Random amplified polymorphic DNA and sequence characterized amplified regions for studies of genetic diversity and downy mildew resistance in cucumber

RAPD and SCAR markers have not been rigorously tested for genetic analysis of cucumber. Therefore, a series of studies were conducted to determine their potential utility. A study was conducted to identify RAPD markers linked to dm, the downy mildew resistance gene and examine their potential applicability for marker-assisted selection (MAS). Analysis of downy mildew evaluations in two populations revealed five RAPD markers linked to dm. The most effective RAPD markers to use for MAS are flanking markers linked in repulsion phase to dm. Estimates of selection efficiency indicate that MAS holds potential as a breeding technique for developing resistant cucumbers.; RAPD markers were used to examine genetic relationships among 118 germplasm accessions and compare the effectiveness of RAPD (71 loci) to that of isozyme (10 loci) and RFLP (104 loci) markers. Germplasm grouping patterns were consistent with geographic origins and morphology. Although elite accessions had unique RAPD banding patterns, their genetic distances indicated limited diversity. Germplasm assessment using RAPD markers was more similar to RFLP than to isozyme markers. It was determined that RAPD markers have utility for analysis of genetic relationships in cucumber.; SCAR markers are theoretically more tolerant to methodological variations than RAPD markers. A study was designed to determine the efficiency of RAPD to SCAR conversion and compare their PCR performance. SCAR primers were constructed from sequences of 14 RAPD PCR products. PCR conditions were altered by varying template DNA type, purity, and concentration; MgCl{dollar}sb2{dollar} concentration; and manufacturers of polymerase and thermocyclers. In eight cases, conversion of RAPD to SCAR markers resulted in the loss of polymorphism. Two SCAR markers produced brighter bands than their corresponding RAPD markers, indicating increased PCR performance. SCAR markers on average were less influenced by MgCl{dollar}sb2{dollar} concentration. One SCAR marker was more sensitive to both template DNA mixtures and concentrations. In contrast, another SCAR marker produced less intense band than its corresponding RAPD over DNA concentrations. No differences in PCR performance were detected for source of either polymerase or thermocycler. Data indicate that judicious consideration must be given when considering SCAR development in cucumber.