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

Lindsay V. Clark, Maria S. Dwiyanti, Kossonou G. Anzoua, Joe E. Brummer, Bimal Kumar Ghimire, Katarzyna Głowacka, Megan Hall, Kweon Heo, Xiaoli Jin, Alexander Edward Lipka, Junhua Peng, Toshihiko Yamada, Ji Hye Yoo, Chang Yeon Yu, Hua Zhao, Stephen P Long, Erik J Sacks

Research output: Contribution to journalArticle

Abstract

To improve the efficiency of breeding of Miscanthus for biomass yield, there is a need to develop genomics-assisted selection for this long-lived perennial crop by relating genotype to phenotype and breeding value across a broad range of environments. We present the first genome-wide association (GWA) and genomic prediction study of Miscanthus that utilizes multilocation phenotypic data. A panel of 568 Miscanthus sinensis accessions was genotyped with 46,177 single nucleotide polymorphisms (SNPs) and evaluated at one subtropical and five temperate locations over 3 years for biomass yield and 14 yield-component traits. GWA and genomic prediction were performed separately for different years of data in order to assess reproducibility. The analyses were also performed for individual field trial locations, as well as combined phenotypic data across groups of locations. GWA analyses identified 27 significant SNPs for yield, and a total of 504 associations across 298 unique SNPs across all traits, sites, and years. For yield, the greatest number of significant SNPs was identified by combining phenotypic data across all six locations. For some of the other yield-component traits, greater numbers of significant SNPs were obtained from single site data, although the number of significant SNPs varied greatly from site to site. Candidate genes were identified. Accounting for population structure, genomic prediction accuracies for biomass yield ranged from 0.31 to 0.35 across five northern sites and from 0.13 to 0.18 for the subtropical location, depending on the estimation method. Genomic prediction accuracies of all traits were similar for single-location and multilocation data, suggesting that genomic selection will be useful for breeding broadly adapted M. sinensis as well as M. sinensis optimized for specific climates. All of our data, including DNA sequences flanking each SNP, are publicly available. By facilitating genomic selection in M. sinensis and Miscanthus × giganteus, our results will accelerate the breeding of these species for biomass in diverse environments.

Original languageEnglish (US)
JournalGCB Bioenergy
DOIs
StatePublished - Jan 1 2019

Fingerprint

Miscanthus sinensis
germplasm
Nucleotides
Polymorphism
single nucleotide polymorphism
genomics
polymorphism
Biomass
genome
Genes
prediction
biomass
breeding
Miscanthus
marker-assisted selection
yield components
DNA sequences
estimation method
Asia
North America

Keywords

  • biomass yield
  • field trials
  • genome-wide association studies
  • genomic selection
  • Miscanthus sinensis
  • Miscanthus × giganteus
  • RAD-seq

ASJC Scopus subject areas

  • Forestry
  • Renewable Energy, Sustainability and the Environment
  • Agronomy and Crop Science
  • Waste Management and Disposal

Cite this

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. / 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 Edward; Peng, Junhua; Yamada, Toshihiko; Yoo, Ji Hye; Yu, Chang Yeon; Zhao, Hua; Long, Stephen P; Sacks, Erik J.

In: GCB Bioenergy, 01.01.2019.

Research output: Contribution to journalArticle

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 Edward ; 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. In: GCB Bioenergy. 2019.
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AU - Anzoua, Kossonou G.

AU - Brummer, Joe E.

AU - Ghimire, Bimal Kumar

AU - Głowacka, Katarzyna

AU - Hall, Megan

AU - Heo, Kweon

AU - Jin, Xiaoli

AU - Lipka, Alexander Edward

AU - Peng, Junhua

AU - Yamada, Toshihiko

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AU - Zhao, Hua

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