Winter hardiness of Miscanthus (III): Genome-wide association and genomic prediction for overwintering ability in Miscanthus sinensis

Hongxu Dong, Lindsay V. Clark, Alexander E. Lipka, Joe E. Brummer, Katarzyna Głowacka, Megan C. Hall, Kweon Heo, Xiaoli Jin, Junhua Peng, Toshihiko Yamada, Bimal Kumar Ghimire, Ji Hye Yoo, Chang Yeon Yu, Hua Zhao, Stephen P. Long, Erik J. Sacks

Research output: Contribution to journalArticle

Abstract

Overwintering ability is an important selection criterion for Miscanthus breeding in temperate regions. Insufficient overwintering ability of the currently leading Miscanthus biomass cultivar, M. ×giganteus (M×g) ‘1993–1780', in regions where average annual minimum temperatures are −26.1°C (USDA hardiness zone 5) or lower poses a pressing need to develop new cultivars with superior cold tolerance. To facilitate breeding of Miscanthus, this study characterized phenotypic and genetic variation of overwintering ability in an M. sinensis germplasm panel consisting of 564 accessions, evaluated in field trials at three locations in North America and two in Asia. Genome-wide association (GWA) and genomic prediction analyses were performed. The Korea/N China M. sinensis genetic group is a valuable gene pool for cold tolerance. The Yangtze-Qinling, Southern Japan, and Northern Japan genetic groups were also potential sources of cold tolerance. A total of 73 marker–trait associations were detected for overwintering ability. Estimated breeding value for overwintering ability based on these 73 markers could explain 55% of the variation for first winter overwintering ability among M. sinensis. Average genomic prediction ability for overwintering ability across 50 fivefold cross-validations was high (~0.73) after accounting for population structure. Common genomic regions for overwintering ability were detected by GWA analyses and a previous parallel QTL mapping study using three interconnected biparental F1 populations. One QTL on Miscanthus LG 8 encompassed five GWA hits and a known cold-responsive gene, COR47. The other overwintering ability QTL on Miscanthus LG 11 contained two GWA hits and three known cold stress-related genes, carboxylesterase 13 (CEX13), WRKY2 transcription factor, and cold shock domain (CSDP1). Miscanthus accessions collected from high latitude locations with cold winters had higher rates of overwintering, and more alleles for overwintering, than accessions collected from southern locations with mild winters.

Original languageEnglish (US)
Pages (from-to)930-955
Number of pages26
JournalGCB Bioenergy
Volume11
Issue number8
DOIs
StatePublished - Aug 2019

Fingerprint

Miscanthus sinensis
winter hardiness
Miscanthus
overwintering
genomics
genome
Genes
prediction
winter
cold tolerance
quantitative trait loci
breeding
cold stress
Transcription factors
gene
cultivar
Japan
Miscanthus giganteus
Biomass
carboxylesterase

Keywords

  • Miscanthus sinensis
  • Overwintering ability
  • breeding
  • genome-wide association analysis
  • genomic prediction
  • germplasm

ASJC Scopus subject areas

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

Cite this

Winter hardiness of Miscanthus (III) : Genome-wide association and genomic prediction for overwintering ability in Miscanthus sinensis. / Dong, Hongxu; Clark, Lindsay V.; Lipka, Alexander E.; Brummer, Joe E.; Głowacka, Katarzyna; Hall, Megan C.; Heo, Kweon; Jin, Xiaoli; Peng, Junhua; Yamada, Toshihiko; Ghimire, Bimal Kumar; Yoo, Ji Hye; Yu, Chang Yeon; Zhao, Hua; Long, Stephen P.; Sacks, Erik J.

In: GCB Bioenergy, Vol. 11, No. 8, 08.2019, p. 930-955.

Research output: Contribution to journalArticle

Dong, H, Clark, LV, Lipka, AE, Brummer, JE, Głowacka, K, Hall, MC, Heo, K, Jin, X, Peng, J, Yamada, T, Ghimire, BK, Yoo, JH, Yu, CY, Zhao, H, Long, SP & Sacks, EJ 2019, 'Winter hardiness of Miscanthus (III): Genome-wide association and genomic prediction for overwintering ability in Miscanthus sinensis', GCB Bioenergy, vol. 11, no. 8, pp. 930-955. https://doi.org/10.1111/gcbb.12615
Dong, Hongxu ; Clark, Lindsay V. ; Lipka, Alexander E. ; Brummer, Joe E. ; Głowacka, Katarzyna ; Hall, Megan C. ; Heo, Kweon ; Jin, Xiaoli ; Peng, Junhua ; Yamada, Toshihiko ; Ghimire, Bimal Kumar ; Yoo, Ji Hye ; Yu, Chang Yeon ; Zhao, Hua ; Long, Stephen P. ; Sacks, Erik J. / Winter hardiness of Miscanthus (III) : Genome-wide association and genomic prediction for overwintering ability in Miscanthus sinensis. In: GCB Bioenergy. 2019 ; Vol. 11, No. 8. pp. 930-955.
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AU - Peng, Junhua

AU - Yamada, Toshihiko

AU - Ghimire, Bimal Kumar

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AU - Sacks, Erik J.

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