Identification of genomic variation in perennial ryegrass (Lolium perenne)

Perennial ryegrass (Lolium perenne) is a species for which high SNP densities in genic regions have previously been reported. We are interested to identify the genomic diversity of candidate genes that are known to regulate important biological processes such as plant growth, development and architecture. Using an in-house optimized probe-capture strategy, 550 candidate loci were resequenced in a collection of 750 L. perenne accessions. SNPs, InDels and copy number variations were identified and are being aggregated into a genomics resource that contains an optimized annotated reference gene set, a description of gene families, and the natural genetic variation within each gene. The resulting database of genomic variation gives an insight in the degree of variation that exists in our collection. Functional consequences of SNPs and InDels can be determined by comparative genomics within each gene family. This way, de novo discovery of rare defective alleles and predictions of other alleles disturbing gene function can be used to select accessions for further analysis or breeding. In addition, phenotypic variation can be linked to genomic variation in genes that are important regulators of the biological processes of interest.