI: 10.1093/aob/mcw137

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
journal, January 1995


Discriminant analysis of principal components: a new method for the analysis of genetically structured populations
journal, January 2010

  • Jombart, Thibaut; Devillard, Sébastien; Balloux, François
  • BMC Genetics, Vol. 11, Issue 1
  • DOI: 10.1186/1471-2156-11-94

    Works referencing / citing this record:

    The impact of population structure on genomic prediction in stratified populations
    journal, January 2014

    • Guo, Zhigang; Tucker, Dominic M.; Basten, Christopher J.
    • Theoretical and Applied Genetics, Vol. 127, Issue 3
    • DOI: 10.1007/s00122-013-2255-x

    A Review on Miscanthus Biomass Production and Composition for Bioenergy Use: Genotypic and Environmental Variability and Implications for Breeding
    journal, September 2014


    A review of the genetic study of the energy crop Miscanthus
    journal, July 2011


    Auxin response factors
    journal, October 2007


    Methyl-CpG-binding domain proteins in plants: interpreters of DNA methylation
    journal, February 2007


    Genomic prediction in CIMMYT maize and wheat breeding programs
    journal, April 2013


    Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement
    journal, February 2016


    Enhancing genomic prediction with genome-wide association studies in multiparental maize populations
    journal, February 2017


    Genomic and metabolic prediction of complex heterotic traits in hybrid maize
    journal, January 2012

    • Riedelsheimer, Christian; Czedik-Eysenberg, Angelika; Grieder, Christoph
    • Nature Genetics, Vol. 44, Issue 2
    • DOI: 10.1038/ng.1033

    Mixed linear model approach adapted for genome-wide association studies
    journal, March 2010

    • Zhang, Zhiwu; Ersoz, Elhan; Lai, Chao-Qiang
    • Nature Genetics, Vol. 42, Issue 4
    • DOI: 10.1038/ng.546

    A unified mixed-model method for association mapping that accounts for multiple levels of relatedness
    journal, December 2005

    • Yu, Jianming; Pressoir, Gael; Briggs, William H.
    • Nature Genetics, Vol. 38, Issue 2
    • DOI: 10.1038/ng1702

    Fast gapped-read alignment with Bowtie 2
    journal, March 2012

    • Langmead, Ben; Salzberg, Steven L.
    • Nature Methods, Vol. 9, Issue 4
    • DOI: 10.1038/nmeth.1923

    A footprint of past climate change on the diversity and population structure of Miscanthus sinensis
    journal, June 2014

    • Clark, Lindsay V.; Brummer, Joe E.; Głowacka, Katarzyna
    • Annals of Botany, Vol. 114, Issue 1
    • DOI: 10.1093/aob/mcu084

    Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia
    journal, July 2016

    • Clark, Lindsay V.; Dzyubenko, Elena; Dzyubenko, Nikolay
    • Annals of Botany, Vol. 118, Issue 5
    • DOI: 10.1093/aob/mcw137

    GAPIT: genome association and prediction integrated tool
    journal, July 2012


    Genetic structure of Miscanthus sinensis and Miscanthus sacchariflorus in Japan indicates a gradient of bidirectional but asymmetric introgression
    journal, January 2015

    • Clark, Lindsay V.; Stewart, J. Ryan; Nishiwaki, Aya
    • Journal of Experimental Botany, Vol. 66, Issue 14
    • DOI: 10.1093/jxb/eru511

    Genetic relationships between spring emergence, canopy phenology, and biomass yield increase the accuracy of genomic prediction in Miscanthus
    journal, October 2017

    • Davey, Christopher L.; Robson, Paul; Hawkins, Sarah
    • Journal of Experimental Botany, Vol. 68, Issue 18
    • DOI: 10.1093/jxb/erx339

    Genetic variation in Miscanthus × giganteus and the importance of estimating genetic distance thresholds for differentiating clones
    journal, June 2014

    • Głowacka, Katarzyna; Clark, Lindsay V.; Adhikari, Shivani
    • GCB Bioenergy, Vol. 7, Issue 2
    • DOI: 10.1111/gcbb.12166

    Mapping the genome of Miscanthus sinensis for QTL associated with biomass productivity
    journal, June 2014

    • Gifford, Justin M.; Chae, Won Byoung; Swaminathan, Kankshita
    • GCB Bioenergy, Vol. 7, Issue 4
    • DOI: 10.1111/gcbb.12201

