Conformity and genetic relatedness estimation in crop species having a narrow genetic base: the case of cucumber (Cucumis sativus L.)*

A set of 155 SSR (107) and SCAR (48) markers were used to evaluate 53 cucumber (Cucumis sativus L.) accessions of diverse origin to characterize genetic relationships and to define a standard marker array that was most effective in detecting genetic differences in this germplasm array. A multivariate marker‐based analysis of diverse germplasm using this standard marker array (17 SSR and 5 SCAR markers) was compared with results from a set of 70 previously reported RAPD markers, and then used to explore the potential value of these genetic markers for plant variety protection (PVP) and the establishment of essential derivation (ED) threshold values in this species using elite lines and hybrids and backcross progeny. Diversity analysis allowed identification of distinctly different lines that were used for the construction of three sets of backcross families (BC₁‐BC₃). While general genetic relationships among accessions were similar in SSR/SCAR analyses (r_s= 0.65) using two genetic distance (GD) estimators, differences in accession relationships were detected between RAPD and SSR/SCAR marker evaluations regardless of the estimator used. The GDs among elite germplasm with known pedigrees were relatively small (0.06‐0.23 for any pairwise comparison). GD values decreased and degree of fixation (at three to seven loci depending on the mating) increased with increased backcrossing such that recurrent parent allelic fixation occurred in least one family of each of the BC₃ families. In many instances the degree of fixation of loci was not uniformly achieved in the BC₃. Although the level of genetic polymorphisms will likely restrict the use of molecular markers for PVP and the establishment of ED values, the use of single nucleotide differences will likely provide opportunities to define specific functional distances that have potential for PVP in cucumber. Nevertheless, without an expanded, genetically robust standard marker array (e.g. 50 codominant markers), ED threshold values will be difficult to define in this species, and perhaps will require the appraisal of single nucleotide polymorphisms as discriminators of difference in this species.