Selection and application of SSR markers for variety discrimination, genetic similarity and relation analysis in gerbera (Gerbera hybrida)

Gerbera is one of the most important floricultural crops worldwide, yet few robust and informative molecular markers were available for use in gerbera breeding and genetic studies. Previously we reported the first set of 99 EST-SSR markers. This study further characterized these markers using a much larger group of gerbera accessions and selected 53 robust, informative markers. The selected markers each amplified two to seven alleles, their PIC value ranged from 0.207 to 0.771, observed heterozygosity from 0.100 to 0.775, and expected heterozygosity from 0.224 to 0.801. Observed heterozygosity varied considerably among gerberas, ranging from 0.245 to 0.615. Similar levels of genetic diversity (observed and expected heterozygosity and Shannon's index) were observed among groups of gerberas for different uses (breeding lines, cut flower, seed-propagated pot-type, and tissue culture-propagated pot-type). The selected markers unequivocally differentiated all gerberas in the study, including six pairs of highly similar varieties that were indistinguishable morphologically. The great majority of the 861 pairwise comparisons among the 40 gerbera accessions showed a Jaccard similarity coefficient between 0.290 and 0.700 and a few pairs between 0.800 and 0.970. The UPGMA dendrogram based on similarity coefficients and population inference analysis with STRUCTURE separated the gerbera accessions into two major clusters that largely correspond to breeding approaches and/or propagation methods. These results showed that the selected markers were very powerful for discriminating gerberas and revealed genetic structures in cultivated gerberas. Application of these markers may also facilitate assessment of clonal fidelity and future DUS tests in gerberas.

► We selected 53 robust, informative EST-SSR markers for use in gerbera breeding and genetic studies.
► These markers differentiated highly similar, morphologically indistinguishable varieties.
► Similar levels of genetic diversity were found among four groups of gerberas for different uses.
► Clustering of gerberas largely corresponded to breeding approach and/or propagation method.