Molecular Identification of Fusarium Solani Sensu Lato And Alternaria Alternata Associated with Pistacia Vera L.: A Critical Review of Markers, Primers and Diagnostic Workflows

Accurate identification of fungi associated with pistachio (Pistacia vera L.) is complicated by two recurring problems: morphologically similar taxa may belong to genetically distinct lineages, and a sequence match from a single barcode may overstate taxonomic certainty. These limitations are particularly relevant to Fusarium solani sensu lato and Alternaria alternata, two names frequently encountered in diagnostic work on diseased pistachio tissues. This critical review re-examines the literature with emphasis on molecular markers, primer choice, sequence interpretation and the distinction between fungal detection and proof of pathogenicity. For the Fusarium solani species complex (FSSC), the internal transcribed spacer (ITS) region is useful for preliminary placement but is often too conserved for reliable species delimitation; translation elongation factor 1-alpha (TEF1-α) and the second largest subunit of RNA polymerase II (RPB2) provide substantially stronger resolution when interpreted against curated reference sequences and phylogenetic trees. For Alternaria section Alternaria, ITS has similar limitations, and multilocus analysis using GAPDH, RPB2, TEF1 and, where useful, Alt a 1 or endopolygalacturonase is more defensible. Pistachio-specific studies provide a comparatively strong molecular precedent for Alternaria late blight, whereas FSSC records in pistachio remain more heterogeneous in marker choice and nomenclature. The review also proposes a practical workflow for isolates from Central Asian pistachio systems and includes original schematic figures for ITS primers, PCR/sequencing workflow and gel interpretation. Molecular identity should ultimately be integrated with morphology and pathogenicity testing; a PCR band or high BLAST identity alone does not establish causal status.

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