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Developing and implementing molecular markers in perennial ryegrass breeding

K.F. Smith1,3, J.W. Forster2,3, T.A. Ciavarella1,3, J.L. Dumsday2, M.P. Dupal2,3, E.S. Jones2,3, B.D. Kirkwood1,3, A. Leddin1,3, N.M. McFarlane1,3, P.J. Trigg1,3 , K.M. Guthridge2,3 and N.L. Mahoney2,3

1Agriculture Victoria Hamilton, Pastoral and Veterinary Institute, Hamilton, Vic.
Plant Biotechnology Centre, Agriculture Victoria, La Trobe University, Bundoora, Vic.
CRC for Molecular Plant Breeding


Molecular genetic markers are being developed for implementation in the breeding of the key forage grass species, perennial ryegrass (Lolium perenne L.). These systems are being used for genetic diversity analysis and cultivar identification, genetic dissection of complex traits and marker assisted selection (MAS). A combination of RFLP, AFLP and SSRP markers are in use for genotypic analysis. For perennial ryegrass, reference genetic map construction is being performed in the p150/112 one-way pseudo-testcross family. Perennial ryegrass SSR (LPSSR) loci which are polymorphic in this cross have been assigned to the genetic map in addition to AFLP and RFLP loci contributed from the activities of the International Lolium Genome Initiative (ILGI). Trait-specific families have been developed for the detection and tagging of genes/QTLs for crown rust resistance, drought tolerance and water-soluble carbohydrate concentration. Progress in phenotypic and genotypic analysis of these families is described in this paper.


Perennial ryegrass (Lolium perenne L.) is the most commonly sown temperate forage grass species in the world, and as such a very large number of cultivars have been developed. The species is also commonly sown as an amenity grass for recreational use.

The development of perennial ryegrass cultivars for pastoral use has largely been based on improving the yield potential of the species through improving the seasonal distribution of dry matter yield and through improvements in disease resistance (9). The self-incompatible, outcrossing nature of the species means that the majority of new cultivars are synthetic cultivars based on the random mating of several parents.

Despite the predominance of perennial ryegrass in temperate agriculture very few attempts have been made to develop cultivars with improvements in specific traits such as nutritive value to grazing animals. This is in part due to a poor knowledge of the genetic control of many traits in perennial ryegrass and on the effects of environment of these traits. Large improvements in the productivity of grazing industries have been predicted to flow from the improvement of nutritive value traits in perennial ryegrass. For instance a 5% unit increase in in vitro digestibility that was observed in experimental synthetics of perennial ryegrass selected for increased water-soluble carbohydrate concentrations was predicted to have the potential to increase milk production from dairy cows by up to 26% over summer (7).

The development of molecular markers in perennial ryegrass has the potential to:

  • increase the ability to discriminate between perennial ryegrass cultivars for cultivar identification purposes,
  • allow dissection of the genetic control of complex traits through the detection of the quantitative trait loci (QTL) that control the expression of these traits,
  • increase the rate of development of cultivars with novel traits through the development of marker assisted selection procedures: using marker loci to select for QTL controlling the expression of traits of agronomic importance.

The development of molecular markers in perennial ryegrass has been limited in comparison to advances in other crops such as maize (Zea mays L.) and tomato (Lycopersicon esculentum L.). The applicability of these molecular markers to breeding programs has also been limited by the small number of traits for which linkage has been determined, and the lack of reproducible, co-dominant markers available for linkage analysis.

This paper describes a series of results from a number of experiments that are developing robust molecular marker systems in perennial ryegrass and determining the linkage of these markers to traits of agronomic importance such as forage quality and disease resistance.

Development of molecular markers in perennial ryegrass

A range of molecular marker systems is now available to detect DNA polymorphism. These marker systems vary according to their method of detection (Southern hybridisation or PCR), multiplex ratio (number of loci detected per assay) and ability to detect heterozygous genotypes (co-dominant vs. dominant). Whilst initial developments of molecular maps in perennial ryegrass were based on restriction fragment length polymorphism (RFLP) or random amplification of polymorphic DNA (RAPD) markers (3), these marker systems are both of limited value in a practical breeding program. RAPD markers show low reproducibility, while RFLPs have high time and labour requirements. More recently marker systems based on amplified fragment length polymorphism (AFLP) and simple sequence repeat polymorphism (SSRP) have replaced RFLP and RAPD systems. SSRP markers are particularly useful in breeding programs as they are co-dominant and highly reproducible. However, the initial isolation and characterisation of SSRP within a species is labour-intensive and costly.

SSR development in perennial ryegrass

We have developed SSRP libraries from perennial ryegrass based on a modification of previously published SSR enrichment procedures (1). Through the optimisation of these procedures for perennial ryegrass a total of 366 unique SSR clones suitable for primer design were obtained (4). Primer pairs for 100 selected SSR loci were tested for efficiency of amplification and detection of genetic polymorphism against a panel of 8 diverse perennial ryegrass genotypes (Table 1).

Table 1. Amplification and polymorphism data for perennial ryegrass SSRs.

