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

Type Abstract
Original languageEnglish
PagesW422
Publication statusPublished - 11 Jan 2014
EventPlant & Animal Genome XXII Conference - San Diego, United States of America
Duration: 10 Jan 201415 Jan 2014

Conference

ConferencePlant & Animal Genome XXII Conference
CountryUnited States of America
CitySan Diego
Period10 Jan 201415 Jan 2014
Links
Handle.net
View graph of relations
Citation formats

Abstract

Increasing demands for food and energy require a step change in the effectiveness, speed and flexibility of crop breeding. The aim of this study was therefore 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 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 M. 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 after Bonferroni corrections. Genome-wide prediction accuracies tended to be moderate to high (average = 0.57) but varied dramatically across traits (range = 0.05-0.95). As expected, predictive abilities (1) were correlated with broad-sense heritabilities (r > 0.57, P < 0.018); (2) 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 (3) 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.