White Clover Seed Yield: A Case Study in Marker-Assisted Selection

Genetic gain from phenotypic selection in open-pollinated forage species is constrained by the inability to accurately use phenotype to estimate genotype, prior to parent selection for polycrossing. The use of marker-assisted selection (MAS) offers the potential to accelerate genetic gain by partially overcoming this constraint. White clover (Trifolium repens L., 2n = 4x = 32) is an open-pollinated, high-quality, perennial forage legume with complex inheritance of traits underpinning pasture persistence, seed production, animal productivity, and animal health. Our legume improvement programme has utilised seed production in white clover as a case study in the application of MAS in outbred forage species, using microsatellite markers linked to quantitative trait loci (QTL) of moderate resolution. The QTL SY03-D2 on the distal end of group D2, was used to explore marker:trait associations in 12 breeding pools, leading to opportunities to conduct reselection experiments, and to monitor response to genotypic selection criteria in experimental polycrosses. Each breeding pool was sampled with 90 or more individuals grown out in an unreplicated field trial to assess seed yield traits, as per standard practice in our cultivar development programme. DNA samples were tested with up to three microsatellite markers associated with the QTL. Significant (p < 0.01) marker:trait associations were observed in 8 of the 12 breeding pools, with the most informative polymorphisms accounting for differences of 30–69% in the mean seed yield values within breeding pools. These data suggest that value can be realised from the current investment in genomics for MAS in white clover, given QTL of moderate resolution, and widely used marker platforms such as microsatellites.