Using Genotyping-by-Sequencing to Identify QTL for Important Traits of Soft Red Winter Wheat

The next generation sequencing technology has reduced costs associated with genotyping to allow the detection of sequence polymorphism in high species with high diversity, complex genome, and lacking reference genomes using genotyping-by-sequencing (GBS).  The development of this methodology allowed a new tool for genome-wide association studies (GWAS) as well as genome assisted breeding methods.  Using GBS coupled the GWAS we can now identify QTL associated with economically important traits of soft red winter wheat.  Our objective was to use these two tools to identify markers associated with QTL for grain yield, fusarium head blight resistance, flour yield, and softness equivalent in a set of elite lines from the Ohio State wheat breeding program.  We used subsets derived from 470 lines with high heritability for each trait.  Lines were genotyped using genotyping by sequencing which produced 33K markers including 28K diversity array technologies and 6K SNPs.  There was 9% missing data across all markers scores which was imputed with the randomForest package in R 3.0.1 using 'na.roughfix'.  We attempted to evenly represent all portions of the genome by determining a subset of 1,715 markers using LD to cluster with ‘hclust’.  A GWAS of all 33K markers will be done using the GAPIT R package.  Results from this study can provide information of regions important for improved selection of these traits when breeding soft red winter wheat and will be presented further.