Double Infection of Onion yellow dwarf virus and Shallot latent virus in Garlic from Several Regions in Indonesia

Viruses have been a problem on garlic cultivations in various countries. There are several viruses reported infecting garlic. Genera Potyvirus and Carlavirus are the most common viruses found infecting garlic. Mixed infection on garlic is often designated as a “garlic viral complex”. These viruses can be transmitted through imported garlic seeds. Therefore, it is necessary to conduct early detection of garlic seeds to prevent the epidemic of these viruses. This study aimed to detect Onion yellow dwarf virus (OYDV) and Shallot latent virus (SLV) on garlic. Garlic samples were obtained from Enrekang, Magelang, Temanggung, Tawangmangu, and Yogyakarta. Total RNA was extracted from the samples and subsequently used for RT-PCR using two pairs of specific primers SLV-F/SLV-R and OYDV-F/OYDV-R. Primary pair SLV-F/SLV-R in amplicons sized 276 bp, while OYDV-F/OYDV-R in amplicons sized 112 bp. RT-PCR results showed that OYDV was found in all samples tested in this study. Meanwhile, double infections (OYDV and SLV) were found in eight out of ten samples tested. These results indicated that double infections on garlic were common in Indonesia.

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.

Characterization of the virome of shallots affected by the shallot mild yellow stripe disease in France

To elucidate the etiology of a new disease on shallot in France, double-stranded RNAs from asymptomatic and symptomatic shallot plants were analyzed by high-throughput sequencing (HTS). Contigs annotation, molecular characterization and phylogenetic analyses revealed the presence in symptomatic plants of a virus complex consisting of shallot virus X (ShVX, Allexivirus), shallot latent virus (SLV, Carlavirus) and two novel viruses belonging to the genera Carlavirus and Potyvirus, for which the names of shallot virus S (ShVS) and shallot mild yellow stripe associated virus (SMYSaV), are proposed. Complete or near complete genomic sequences were obtained for all these agents, revealing divergent isolates of ShVX and SLV. Trials to fulfill Koch’s postulates were pursued but failed to reproduce the symptoms on inoculated shallots, even though the plants were proved to be infected by the four viruses detected by HTS. Replanting of bulbs from SMYSaV-inoculated shallot plants resulted in infected plants, showing that the virus can perpetuate the infection over seasons. A survey analyzing 351 shallot samples over a four years period strongly suggests an association of SMYSaV with the disease symptoms. An analysis of SMYSaV diversity indicates the existence of two clusters of isolates, one of which is largely predominant in the field over years.The sequences reported in the present manuscript have been deposited in the GenBank database under accession numbers MG571549, MH292861, MH389247 to MH389255, and MG910501 to MG910598.

Elimination of shallot bulb viruses through heat treatment

Shallot (Allium cepa L. Aggregatum group) is usually cultivated vegetatively. As a result, viruses tend to accumulate within the host plants and spread to healthy plants every crop cycle, reducing yield and bulb quality. There are a very limited number of studies about the elimination of shallot viruses through heat treatment. The objective of this research was to eliminate shallot viruses through heat treatment to produce virus-free plantlets. The leaves of Biru Lancor with specifc visual virus symptoms were detected by Reverse Transcription–Polymerase Chain Reaction (RT-PCR). Then bulbs of Biru Lancor that were positively infected by viruses were used as materials for heat treatment. The treatments were a control (without treatment), electric treatment at 15 mA for 10 minutes, heat treatment in an incubator at 37°C for 4 weeks, heat treatment in a waterbath at 45°C for 60 minutes, and combination of heat treatment in an incubator at 37°C for 4 weeks and heat treatment in a waterbath at 45°C for 60 minutes. After being subjected to heat treatment, the pseudo stem were cultivated in the MS Medium + 1 mg/L BAP + 1 mg/L IBA.Virus detection by RT-PCR was conducted 28 days after planting using samples of leaves from each plantlet. The results of this research showed that the treatments of electric treatment at 15 mA for 10 minutes and combination of heat treatment in the incubator at 37°C for 4 weeks and heat treatment in the waterbath at 45°C for 60 minutes could suppress the incidence of Shallot latent virus (SLV) until 100%. Heat treatment might have an important role in the degradation of virus particles by boosting Virus-Induced Gene Silencing (VIGS) as plant responses to virus infection.

Distribution of viruses in the shallot germplasm collection of the Czech Republic – Short Communication

The Czech collection of shallot (Allium cepa var. ascalonicum) genetic resources (122 accessions) was surveyed for the presence of four different viruses, i.e. Onion yellow dwarf virus, Leek yellow stripe virus, Garlic common latent virus (GCLV), and Shallot latent virus, by DAS-ELISA. The shallot seems to be resistant against GCLV because none of the tested plants was infested by this virus. Other three viruses were found with an incidence ranging from 53% to 93% for genotypes and 48% to 87% for plants. Most of the tested shallot genotypes were simultaneously infected with two or three viruses. These results were compared with neighbouring collection of garlic where all four viruses were found widespread with an incidence ranging from 65% to 83% for genotypes and 39% to 61% for plants.

Deteksi Virus pada Bawang Merah (Allium cepa var. ascalonicum) dengan Metode Dot Immuno Binding Assay

<p>Bawang merah umumnya diperbanyak secara vegetatif menggunakan umbi. Bibit unggul bawang merah ditentukan<br />antara lain oleh status kesehatan benihnya termasuk bebas dari infeksi virus. Penyakit yang disebabkan oleh virus yang bersifat<br />tular umbi merupakan salah satu kendala dalam meningkatkan produksi bawang merah. Penelitian bertujuan untuk mengetahui<br />jenis-jenis virus terbawa umbi pada beberapa varietas bawang merah yang berasal dari Jawa Tengah (Brebes) dan Jawa Barat<br />(Cirebon, Kuningan, Majalengka, Bandung), yaitu Bima Curut, Bima Brebes, Sumenep, Jawa, Batu Merah, Batu Putih, Nganjuk,<br />Timur Carwan, Ilokos, dan Jalaksana. Deteksi virus dilakukan dengan metode dot immuno binding assay (DIBA) menggunakan<br />antibodi spesifik. Deteksi virus pada umbi bawang dilakukan dengan dua teknik, yaitu deteksi langsung dari umbi dan deteksi daun<br />muda yang diambil dari umbi yang ditumbuhkan selama 30 hari. Hasil deteksi menunjukkan adanya infeksi onion yellow dwarf<br />virus (OYDV), shallot latent virus (SLV), dan garlic common latent virus (GCLV) dengan infeksi tertinggi OYDV dan SLV. Infeksi <br />virus lebih banyak terdeteksi dari sampel daun muda dibandingkan dengan dari sampel umbi. Infeksi virus tertinggi ditemukan pada <br />sampel umbi varietas Nganjuk, Batu Putih, Jawa, dan Sumenep asal Majalengka, Kuningan, dan Bandung.</p>