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

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Winter hardiness of Miscanthus (III): Genome-wide association and genomic prediction for overwintering ability in Miscanthus sinensis. / Dong, H.; Clark, L.V.; Lipka, A.E. et al.
In: GCB Bioenergy, Vol. 11, No. 8, 01.08.2019, p. 930-955.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Harvard

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

APA

Dong, H., Clark, L. V., Lipka, A. E., Brummer, J. E., Głowacka, K., Hall, M. C., Heo, K., Jin, X., Peng, J., Yamada, T., Ghimire, B. K., Yoo, J. H., Yu, C. Y., Zhao, H., Long, S. P., & Sacks, E. J. (2019). Winter hardiness of Miscanthus (III): Genome-wide association and genomic prediction for overwintering ability in Miscanthus sinensis. GCB Bioenergy, 11(8), 930-955. https://doi.org/10.1111/gcbb.12615

Vancouver

Dong H, Clark LV, Lipka AE, Brummer JE, Głowacka K, Hall MC et al. Winter hardiness of Miscanthus (III): Genome-wide association and genomic prediction for overwintering ability in Miscanthus sinensis. GCB Bioenergy. 2019 Aug 1;11(8):930-955. Epub 2019 Apr 14. doi: 10.1111/gcbb.12615

Author

Dong, H. ; Clark, L.V. ; Lipka, A.E. et al. / 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.

Bibtex

@article{0e2daab5d24347d082af6caf4ad45dea,
title = "Winter hardiness of Miscanthus (III): Genome-wide association and genomic prediction for overwintering ability in Miscanthus sinensis",
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) {\textquoteleft}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.",
keywords = "breeding, genome-wide association analysis, genomic prediction, germplasm, Miscanthus sinensis, Overwintering ability, Location, Plants (botany), Transcription, Genome-wide association, Genomic predictions, Germplasms, Forecasting, Miscanthus",
author = "H. Dong and L.V. Clark and A.E. Lipka and J.E. Brummer and K. G{\l}owacka and M.C. Hall and K. Heo and X. Jin and J. Peng and T. Yamada and B.K. Ghimire and J.H. Yoo and C.Y. Yu and H. Zhao and S.P. Long and E.J. Sacks",
year = "2019",
month = aug,
day = "1",
doi = "10.1111/gcbb.12615",
language = "English",
volume = "11",
pages = "930--955",
journal = "GCB Bioenergy",
issn = "1757-1693",
publisher = "Blackwell Publishing Ltd",
number = "8",

}

RIS

TY - JOUR

T1 - Winter hardiness of Miscanthus (III)

T2 - Genome-wide association and genomic prediction for overwintering ability in Miscanthus sinensis

AU - Dong, H.

AU - Clark, L.V.

AU - Lipka, A.E.

AU - Brummer, J.E.

AU - Głowacka, K.

AU - Hall, M.C.

AU - Heo, K.

AU - Jin, X.

AU - Peng, J.

AU - Yamada, T.

AU - Ghimire, B.K.

AU - Yoo, J.H.

AU - Yu, C.Y.

AU - Zhao, H.

AU - Long, S.P.

AU - Sacks, E.J.

PY - 2019/8/1

Y1 - 2019/8/1

N2 - 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.

AB - 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.

KW - breeding

KW - genome-wide association analysis

KW - genomic prediction

KW - germplasm

KW - Miscanthus sinensis

KW - Overwintering ability

KW - Location

KW - Plants (botany)

KW - Transcription

KW - Genome-wide association

KW - Genomic predictions

KW - Germplasms

KW - Forecasting

KW - Miscanthus

U2 - 10.1111/gcbb.12615

DO - 10.1111/gcbb.12615

M3 - Journal article

VL - 11

SP - 930

EP - 955

JO - GCB Bioenergy

JF - GCB Bioenergy

SN - 1757-1693

IS - 8

ER -