Evaluation of different microsatellite motifs for analysing genetic relationships in cultivated sunflower (Helianthus annuus L.)

A total of 16 different simple sequence repeat motifs and an M13 repeat sequence were used as hybridization probes in order to examine the molecular relationships between two German inbred and eight North American sunflower lines of known pedigree, and to determine the suitability of the individual short tandem repeats for genetic analyses and their occurrence in the sunflower genome. Only the oligonucleotides (ACA)6, (CAT)6, (CATA)5, (GACA)4 and (GATA)4 proved to be well suited for the generation of scorable fingerprinting patterns, while the other (microsatellite) sequences were either too abundant or too rare. Although different levels of polymorphism were present in hybridizations with the different simple sequence repeats (SSRs), a clear separation of the German material from the USDA Hnes was feasible not only by evaluating 20 probe‐enzyme combinations, but also by combining every individual probe with four different restriction enzymes. In the American material, the expected relationships could be proved with the single exception of a line that did not group in accordance with its pedigree.