Genome-wide association studies and prediction of 17 traits related to phenology, biomass and cell wall composition in the energy grass Miscanthus sinensis

• Published in: The New phytologist Vol. 201; no. 4; pp. 1227 - 1239
• Main Authors: Slavov, Gancho T., Nipper, Rick, Robson, Paul, Farrar, Kerrie, Allison, Gordon G., Bosch, Maurice, Clifton‐Brown, John C., Donnison, Iain S., Jensen, Elaine
• Format: Journal Article
• Language: English
• Published: England New Phytologist Trust 01.03.2014; Wiley Subscription Services, Inc; BlackWell Publishing Ltd
• Subjects: Biomass; Breeding; Cell Wall - metabolism; Cell walls; Deoxyribonucleic acid; DNA; DNA sequencing; DNA, Plant - genetics; Energy; Gene mapping; Genetic Markers; Genome, Plant - genetics; Genome-wide association studies; Genome-Wide Association Study; Genomes; genome‐wide association studies (GWAS); genomic selection; Genomics; Genotype; Genotypes; Geography; Grasses; Human genetics; Linear regression; Markers; Metagenomics; Miscanthus; Miscanthus sinensis; molecular markers; Nucleotides; Phenotype; Phenotypes; Phenotypic traits; Plant breeding; Poaceae - cytology; Poaceae - genetics; Polymorphism, Single Nucleotide - genetics; Population characteristics; Population Dynamics; Population structure; Predictions; Principal Component Analysis; Quantitative Trait, Heritable; RAD‐Seq; Restriction Mapping; Sequence Analysis, DNA; single‐nucleotide variants; Sorghum; Subpopulations; genomic selection; genome-wide association studies (GWAS); RAD-Seq; Miscanthus sinensis; single-nucleotide variants; molecular markers
• ISSN: 0028-646X; 1469-8137
• DOI: 10.1111/nph.12621

Increasing demands for food and energy require a step change in the effectiveness, speed and flexibility of crop breeding. Therefore, the aim of this study was to assess the potential of genome-wide association studies (GWASs) and genomic selection (i.e. phenotype prediction from a genome-wide set of markers) to guide fundamental plant science and to accelerate breeding in the energy grass Miscanthus. We generated over 100 000 single-nucleotide variants (SNVs) by sequencing restriction site-associated DNA (RAD) tags in 138 Micanthus sinensis genotypes, and related SNVs to phenotypic data for 17 traits measured in a field trial. Confounding by population structure and relatedness was severe in naïve GWAS analyses, but mixed-linear models robustly controlled for these effects and allowed us to detect multiple associations that reached genome-wide significance. Genome-wide prediction accuracies tended to be moderate to high (average of 0.57), but varied dramatically across traits. As expected, predictive abilities increased linearly with the size of the mapping population, but reached a plateau when the number of markers used for prediction exceeded 10 000–20 000, and tended to decline, but remain significant, when cross-validations were performed across subpopulations. Our results suggest that the immediate implementation of genomic selection in Miscanthus breeding programs may be feasible.