Extent of Genome Wide Linkage Disequilibrium in a Collection of Perennial Ryegrass Forage and Turf Genotypes, and Identification of Alleles Differentiating Between Both Types

Knowledge on Linkage Disequilibrium (LD) is important when considering genotyping strategies for genomic selection. A rapid decay of LD necessitates the need for a higher marker density to enable markers to capture the entire phenotypic variation in the population. Outbreeding species with large effective population sizes are expected to have very low levels of LD. We have utilised a draft assembly of the perennial ryegrass genome to assess the extent of genome wide LD in a perennial ryegrass association population. The population consists of 174 single individuals originating from 72 varieties and 22 ecotypes, and there is a 92, 82 split between forage and turf types. The population was genotyped using a genotype by sequencing approach with the restriction enzyme APEKI (5bp cutter). Sequence tags were mapped onto scaffolds from the draft genome assembly that were greater than 10Kb in size, in order to identify SNPs. The genotypes were determined for each individual at these SNP sites, and used to calculate the squared correlation of allele frequencies between SNP pairs falling within the same genomic scaffold. The LD decayed rapidly between inter-SNP distances of 1-4Kb. The population was then used to find alleles that were differentiated between forage and turf types. This identified variation in a gene involved in sterol synthesis, a precursor in brassinosteroid hormone synthesis. Mutations in the brassinosteroid pathway have previously been associated with dwarfism in other plant species.