Development of a database containing DNA barcodes of the Canadian Aphelenchoides species for accurate identification of the foliar nematodes, Aphelenchoides fragariae

Design and validation of PCR primers for barcoding foliar nematodes in diagnostic testing. Seven PCR primers were tested on 18 nematode specimens to amplify the 5′ third of the ~1600 base pair SSU gene, which contains about 50% of the nucleotide variability of the whole gene. Two primer pairs were reliable and consistently yielded specific and reasonable amounts of PCR product. However, other primer combinations either frequently failed to amplify anything or produced a low yield of PCR product, which was insufficient for DNA sequencing. As a result, the two pairs of primers were validated for barcoding foliar nematodes in diagnostic tests.

Database harboring SSU sequences for Aphelenchoides species. A database was created using Geneious Prime DNA software. Combined with an Excel spreadsheet, the DNA sequences and information of specimens, including host and origin, were well recorded and organized. Overall, this research improved the efficiency and accuracy of diagnostic tests for foliar nematodes, specifically Aphelenchoides fragariae, to support the export certification of Canadian agricultural commodities for international market access.