Frequency, type, and distribution of EST-SSRs from three genotypes of Lolium perenne, and their conservation across orthologous sequences of Festuca arundinacea, Brachypodium distachyon, and Oryza sativa

From 25,744 ESTs, representing 8.53 megabases of nucleotide information from three genotypes of L. perenne, 1,458 ESTs (5.7%) contained one or more SSRs. Of these SSRs, 955 (3.7%) were non-redundant. Tri-nucleotide repeats were the most abundant type of repeats followed by di- and tetra-nucleotide repeats. The EST-SSRs from the three genotypes were analysed for allelic- and/or genotypic SSR motif polymorphisms. Most of the SSR motifs (97.7%) showed no polymorphisms, whereas 22 EST-SSRs showed allelic- and/or genotypic polymorphisms. All polymorphisms identified were changes in the number of repeat units. Comparative analysis of the L. perenne EST-SSRs with sequences of Festuca arundinacea, Brachypodium distachyon, and Oryza sativa identified 19 clusters of orthologous sequences between these four species. Analysis of the clusters showed that the SSR motif generally is conserved in the closely related species F. arundinacea, but often differs in length of the SSR motif. In contrast, SSR motifs are often lost in the more distant related species B. distachyon and O. sativa.The results indicate that the L. perenne EST-SSR markers are a valuable resource for genetic mapping, as well as evaluation of co-location between QTLs and functionally associated markers.Lolium perenne is one of the major grass species used for turf and forage in the temperate regions of the world. It belongs to the grass family Poaceae. L. perenne (2n = 2x = 14) is taxonomically related to many important plant species in the Poaceae family, including rice (Oryza sativa), wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), maize (Zea mays L.), and sorghum (Sorgum bicolor L.) [1].Several anonymous molecular markers have been developed for L. perenne, including restriction fragment length polymorphism and random amplified polymorphic DNA [2,3], amplified fragment length polymorphism [4], as well as SSR markers [5,6]. More recently, gene-tagged markers [7] have been developed and used to constru