Paternity and Nested-within-Family Marker Assisted Selection In Space Planted Red Clover Nurseries.

Presented is a cost effective marker assisted selection methodology that utilizes individual plant phenotypes, seed production based knowledge of maternity, molecular marker determined paternity, and nested within halfsib family linkage relationships.  Combining all above listed components, selection gains in red clover are easily doubled compared to standard maternal halfsib family based selection.  The efficacy of this scheme is demonstrated in a red clover populations derived from 96 parent polycrosses with 19 maternal halfsib families evaluated in multi-environment space plant nurseries.  A simple permutation based validation approach is used to demonstrate selection gains, in which multiple randomly chosen 80% of nursery plants with genotypic and phenotypic information are used to estimate breeding values and selection rankings.  The selection rankings from the 80% estimation sets are used to rank their corresponding 20% validation sets based on maternal and molecular marker determined paternal familial structure, and molecular marker determined cumulative linkage effects.  Positive and negative selection was practiced for the full range of selection intensities on the validation sets with corresponding average selection gains determined across all 20% validation sets.  Using 11 SSR markers multiplexed into two PCR reactions paternity was determined for progeny plants from the 96 parent polycrosses.  These same SSR markers were used for nested-within-family based linkage selection.  In all cases selection gains were greatly increased with the additional information provided by the molecular markers.