Detection and Distribution of Viruses Infecting Garlic Crops in Australia

The distribution of viruses in eastern Australian field garlic was evaluated. Detection assays were developed that involved generic RT-PCR for viruses in the Allexivirus, Carlavirus and Potyvirus genera followed by virus-specific colorimetric dot-blot hybridization. Assays targeted the potyviruses (onion yellow dwarf virus (OYDV), shallot yellow stripe virus (SYSV), and leek yellow stripe virus (LYSV)), the carlaviruses (garlic common latent virus (GCLV) and shallot latent virus (SLV)), and the allexiviruses (garlic viruses A, B, C, X (GarVA, -B, -C, -X) and shallot virus X (ShVX)). Virus incidence in crops was consistently high, with most plants infected with at least one virus from each genus. OYDV, LYSV, SLV, and GCLV were commonly detected. Three of the four allexiviruses were in all districts surveyed but varied in incidence, whereas ShVX and SYSV were not detected. There was no association between virus species complement and bulb size, indicating size is not a good predictor of the virus status of planting material. The variation of virus incidence across different Australian growing districts and in different cultivars implies multiple introductions of viruses rather than spread within the country. The genetic diversity observed within coat protein sequences of some virus species also supports multiple separate introductions.

Production of Virus-Free Garlic Plants through Somatic Embryogenesis

The present study was conducted to establish a protocol for the regeneration of virus-free garlic plants through somatic embryogenesis of two Croatian garlic ecotypes. Basal parts of cloves from mother plants were cultured on a full Murashige and Skoog (MS) or modified MS medium (¼ of KNO3 and NH4NO3 and 2xMgSO4) containing 0.1 mg L−1 2,4-dichlorophenoxyacetic acid (2,4-D) or 1 mg L−1 2,4-D + 0.5 mg L−1 kinetin (Kin) and representing four different treatments. Plants were regenerated in MS medium containing 0.1 mg L−1 2,4-D and rooted in a medium containing 0.05 mg L−1 1-naphthaleneacetic acid (NAA) + 0.005 mg L−1 6-(γ,γ-dimethylallylamino)purine (2iP). The presence of viruses (i.e., sanitary status) of the mother plants and regenerants was checked by enzyme-linked immunosorbent assay (ELISA) and reverse transcription-polymerase chain reaction (RT-PCR). The mother plants were infected with onion yellow dwarf virus (OYDV) and leek yellow stripe virus (LYSV). In addition, the presence of garlic common latent virus (GCLV) was confirmed in four mother plants. Embryogenic callus developed in all four treatments with success ranging from 55% to 81% depending on treatment and ecotype. Plant conversion was significantly higher in somatic embryos developed in media containing 0.1 mg L−1 2,4-D than those developed in media containing 1 mg L−1 2,4-D + 0.5 mg L−1 Kin. Virus elimination success ranged from 13.3% up to 62.5% depending on garlic ecotype and treatment. The overall rate of virus elimination by somatic embryogenesis for both treatments and ecotypes were 20.7%, 22.9%, and 30.5% for OYDV, GCLV, and LYSV, respectively. Based on these results, somatic embryogenesis has been shown to be equally or more successful in eliminating garlic viruses compared to other in vitro methods.

Phylogenetic and diversity analyses revealed that leek yellow stripe virus population consists of two types: S and N

Leek yellow stripe virus (LYSV, Potyvirus), a pathogen affecting Allium spp. worldwide, has been suspected to consist of two types: S and N, based on genetic and host species differences. In this study, phylogenetic and evolutionary analyses were performed to P1 and CP regions of genome of global LYSV isolates to clarify the variation among members of S-type and N-type. Constructed phylogenetic trees clearly divided isolates into S-type and N-type, with N-type was further split into L and N groups, according to hosts. Significant nucleotide (nt) and amino acids (aa) sequence variation were observed on full ORF, P1, HC-Pro, P3, VPg coding regions. The dN/dS values of P1 and CP confirmed that both genes are under strong negative selection pressure. Neutrality tests on Eastern Asian isolates argued that ancestor of current LYSV isolates may had evolved with garlic while they were in Asia before spread to other world regions through garlic propagative materials. The genetic differentiation and gene flow analysis showed that there was very frequent gene flow from S-type to L and N groups and these phylogroups differentiated from each other over time. Host differences, substantial nt and aa variation, inconsistent serological test results, and phylogenetic and diversity analyses results highly suggested that LYSV can be separated into two types: S and N.

Incidence of viruses in cloves and bulbils of garlic ecotypes in Croatia

In a survey on the sanitary status of garlic collection performed in 2016 at the Institute of Agriculture and Tourism in Poreč (Croatia), 24 ecotypes and cultivars were tested by DAS-ELISA test for the presence of four main garlic viruses: Garlic common latent virus (GCLV), Shallot latent virus (SLV), Leek yellow stripe virus (LYSV) and Onion yellow dwarf virus (OYDV). The least frequent virus was SLV, whereas the most frequent was LYSV. In most ecotypes the infection of cloves was lower than infection of bulbils, while for SLV we found higher infection in cloves. Total virus infection of Istrian ecotypes was lower than infection of Dalmatian ones. Total incidence of viruses in Croatian garlic material ranged from 40.6% to 100.0%, depending on ecotype. In imported cultivar ‘Rose de Lautrec’ we found no infection with SLV. A high percentage of mixed infections in garlic cloves was also found and for double infections it ranged from 69% to 88%. Infection with all tested viruses was observed in 78% cloves. The most infected combination was double infections with potyviruses LYSV+OYDV. To the best of our knowledge, this is the first report of SLV infection in garlic in Croatia.