Unraveling Shallot Viral Diversity: PCR Detection and In Vitro Culture

Shallot (Allium cepa var. aggregatum) is an annual herbaceous plant of the Amaryllidaceae family cultivated worldwide for its gastronomic importance, unique flavour, and nutritional properties. In Ecuador, shallot is considered an emerging crop; however, the lack of effective detection and treatment options for phytoviruses remains a challenge for farmers. These viruses negatively impact crop yield, leading to substantial economic losses and declining crop quality. Simultaneous infections can synergistically exacerbate crop damage. In this study, the molecular detection of the five most common shallot viruses—Shallot latent virus (SLV), Onion yellow dwarf virus (OYDV), Shallot virus X (ShVX), Leek yellow stripe virus (LYSV), and Iris yellow spot virus (IYSV)—were investigated in shallots obtained from different market suppliers in Quito, Ecuador. We identified two viruses using RT-PCR: SLV (latent) and IYSV (responsible for severe disease symptoms). Shoot tip culture produced shallot plants completely free of IYSV, while SLV persisted in the regenerated plants. This study reports IYSV for the first time in shallots in Ecuador and shows that shoot tip culture can serve as a partial cleaning method to improve crop quality and support more effective pathogen management and control strategies.