Development and mapping of DArT markers within the Festuca - Lolium complex

Abstract

Background: Grasses are among the most important and widely cultivated plants on Earth. They provide high quality fodder for livestock, are used for turf and amenity purposes, and play a fundamental role in environment protection. Among cultivated grasses, species within the Festuca-Lolium complex predominate, especially in temperate regions. To facilitate high-throughput genome profiling and genetic mapping within the complex, we have developed a Diversity Arrays Technology (DArT) array for five grass species: F. pratensis, F. arundinacea, F. glaucescens, L. perenne and L. multiflorum.

Results: The DArTFest array contains 7680 probes derived from methyl-filtered genomic representations. In a first marker discovery experiment performed on 40 genotypes from each species (with the exception of F. glaucescens for which only 7 genotypes were used), we identified 3884 polymorphic markers. The number of DArT markers identified in every single genotype varied from 821 to 1852. To test the usefulness of DArTFest array for physical mapping, DArT markers were assigned to each of the seven chromosomes of F. pratensis using single chromosome substitution lines while recombinants of F. pratensis chromosome 3 were used to allocate the markers to seven chromosome bins.

Conclusion: The resources developed in this project will facilitate the development of genetic maps in Festuca and Lolium, the analysis on genetic diversity, and the monitoring of the genomic constitution of the Festuca x Lolium hybrids. They will also enable marker-assisted selection for multiple traits or for specific genome regions.

Figure 1

UPGMA dendrogram (shown as Radial tree). UPGMA dendrogram (shown as Radial tree) based on hybridization of 80 Lolium and 87 Festuca genotypes to 2629 DArT markers and Felsenstein's modified Nei/Li restriction fragment distance. Two major groups representing the fescue and ryegrass genera are clearly differentiated. Both ryegrass species display higher genetic diversity than fescue species. Note that the accession of F. arundinacea Fa-35 (Moroccan ecotype 599533) was found distant of the major group. Similarly, one accession of F. glaucescens (Fg-7) clustered with the subgroup of F. arundinacea. Another inconsistent accession, F. pratensis Fp-40 (Norwegian cultivar Norild), was located separately outside of all other species in the dendrogram.

Figure 2

UPGMA dendrogram (shown as Rectanglar cladogram). UPGMA dendrogram (shown as Rectanglar cladogram) based on hybridization of 80 Lolium and 87 Festuca genotypes to 2629 DArT markers and Felsenstein's modified Nei/Li restriction fragment distance. Groups of Festuca and Lolium accessions are marked using colored lines. Inconsistent accessions (Fp-40, Fg-7 and Fa-35) are marked using arrows.

Figure 3

DArT markers for hybrids. Number of DArT markers which can be used to estimate the genomic constitution in hybrids within the Festuca-Lolium complex. In each pair-wise combination, a high proportion of markers is shared by both species. The markers shared by both parental genomes are in the middle section of the bar.

Figure 4

DArT markers physically mapped to bins of F. pratensis chromosome 3. Nine out of 36 markers co-localized to one or more chromosomes (chromosome numbers in brackets).