CONFORMITY AND GENETIC RELATEDNESS ESTIMATION IN CROP SPECIES HAVING A NARROW GENETIC BASE: THE CASE OF CUCUMBER (CUCUMIS SATIVUS L.)

Authors: Staub, Jack; CHUNG, SANG-MIN - UNIV OF WISCONSIN; Fazio, Gennaro

Submitted to: Plant Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/20/2003
Publication Date: 3/10/2004
Citation: Staub, J.E., Chung, S., Fazio, G. 2004. Conformity and genetic relatedness estimation in crop species having a narrow genetic base: the case of cucumber (Cucumis sativus l.). Plant Breeding. 124:44-53.

Interpretive Summary: Intellectual property rights (e.g, plants and other plant-related inventions) in the United States can be protected by the Plant Patent Act of 1930, utility patents, and the Plant Variety Protection Act of 1970 as amended in 1994. Potential infringement of intellectual property (using property and their associated rights illegally) related to germplasm (protected plant species) necessitated the establishment of the concept of an Essentially Derived Variety (EDV) in 1991. New varieties are often created from old varieties. The new variety must be genetically different from the old variety such that they cannot be mistaken for one another. The EDV is said to be distinct from the initial variety (IV) from which it was predominantly derived, but conforms in its expression with the essential characteristics of the IV but is different from the IV such that it is obvious to the scientific world. The question is how different does the EDV have to be from the IV to allow it to not infringe on the illegal rights of the IV. Genetic differences between plants can be determined at the molecular level by differences in their DNA (the substance that makes up genes which control how plants look). Cucumber varieties are very closely related and thus the issue of differences between the IV and EDV are extremely important to the legal arena. An experiment was designed to determine how genetically different the EDV has to be from the IV to ensure that it is unique and distinct from the IV. Data indicate that such differences can only be determined at the DNA level between individual genes at which the EDV and IV differ. Information from this study sets guidelines for genetic distances between IV and EDV in cucumber. This will allow an inventor (public or private breeding programs) of a new and improved variety to better describe their new invention for plant variety protection. Such protect will allow for less cases of infringement to burden the legal system and increase profitability for the inventor. The grower and consumer will thus be able to grow and consumer plants for a more reasonable price.

Technical Abstract: 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 to 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 (rs = 0.65) using two 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 3 to 7 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 SNPs as discriminators of difference in this species.