Cultivating Marker-Assisted Selection in Forage Legumes

Intensively grazed temperate pastoral grasslands are commonly based on perennial ryegrass (Lolium perenne L.) and white clover (Trifolium repens L.).  Both species are adapted and bred as heterogeneous populations of heterozygous individuals – offering challenges and opportunities for marker-assisted selection (MAS).  After successful large-scale microsatellite marker discovery projects, genetic tools have been developed including linkage maps, quantitative trait loci (QTL) and marker:trait associations.  These are backed by functional genomics, metabolomics, genome sequence data and field-based multi-site phenomics resources in programmes such as Pastoral Genomics, a research consortium jointly funded by the NZ government and pasture-based industries.  We explored a MAS strategy in an elite breeding population of white clover, identifying population-specific allele:trait associations and increasing beneficial allele frequency by recurrent selection.  The strategy focused on two traits related to persistence: Internode Length (IL); and Average Node Number (ANN).  For each trait, markers subtending QTL discovered and verified in replicated, mixed-sward field trials across years and sites were used to screen a multi-parent complex population sampled from cultivar ‘Kopu II’.  Significant (p<0.0001) marker:trait associations were identified, with plants carrying beneficial marker alleles exhibiting a 21% and 19% increase in trait mean for IL and ANN, respectively.  Contrasting selections were made on the basis of phenotypic and marker-based selection indices.  Results from progeny assessment indicate the marker effects are heritable in complex elite populations, evidence that QTL-informed MAS in forage populations is a viable option.  These findings will be discussed in context of novel selection strategies, genome sequence resources, and improved marker platforms.