Exploring an Annotated Sequence Assembly of the Perennial Ryegrass Genome for Genomic Regions Enriched for Trait Associated Variants

Perennial ryegrass (Lolium perenne L.) is an outbreeding diploid species and one of the most important forage crops used in temperate agriculture. We have developed a draft sequence assembly of the perennial ryegrass genome and annotated it with the aid of RNA-seq data from various genotypes, plant components, and treatments. We predicted 39,795 high quality proteins originating from 28,182 genetic loci.  We wanted to use the annotated assembly to study if SNPs falling within various annotation classes explain differing proportions of the variance for traits such as heading date and rust resistance.  A population consisting of 995 breeding families was densely genotyped via Genotyping-By-Sequencing (GBS), and we identified variants at over 1.8 million positions after aligning data against the annotated sequence assembly. Variants were found in 20,594 (73%) of the gene loci, and these had on average 22.3 SNPs per gene.  SNPs were partitioned according to various annotation features and genomic relationship matrices were created for each annotation class. The SNP-explained variances for heading date and disease resistance were calculated for each class.