A size-fractionated library of Brassica napus L. (rapeseed), composed of 15000 clones, was screened for the presence of GA-, CA-, and GATA-simple-sequence repeats (SSRs). GA-SSRs were four- and five-fold more abundant than CA- and GATA-SSRs, respectively, and present at a frequency of approximately one SSR for every 100 kb of DNA. Following the sequencing of 124 positive clones, primer pairs were designed and evaluated for seven selected SSRs. Products were amplified in an array of individuals of B. napus, B. oleracea and B. rapa, demonstrating that the seven SSRs were conserved among species. Two SSRs were polymorphic. Among 11 accessions, the dinucleotide (GA)-repeat, B.n.9A, yielded 12 fragments, while the tetranucleotide-repeat (GATA), B.n.6A2, revealed two fragments. Automated, fluorescence-based detection of polyacrylamide gels has been employed to simultaneously increase throughput, reduce unit cost, improve analytical resolution, and expedite data acquisition of SSR analysis. Though initial financial investment and technical capabilities may prevent some from directly employing our documented approach, SSR analysis warrants further investigation as a tool in genetic studies for enhancing both the conservation and utilization of genetic resources.

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Because (i) origins and genealogies of vetiver grass have been poorly documented, and (ii) morphological uniformity and infrequent flowering precluded accurate identification of selected clones, an investigation was undertaken to link molecular methods with rigorous biometric analysis to discriminate accessions and clones. Successful DNA profiling is highly dependent on the reproducibility of the assay. Our ability to generate consistent results may have been a result of (i) genomic DNA quality, (ii) rigorous oligonucleotide primer selection, and (ill) DNA amplification protocol stringency. Because of the low level of replicate variability, we were able to bring a high level of resolution to the analysis of identity. Though genetic redundancy may be more difficult to establish than genetic uniqueness, the data support with a high degree of certainty that the accessions ‘Huffman’ and ‘Boucard’ were essentially the same genotype. A contrasting case to the Huffman‐Boucard example was found among the putative clones of ‘PI 196257’. Our analysis indicated that each clone of PI 196257 was genetically unique.

Simple-sequence repeats (SSRs) are efficient and informative DNA markers with great potential for germplasm characterization. When used to characterize large arrays of accessions, such as the core subset of the USDA/ARS Malus collection, SSRs may be more effective than other approaches, such as restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD). For example, SSRs can be PCR-amplified and fluorescence-based detected; they also appear to be abundantly disbursed throughout plant genomes and yield abundant polymorphisms in most taxa studied. We are conducting an extensive screening of a size-fractionated library of Malus ×domestica cv. Golden Delicious to identify and characterize selected SSR loci. We are applying genetic information revealed by SSR loci in combination with passport and horticultural data to better comprehend genetic identity and relatedness in Malus germplasm collections and help develop the Malus core subset. Ultimately, application of molecular marker data will permit improved conservation and use of genetic resources.