    Genetic mapping of biomass yield in three interconnected Miscanthus populations
    journal, August 2017

    • Dong, Hongxu; Liu, Siyao; Clark, Lindsay V.
    • GCB Bioenergy, Vol. 10, Issue 3
    • DOI: 10.1111/gcbb.12472

    Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar
    journal, October 2018

    • Clifton-Brown, John; Harfouche, Antoine; Casler, Michael D.
    • GCB Bioenergy, Vol. 11, Issue 1
    • DOI: 10.1111/gcbb.12566

    Winter hardiness of Miscanthus (I): Overwintering ability and yield of new Miscanthus × giganteus genotypes in Illinois and Arkansas
    journal, January 2019

    • Dong, Hongxu; Green, Steven V.; Nishiwaki, Aya
    • GCB Bioenergy, Vol. 11, Issue 5
    • DOI: 10.1111/gcbb.12588

    Biomass yield in a genetically diverse Miscanthus sinensis germplasm panel evaluated at five locations revealed individuals with exceptional potential
    journal, March 2019

    • Clark, Lindsay V.; Dwiyanti, Maria S.; Anzoua, Kossonou G.
    • GCB Bioenergy, Vol. 11, Issue 10
    • DOI: 10.1111/gcbb.12606

    An Analysis of Transformations
    journal, July 1964


    Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
    journal, January 1995


    Crop genome-wide association study: a harvest of biological relevance
    journal, December 2018

    • Liu, Hai-Jun; Yan, Jianbing
    • The Plant Journal, Vol. 97, Issue 1
    • DOI: 10.1111/tpj.14139

    Discriminant analysis of principal components: a new method for the analysis of genetically structured populations
    journal, January 2010

    • Jombart, Thibaut; Devillard, Sébastien; Balloux, François
    • BMC Genetics, Vol. 11, Issue 1
    • DOI: 10.1186/1471-2156-11-94

    The WUS homeobox-containing (WOX) protein family
    journal, January 2009


    Genomic prediction accuracy for switchgrass traits related to bioenergy within differentiated populations
    journal, July 2018

    • Fiedler, Jason D.; Lanzatella, Christina; Edmé, Serge J.
    • BMC Plant Biology, Vol. 18, Issue 1
    • DOI: 10.1186/s12870-018-1360-z

    Bottlenecks for genome-edited crops on the road from lab to farm
    journal, October 2018


    Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol
    journal, January 2013


    Genetic Diversity and Population Structure of Miscanthus sinensis Germplasm in China
    journal, October 2013


    Accelerating the Switchgrass (Panicum virgatum L.) Breeding Cycle Using Genomic Selection Approaches
    journal, November 2014


    Association Analysis of Historical Bread Wheat Germplasm Using Additive Genetic Covariance of Relatives and Population Structure
    journal, October 2007


    Accuracy of Genomic Selection Methods in a Standard Data Set of Loblolly Pine ( Pinus taeda L.)
    journal, January 2012


    A Foundation for Provitamin A Biofortification of Maize: Genome-Wide Association and Genomic Prediction Models of Carotenoid Levels
    journal, September 2014


    Population structure correction for genomic selection through eigenvector covariates
    journal, December 2017

    • Azevedo, Camila Ferreira; Resende, Marcos Deon Vilela de; Silva, Fabyano Fonseca e.
    • Crop Breeding and Applied Biotechnology, Vol. 17, Issue 4
    • DOI: 10.1590/1984-70332017v17n4a53

    Fitting Linear Mixed-Effects Models Using lme4
    journal, January 2015

    • Bates, Douglas; Mächler, Martin; Bolker, Ben
    • Journal of Statistical Software, Vol. 67, Issue 1
    • DOI: 10.18637/jss.v067.i01

    Performance of 15 Genotypes at Five Sites in Europe
    journal, January 2001


    Characterizing a Germplasm Collection for Yield, Yield Components, and Genotype × Environment Interactions
    journal, January 2015


    Efficient Methods to Compute Genomic Predictions
    journal, November 2008


    Marker-Trait Association for Biomass Yield of Potential Bio-fuel Feedstock Miscanthus sinensis from Southwest China
    journal, June 2016


    Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP
    journal, January 2011


    Genomic Selection in Wheat Breeding using Genotyping-by-Sequencing
    journal, January 2012


    Genetics of Tillering in Rice and Barley
    journal, January 2014


    Genomic Selection for Predicting Head Blight Resistance in a Wheat Breeding Program
    journal, January 2015