DNA profiling of fresh and processed fruits in pear

A DNA profiling method was developed for fresh and processed fruits in pear. Four different DNA extraction methods were examined to isolate genomic DNAs from fresh pear fruits, i.e., CTAB-based method and methods based on 3 kinds of DNA extraction kits (DNeasy Plant Mini Kit, G2 buffer & Genomic-tip20/G, Nucleon Phytopure Plant DNA Extraction Kit). All the methods enabled to recover genomic DNAs from samples of fresh fruits with such a high quality that cultivar identification could be performed based on SSR markers. Among them, the G2 buffer & Genomic-tip20/G method gave the best results for samples of fresh as well as processed fruits. Partially degraded genomic DNAs that were isolated from samples of dried fruits could be amplified by all the tested SSR markers. SSR analysis revealed that genotypes from dried fruits were identical with those of the European pear cultivar 'Bartlett', indicating that cultivar identification could be successfully performed. Severely degraded genomic DNAs less than 500 bp in size were recovered from samples of canned fruits and fruit juice. The amount and quality of the extracted DNAs were sufficient to enable amplification by primers corresponding to high copy rDNA sequences, whereas no bands were produced by primers of chloroplast DNA sequences. Out of 15 SSR loci, 9 SSRs with target sequences less than 150-160 bp could successfully amplify fragments for genomic DNAs from samples of canned fruits and fruit juice. In contrast, no amplified fragments were observed for the remaining 6 SSRs with longer target sequences. DNA profiling and cultivar identification were successfully performed by using SSR markers to amplify short target sequences less than 150 bp.