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 E. Lipka,
Junhua Peng,
Toshihiko Yamada,
Ji Hye Yoo,
Chang Yeon Yu,
Hua Zhao,
Stephen P. Long,
Erik J. Sacks
Affiliations
Lindsay V. Clark
Department of Crop Sciences University of Illinois, Urbana‐Champaign Urbana Illinois
Maria S. Dwiyanti
Field Science Center for Northern Biosphere Hokkaido University Sapporo Japan
Kossonou G. Anzoua
Field Science Center for Northern Biosphere Hokkaido University Sapporo Japan
Joe E. Brummer
Department of Soil and Crop Sciences Colorado State University Fort Collins Colorado
Bimal Kumar Ghimire
Department of Applied Bioscience Konkuk University Seoul South Korea
Katarzyna Głowacka
Department of Biochemistry University of Nebraska‐Lincoln Lincoln Nebraska
Megan Hall
Bio Architecture Lab Berkeley California
Kweon Heo
Department of Applied Plant Sciences Kangwon National University Chuncheon, Gangwon South Korea
Xiaoli Jin
Department of Agronomy Zhejiang University Hangzhou China
Alexander E. Lipka
Department of Crop Sciences University of Illinois, Urbana‐Champaign Urbana Illinois
Junhua Peng
HuaZhi Biotechnology Institute Changsha China
Toshihiko Yamada
Field Science Center for Northern Biosphere Hokkaido University Sapporo Japan
Ji Hye Yoo
Department of Applied Plant Sciences Kangwon National University Chuncheon, Gangwon South Korea
Chang Yeon Yu
Department of Applied Plant Sciences Kangwon National University Chuncheon, Gangwon South Korea
Hua Zhao
College of Plant Science and Technology Huazhong Agricultural University Wuhan China
Stephen P. Long
Department of Crop Sciences University of Illinois, Urbana‐Champaign Urbana Illinois
Erik J. Sacks
Department of Crop Sciences University of Illinois, Urbana‐Champaign Urbana Illinois
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.