Characterization of underutilized fruits by molecular markers. A case study of loquat.

The usefulness of RAPD markers for genotyping a minor fruit species such as loquat has been tested in order to assess their ability for identifying accessions and to provide a set of markers suitable for use by different groups of scientists and curators. Twenty-nine polymorphic markers selected from a previous study of 33 accessions were tested in 46 new accessions added to the collection. Using the same PCR standard conditions, only 20 markers out of 29 selected in the previous study gave consistent amplifications in the new set of plant material. The rest required optimization of reaction conditions. This fact pointed out that RAPD markers were sensitive to the experimental conditions, hence a standard technique did not guarantee reproducibility. To overcome this problem markers for plant fingerprinting should be selected after comparison across accession sets. Only those markers reproducible with different sampling and checked in several sets of accessions are suitable for germplasm fingerprinting. In the present study we propose 31 RAPDs for fingerprinting loquat that accomplished these characteristics. The markers obtained were sufficient for determining origin and relationships of cultivars, for identifying synonyms and derived varieties from bud-sports. All bud sports were identical for all RAPDs selected.