Investigation of the basis behind selection of superior and inferior garlic lines from uniformly virus-infected cultivars

Viruses infecting garlic and shallot are economically important in many countries, including Australia and Indonesia. These viruses are transmitted through planting material and by insect vectors. Infected planting material is the primary source of inoculum, as garlic and shallot are vegetatively propagated by farmers. Worldwide, garlic is infected by a complex of viruses, including potyviruses, carlaviruses and allexiviruses, and the majority have been identified on garlic in Australia. Chronically infected garlic plants show symptoms of yellow stripes, mosaic, stem lesions, and leaf deformation. The objective of this study was to investigate why inferior and superior lines of garlic can be selected and maintained from a uniformly, chronically-infected garlic crop and whether improvements are associated with the loss of one or more viruses. As an indexing tool, ten virus-specific PCR primer pairs for the main viruses infecting garlic in Australia have been developed. Field trials were conducted in two successive seasons, in which the second trial was planted with cloves that derived from either mildly or severely diseased plants in the first trial. Second-generation plants from severely diseased plants had significantly lower yields than those from mildly diseased plants. The severe-disease phenotype was highly heritable, although there were some reversions, mild to severe and severe to mild. No consistent association was found between the severity of disease symptoms and the profile of viruses but there were some instances where a virus species was lost during the vegetative propagation process. We speculate that differences in disease severity may related to differences in virus titre, which may be associated with RNAi silencing mechanisms. During the course of virus indexing, we detected garlic virus E in some plants, which is the first detection of this allexivirus in Australia