Probing genome diversity in natural and breeding populations of Lolium perenne

Population-scale genome resequencing has revealed the rich genome sequence diversity in model organisms and agriculturally important crops, and has great potential to identify target loci for breeding and selection or to investigate the genetic basis of adaptive traits. With the dual purpose to provide molecular markers for association mapping and to catalogue the functional sequence variation in the gene pool, we have resequenced several hundred candidate genes in natural accessions, elite breeding material, and commercial varieties of L. perenne. Target loci included key regulatory genes controlling plant growth and development, plant architecture, meristem activity, induction of flowering, light signaling, cell wall biogenesis, and phytohormone biosynthesis, signaling, and response. Based on phylogenetic analysis, we assigned more than 2900 L. perenne proteins predicted on the draft genome to 180 gene families and selected 539 representative family members for targeted resequencing. We constructed indexed shotgun gDNA libraries of 736 independent L. perenne genotypes. These libraries were pooled, probe capture-enriched and sequenced on a HiSeq2000 flowcell. To validate the method, we analysed target region coverage, read depth and polymorphism density, as a function of experimental and SNP calling parameters. Our data provide novel insights into the sequence diversity present in genes and physiological pathways potentially controlling architectural traits and cell wall digestibility, and provide high quality genotyping data for association studies. Furthermore, we aim to predict functional sequence variation based on haplotype reconstruction combined with within- and between-species sequence conservation, and to provide further molecular genetic insight into the causative variation underlying phenotypic diversity.