ESTIMATION OF SAMPLING VARIANCE OF MOLECULAR MARKER DATA USING THE BOOTSTRAP PROCEDURE

Knowledge of genetic relationships among genotypes is useful in a plan t breeding program because it permits the organization of germplasm an d provides for more efficient sampling. The genetic distance (GD) amon g genotypes can be estimated using random restriction fragment length polymorphisms (RFLPs) as molecular markers. Knowledge of the sampling variance associated with RFLP markers is needed to determine how many markers are required for a given level of precision in the estimate of GD. The sampling variance for GD among all pairs of 37 maize (Z. mays L.) inbred lines was estimated from 1202 RFLPs. The 1202 polymorphism s were generated from 251 enzyme-probe combinations (EPC). The samplin g variance was used to determine how large a sample of RFLPs was requi red to provide a given level of precision. The coefficient of variatio n (CV) associated with GD has a nearly linear relationship between its expected standard deviation and mean. The magnitude of the decrease i n the mean CV for GD with increasing numbers of bands was dependent up on the sampling unit; e.g., individual polymorphic bands vs EPC, and t he degree of relatedness among the inbreds compared. The rate of reduc tion in mean CV with increasing sample size was the same regardless of the restriction enzyme used, BamHI, EcoRI or HindIII, when the bootst rap sampling units were individual polymorphic bands. In constrast, al though the rate of reduction (slopes) was the same, the intercepts of the mean CVs were different when EPCs were used as the bootstrap sampl ing unit. This difference was due to the higher number of bands per EP C in BamHI (4.94) compared with EcoRI (4.83) and HindIII (4.63).