Genome-Wide Association Analysis of Flowering Time in Miscanthus sinensis

The perennial C4 grass Miscanthus sinensis is one of the parental species of the agronomically important hybrid biomass crop M. ×giganteus, and also a close relative of sugarcane. Given that M. sinensis has a broad native range spanning subtropical to cold temperate regions of East Asia, we expect to find wide variation for climatic adaptation within this species. Here we characterize a collection of 625 genotypes from China, South Korea, Japan, and the US. Replicated field trials were planted in Ontario, Canada, Hokkaido, Japan, and Gangwon, South Korea in 2012, with a subset planted in Colorado, USA. Four measures of flowering date were recorded in 2013, and were transformed into one variable per location by principal components analysis. More than 20,000 SNPs were genotyped by RAD-seq using PstI-MspI and the UNEAK pipeline, and an additional 424 SNPs were genotyped by GoldenGate. Alignments to the Sorghum bicolor genome were used to order the SNPs for GWAS. The Q-K mixed model, implemented in JMP Genomics, was used to identify SNP-trait associations. The majority of significantly-associated SNPs were in or immediately adjacent to transcribed regions of genes, suggesting low linkage disequilibrium typical of an outcrossing wild species. As we obtain additional adaptation and yield data from our population, it will become possible to use genomic selection to identify ideal parents for Miscanthus breeding.