Molecular identification, incidence and phylogenetic analysis of seven viruses infecting garlic in Ethiopia

Little information exists on the type and incidence of viruses infecting garlic ( Allium sativum L ) in Ethiopia. Attempts were made to identify the viruses using molecular techniques from 95 composite leaf samples collected from 44 farmers’ fields and 51 germplasm accessions. Reverse transcription (RT-) PCR using genus and/or virus specific primers was used to amplify partial genome sequences of potyviruses, allexiviruses, carlaviruses and a tospovirus followed by sequencing of PCR products. Results indicated that ~73.7% of the samples are infected with at least one virus. Onion yellow dwarf virus (OYDV, genus Potyvirus , family Potyviridae ) is the most common virus detected followed by Garlic virus C (genus Allexivirus ) and Shallot latent virus (SLV, genus Carlavirus ). Other viruses detected at lower frequency include Garlic virus X and Garlic virus D (genus Allexivirus ), Leek yellow stripe virus (genus Potyvirus ) and Iris yellow spot virus (IYSV , genus Tospovirus ). Mixed infection of two or more viruses was detected in 65.7% of the samples. Phylogenetic analysis suggested that the different viruses may have been introduced to Ethiopia from Europe or Asia. This is the first report of Garlic virus X , Garlic virus D , IYSV and SLV in garlic in Ethiopia. The high incidence of OYDV and IYSV which cause severe yield loss alone or in mixed infection with allexiviruses and carlaviruses is a cause of concern to growers.