Ryegrasses (Lolium spp.) include the economically most important forage and amenity grass species and their economic value is likely to rise in future with increasing demand for meat and milk production and the development of environmentally friendly biofuels . Perennial ryegrass (Lolium perenne L.) and Italian ryegrass (Lolium multiflorum Lam.) are naturally diploid (2n = 2x = 14) and outbreeding members of the Poaceaea family with a highly efficient two-locus self-incompatibility system. Current breeding methods are complemented by molecular genetic approaches, with genetic mapping as a prerequisite for marker-assisted selection and map-based cloning. In the case of perennial ryegrass, the International Lolium Genome Initiative (ILGI) reference mapping population  has been extensively characterised for a range of morphophysiological traits [3–7]. Additional mapping populations have been developed and characterised for various traits such as, VrnA (vernalization response, disease resistance, seed yield and fertility traits) [8–11], pop8490 (morphogenetic traits and resistance to crown rust) [12, 13], WSC (water soluble carbohydrate accumulation and fertility traits) [7, 14, 15], TC1*SB2 (resistance to crown rust) , lpOA (resistance to crown rust and seed set), ZX (nitrogen use efficiency)  and F2 biomass (forage yield) . The research focus for Italian ryegrass has been primarily on morphological and disease resistance traits [19–23].
Some of these mapping populations were evaluated for the same traits. Resistance to crown rust, for example, is one of the most important traits in ryegrass breeding. This is reflected in the number of populations in which this trait has been mapped (VrnA, pop8490, lpOA, Xtg-ART, TC1*SB2). Major and minor QTL for resistance to crown rust have been detected on all LGs in different mapping populations from both perennial [9, 21, 24–26] and Italian ryegrass , providing the opportunity to compare the source of resistance among mapping populations. Although some genetic linkage maps developed from these populations have been aligned with each other using publicly available markers , the number of common markers among genetic maps is very low, limiting the ability to infer cosegregation of QTL for a specific trait across populations. This is mainly due to the limited number of publicly available genetic markers for Lolium spp., and to some extent due to the limited transferability of markers across mapping populations. While traditionally a genetic map has been generated from a single population, recent efforts to create maps from multiple populations, referred to as consensus maps, have gained much interest in the scientific and breeding community. Integration of mapping data from individual maps into one consensus map has been reported in other forage  and cereal species [29–31] and aims at determining the relative positions of transferable markers in order to compare candidate gene and QTL locations across a broad variety of genetic backgrounds. A first effort towards a consensus linkage map in Lolium was based on two mapping populations  and used comparative RFLP probes as the core mapping set. Later, Jensen et al.  produced a consensus map from four mapping populations which contained 65 SSR markers. While this represented an improvement in terms of marker technology, some LGs were not adequately covered and large gaps were found on LG 5 and LG 6. Therefore, a large set of publicly available genetic markers with a high inter- and intraspecific amplification rate is crucial for map alignment, consensus map construction and, finally, for the assessment of co-location of QTL and candidate genes across populations.
SSR markers are hypervariable, multiallelic, often codominant, highly reproducible and, therefore, ideal to anchor molecular linkage maps . Gene-associated SSRs derived from ESTs are of particular interest for linkage map alignments, since they are highly transferable to other pedigrees [34–36] and may functionally determine trait variation.
A large set of ryegrass EST-SSR markers has recently become available . Here we report on the collective effort of seven European institutions (ART, Switzerland; DJF, Denmark; IBERS, United Kingdom; ILVO, Belgium; INRA, France; PRI, The Netherlands; and TEAGASC, Ireland) to i) provide the map positions of a large set of publicly available EST-SSRs, ii) to establish the first comprehensive consensus linkage map for Lolium spp. using EST-derived anchor SSR markers, iii) to complement this map with a reference set of publicly available SSR markers and iv) to assess the usefulness of EST-SSRs for comparative genetics across existing mapping populations in ryegrass.