Water-soluble carbohydrate provides an easily fermentable energy source in perennial ryegrass fodder. Previously the considerable genetic variation available within the species has been characterised by quantitative trait locus mapping and regions of the genome with significant control over trait expression validated by individual test crosses. However, only limited extents of the large variation available within the source population were recovered. Here a quantitative trait locus marker index has been devised to test the potential of this strategy to exploit the available variation more efficiently. Parents for polycrossing were chosen on the basis of an index weighted for the size of leaf water-soluble carbohydrate effects. Populations of one hundred plants from the crosses were maintained in a glasshouse and the water-soluble carbohydrate content of tiller bases and leaves was measured. The fructan and total water-soluble carbohydrate content of the high populations were always greater than in the low populations. However the differences were not always significant and were generally lower than for the parental populations. This highlights the confounding effects of genome-wide, uncontrolled, segregation for carbohydrate content outside marker-selection regions and the challenges ahead for marker selection of polygenic, complex traits in outbreeding species.