Core set of primers to evaluate genetic diversity in soybean

A large number of random primers are available to generate random amplified polymorphic DNA (RAPD) markers; however, not all primers are equally informative, The focus of this research was to identify a small set of RAPD primers that ran adequately describe the relationships among major North American soybean [Glycine max (L.) Merr,] ancestors and selected plant introductions (PIs). Two hundred eighty one polymorphic RAPD fragments evaluated on 35 ancestors and PIs were screened for reproducibility and levels of diversity. Principal components analysis (PCA) was employed to identify RAPD fragments associated with the largest sources of variation. Hierarchical and nonhierarchical cluster analyses were used to depict the relationships among the 35 genotypes, One hundred twenty RAPD fragments from 64 random primers were highly reproducible and had polymorphism information content (PIC) scores greater than or equal to 0.30. Principal-components analysis revealed that eight components explained 60% of the total variation. Stepwise removal of fragments from individual primers revealed that fragments from only 35 primers were critical to the analysis. The product-moment correlation of pairwise distances estimated from the complete RAPD fragment data set and this core data set was 0.86 (P < 0.0001), Results from cluster analysis confirmed that this set of 35 primers provides an accurate measurement of the relationships among the 35 genotypes, These primers will be useful for estimating relationships between exotic accessions and the current North American genetic base.