Number of primers screened




Polymorphism in screening panel (% of primers amplified)


Range of allele number detected


Average polymorphism information content


A typical SSR amplification profile in perennial ryegrass is shown in Figure 1.

Figure 1. SSR amplification products amplified by locus LPSSRH02D12 for eight genotypes of L. perenne. 1: North African; 2: Aries; 3: Aurora; 4: Victorian; 5: Ellett; 6: Yatsyn; 7: Vedette; 8: DH297. The SSR structure in the cloned sequence is [CA]12 and the predicted amplification product size is 219 bp. Six alleles designated A (largest) to F (smallest) are indicated.

A reference genetic map for perennial ryegrass based on the cross between a multiply heterozygous individual of complex descent and a double haploid plant (p150/112) has been developed by members of the International Lolium Genome Initiative (ILGI) using AFLP and RFLP markers. The perennial ryegrass SSR markers described are being added to that map with an initial density of 100 loci. These markers will be hen be transferred to trait-specific mapping families with high efficiency.

Using molecular markers for cultivar identification

Perennial ryegrass cultivars are usually synthetic cultivars based on the intercrossing of a number of parental clones with large amounts of genetic variation present within a cultivar. The application of Plant Breeders Rights (PBR) to new perennial ryegrass cultivars is currently based on using morphological characters such as flowering time, plant height and growth habit to distinguish cultivars that may be phenotypically similar but have contrasting agronomic performance. These parameters may also be influenced by the environment in which plants are grown or the stage of development of the plants creating problems for consistent cultivar identification. Biochemical and molecular markers are unaffected by environmental factors and may be applied to plants at any stage of growth, providing new tools to support cultivar identification (6) and are accepted as supplementary characters in Australian PBR (5).

Ideally the use of molecular markers for the identification of cross-pollinated forage species should be based on a strategy of bulking of samples as herbage or DNA to reduce the number of samples to be analysed. We have shown that AFLP markers can be used to discriminate between perennial ryegrass cultivars, even when the cultivars are closely related (2). Analyses based on combining genomic DNA from 20 individuals within a population (a bulking strategy) were consistent with those based on the analysis of individual genotypes. A dendrogram showing the relationship between genotypes of perennial ryegrass is shown in Figure 2. This figure clearly demonstrates the ability of molecular markers to distinguish perennial ryegrass cultivars. We are currently evaluating other marker systems such as SSRP for their applicability for cultivar identification.

Developing molecular markers for agronomic traits in perennial ryegrass

Several trait mapping populations have been developed based on the cross between perennial ryegrass genotypes. These populations are the F1 progeny of the cross between two diverse perennial ryegrass genotypes. The progeny of these crosses are currently being assessed for phenotypic variability in a number of agronomic traits including rust resistance, drought tolerance, waterlogging tolerance, forage quality, photosynthetic parameters, biomass accumulation and partitioning. The results of several of these projects are described elsewhere in these proceedings.

Figure 2. UPGMA phenogram for individual plants (20) of L. perenne cultivars Yatsyn1, Banks and Embassy.

Implementing molecular markers in perennial ryegrass breeding

The development of robust, co-dominant molecular markers that are tightly linked to loci controlling traits of agronomic importance will be of great assistance in the development of perennial ryegrass cultivars with novel characteristics. For instance, the development of perennial ryegrass cultivars with improved forage quality is hampered by environmental influences on the expression of forage quality parameters during half-sib family evaluation (8). Having molecular markers linked to QTL controlling the expression of forage quality components will allow these traits to be selected at the genome level without phenotypic evaluation.


1. Edwards, K.J., Barker, J.H.A., Daly, A., Jones, C., Karp, A. 1996. Biotechniques 20,758-759.

2. Guthridge, K.M., Dupal, M.P., Klliker, R., Jones, E.S., Smith, K.F., Forster, J.W. Euphytica (submitted)

3. Hayward, M.D., Forster, J.W., Jones, J.G., Dolstra, O., Evans, C., McAdam, N.J., Hossain, K.G., Stammers, M., Will, J.A.K., Humphreys, M.O., Evans, G.M. 1998. Plant Breed 117, 451-455.

4. Jones, E.S., Dupal, M.P., Klliker, R., Drayton, M.C., Forster, J.W. 2000. Theor.Appl.Genet. (in press).

5. Morrell, M.K., Peakall, R., Appels, R., Preston, L.R., Lloyd, H.L. 1995. Aust. J. Exp. Agr. 35, 807-819.

6. Preston, L.R., Harker, N., Holton, T., Morrell, M.K. 1999. Plant Var Seeds 12, 191-205.

7. Smith, K.F., Simpson, R.J., Oram, R.N., Dove, H., Culvenor, R.A. and Humphreys, M.O. 1998. Proceedings 21st Meeting of the Fodder Crops and Amenity Grasses Section of EUCARPIA, Zurich, pp. 16-19.

8. Smith, K.F., Rebetzke, G.R., Eagles, H.A., Anderson, M.W., Easton, H.S. 1999. Aust. J. Agric. Res 50, 79-86.

9. Wilkins, P.W. 1991. Euphytica 52, 201-214.

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