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

Abstract

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.

Occurrence of leek yellow stripe virus and onion yellow dwarf virus from edible Allium plants in the south Marmara region of Turkey

“…It is thought that twothirds of the collected samples were not infected with the viruses in question and were instead infected with other viral diseases that affect Allium plants. Furthermore, Alliaceae plants are frequently reported to be infected with carlavirus, allexivirus, and phytoplasma infections in addition to potyvirus infections (Wylie et al 2012;Abraham et al 2019). In particular, the fact that the virus entities in question cannot be identified in any of the collected onion samples supports the idea that the observed symptoms may be caused by infections of other viruses and virus-like diseases (Baghalian et al 2010;Gupta et al 2017).…”

“…Among these phytopathogens, viruses are of particular importance because they do not respond to chemical control and cause significant yield losses. Studies conducted worldwide have reported frequent infections of potyvirus species in addition to infections caused by tospovirus, carlavirus, and allexivirus species in leek, garlic, and onion cultivation (Dovas et al 2001;Katis et al 2012;Taglienti et al 2018;Abraham et al 2019).…”

“…Members of the potyvirus genus cause significant losses among plants of the Allium genus (Lot et al 1998). Leek yellow stripe and onion yellow dwarf viruses (LYSV and OYDV, respectively), the two viruses first characterized among this group of viruses, have been reported to be frequently observed in areas in which these plants are cultivated (Winiarczyk et al 2014;Fernández-Tabanera et al 2018;Abraham et al 2019). Therefore, LYSV and OYDV are the two most important plant pathogens of the potyvirus genus, causing economic losses in plants of the Allium genus.…”

Efficient Elimination of Viruses from Garlic Using a Combination of Shoot Meristem Culture, Thermotherapy, and Chemical Treatment

“…Numerous viruses can infect garlic through different modes of transmission. Garlic can be infected by viruses of various genera, including Potyviruses such as Onion yellow dwarf virus (OYDV), Leek yellow stripe virus (LYSV), and Shallot yellow stripe virus; Carlaviruses such as Garlic common latent virus (GCLV) and Shallot latent virus (SLV); Tospovirus (Iris yellow spot virus, IYSV), and Allexiviruses (Garlic virus-A, Garlic virus-B, Garlic virus-C, Garlic virus-D, Garlic virus-E, and Garlic virus-X) [ 9 , 10 , 11 , 12 , 13 ]. Generally, under field conditions, garlic is infected by multiple viruses, known as the virus complex, which severely reduces the crop yield [ 14 , 15 , 16 ].…”

Molecular characterization of the coat protein gene revealed considerable diversity of viral species complex in Garlic (Allium sativumL.)

“…Furthermore, almost all garlic production systems of Ethiopia used bulbs as a planting material which raises a concern about the presence of considerable diversity of garlic viral species complex. However, so far very little is known on identification, diversity and dissemination of garlic infecting viruses in the country [26][27][28][29]. In order to address this problem, a comprehensive study to evaluate the prevalence and characterization of the viruses existing at the moment in the country is inevitable.…”