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, L.V. and Dwiyanti, M.S. and Anzoua, K.G. and Brummer, J.E. and Ghimire, B.K. and Głowacka, K. and Hall, M. and Heo, K. and Jin, X. and Lipka, A.E. and Peng, J. and Yamada, T. and Yoo, J.H. and Yu, C.Y. and Zhao, H. and Long, S.P. and Sacks, E.J. (2019) 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. GCB Bioenergy, 11 (8). pp. 988-1007. ISSN 1757-1693

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. © 2019 The Authors. GCB Bioenergy Published by John Wiley & Sons Ltd