Nuclear RFLPs were used to estimate relationships among 14 elite commercial inbreds of bulb onion (Allium cepa) from Holland, Japan, and the United States. Variability for known alleles at 75 RFLP loci and 194 polymorphic fragments revealed by 69 anonymous cDNA probes and a clone of alliinase were scored to yield genetically characterized and uncharacterized data sets, respectively. The inbred onion populations possessed more than two alleles at 20 of 43 (46%) codominant RFLP loci. Relationships among the inbreds were estimated by cluster analysis of simple-matching (genetically characterized data) and Jaccard (genetically uncharacterized data) coefficients using the unweighted pair group method and agreed with known pedigrees. RFLPs confidently distinguished among elite inbreds within and between specific market classes. RFLP profiles for virtual hybrids were computer-generated by combining gametic arrays among inbreds of the same market class and analyzed as described above. Allelic and genetically uncharacterized RFLPs confidently distinguished among these hybrids, even though heterozygosity for many markers produced a majority of monomorphic fragments. We randomly sampled decreasing numbers of RFLPs from the complete data sets and calculated simple-matching and Jaccard distances, noting the numbers of probes that were unable to distinguish any two inbreds or hybrids. As few as 10 polymorphic probe-enzyme combinations distinguished among all the inbreds and samples of 20 genetically characterized or 10 genetically uncharacterized clones distinguished all the virtual hybrids. This study demonstrated that the previously reported few RFLPs observed among open-pollinated (OP) onion populations were due to the highly heterozygous nature of the OP population.
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