Development of Specific Diagnostic Assays for the Eleven Main Viruses Infecting Garlic (Allium sativum)

Commercially grown garlic is usually infected by complex mixtures of carla-, poty-, and allexiviruses. Specific detection of these viruses is difficult, particularly as some such as the allexiviruses exhibit serological cross-reactivity, and intraspecific nucleic acid sequence diversity is relatively large. While next generation sequencing shows much promise as a diagnostic method, it is not yet widely used for routine virus screening, especially in developing countries. The main objective of this study was to develop reverse transcription (RT)-PCR assays for each of the most common viruses associated with garlic. Primer specificity was examined in silico using sequences available on GenBank. The assays were then validated using virus isolates of known infection status, and application of the assays demonstrated by testing plants representing forty garlic cultivars grown in a major germplasm collection held at a government research station in South-east Queensland.