ARS | Publication request: ANALYSIS OF MOLECULAR EFFICACY IN GERMPLASM EVALUATION

Submitted to: Cucurbitaceae Proceedings
Publication Type: Proceedings
Publication Acceptance Date: November 15, 2002
Publication Date: December 1, 2002
Citation: Staub, J.E., Lopez Sese, A. 2002. Analysis of molecular efficacy in germplasm evaluation. Cucurbitaceae Proceedings.

Technical Abstract: Curatorial decisions regarding the use of molecular markers for germplasm management requires an assessment of human and fiscal resources. For large collection analysis the use of reference accessions and standardized molecular marker arrays (SMA) is recommended for increasing the efficacy of germplasm analysis. Experiments were designed to determine the impact of reducing the number of markers in the current melon SMA and thus reducing costs of analysis. Stepwise elimination of primers in the SMA was accomplished by examination of previous data on efficacy of marker loci in the SMA for detection of polymorphisms. Four strategic eliminations were compared to an outcome where all primers (57) in the SMA were retained. Comparisons were made by cluster analysis of a data set obtained from RAPD analysis of 46 melon (Cucumis melo L.) accessions that represented economically important market classes. Random elimination of primers was used to simulate the case where exclusion of primers might occur when no previous data on marker efficacy was available. Data suggest that strategic elimination of 17 (30%) or 27 (59%) of the primers in the SMA would result in the misclassification of 2 of 46 accessions (4%) of the accessions in this accession array.