Lolium perenne isolate:4540-9 Genome sequencing and assembly

Microsatellite markers are extremely valuable molecular genetic markers for conservation ecology, paternity testing, pedigree reconstruction, population genetics, and linkage mapping. Traditional methods for the development of microsatellite markers can be time-consuming, laborious and expensive. Next-generation sequencing (NGS) is a more recent, and potentially more promising, approach to microsatellite marker development. Perennial ryegrass (Lolium perenne L.) is an important turfgrass species with a limited set of publicly available microsatellite markers. In the current study we conducted Illumina NGS, as well as genotyping of a Lolium test population, to identify and characterize perennial ryegrass microsatellite markers. Sequencing and assembly results returned a microsatellite marker database containing 10,830 perfect di- and 42,718 perfect trinucleotide microsatellites with repeat unit lengths equal to or greater than 6 and 4 repeat units, respectively, as well as sufficient flanking sequence to enable PCR primer design. Genotyping results from a subset of 172 di- and trinucleotide microsatellite markers indicated that 38.7% of these markers were polymorphic in Lolium perenne, and 21.5% were transferable to and polymorphic in Lolium multiflorum (Lam.). The thousands of expected polymorphic markers reported herein represent a significant new source of microsatellite markers for Lolium genetic diversity research, parentage analysis, linkage analysis, and turf and forage breeding programs.