title: Genome-wide association studies and prediction of 17 traits related to phenology, biomass and cell wall composition in the energy grass Miscanthus sinensis.
abstract: • 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.
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK.
authors.forename: Gancho T
authors.initials: GT
authors.lastname: Slavov
authors.affiliation: Floragenex Inc., Eugene, OR, 97403, USA.
authors.forename: Rick
authors.initials: R
authors.lastname: Nipper
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK.
authors.forename: Paul
authors.initials: P
authors.lastname: Robson
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK.
authors.forename: Kerrie
authors.initials: K
authors.lastname: Farrar
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK.
authors.forename: Gordon G
authors.initials: GG
authors.lastname: Allison
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK.
authors.forename: Maurice
authors.initials: M
authors.lastname: Bosch
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK.
authors.forename: John C
authors.initials: JC
authors.lastname: Clifton-Brown
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK.
authors.forename: Iain S
authors.initials: IS
authors.lastname: Donnison
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK.
authors.forename: Elaine
authors.initials: E
authors.lastname: Jensen
mesh_terms: D018533:Biomass; D002473:Cell Wall / Q000378:metabolism*; D018744:DNA, Plant / Q000235:genetics; D005819:Genetic Markers; D018745:Genome, Plant / Q000235:genetics; D055106:Genome-Wide Association Study; D005838:Genotype; D005843:Geography; D010641:Phenotype; D006109:Poaceae / Q000166:cytology* / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011157:Population Dynamics; D025341:Principal Component Analysis; D019655:Quantitative Trait, Heritable; D015183:Restriction Mapping; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers
keywords: Miscanthus sinensis; RAD-Seq; genome-wide association studies (GWAS); genomic selection; molecular markers; single-nucleotide variants