Detection and identification of viruses infecting onion crops in Bantul District, Yogyakarta

Abstract

Swari FSP, Subandiyah S, Hartono S. 2015. Detection and identification of viruses infecting shallot crops in Bantul District, Yogyakarta. Pros Sem Nas Masy Biodiv Indon 1: 961-968. Onion (Allium cepa var. aggregatum) is a horticultural commodity having important values for Indonesian people like fresh food, seasoning, natural flavoring, and herbal medicine. It is commonly seen that the increasing demand for onion has not been balanced with production, which is often lead to supply shortage and price fluctuation in the market. So far farmers assume that low productivity of onion is caused by severe attacks of armyworms, fungi, or bacteria. As a result, the reduction of quality and yield of shallot due to viral infection has not received sufficient attention, especially in Bantul which is the major shallot production area in the special region of Yogyakarta. The aims of this study were to determine the infection rate of Potyvirus, Carlavirus, and Allexivirus in shallot crops in Bantul and to identify viruses infecting shallot cultivars which are planted in wet and dry seasons in 2014. The molecular assessment was executed on 100 shallot leaf sample at Clinical Laboratory of Plant Disease, Faculty of Agriculture, Gadjah Mada University, Yogyakarta. Leaf samples were collected randomly from 10 fields in Kretek, Sanden, Imogiri, and Jetis, four districts of Bantul Regency. The results showed that the samples of Biru, Crok, Tiron, Bauji, and local Parangkusumo cultivars were infected with Carlavirus and Potyvirus. Crok was the most susceptible cultivar, while Biru was relatively tolerant to viral infection. Infection of Allexivirus was only found in local Parangkusumo cultivar in the dry season with the lowest rate of infection, 2%. Carlavirus was more dominant than Allexivirus and Potyvirus. The infection rate of Carlavirus and Potyvirus in the wet season, 78% and 62% respectively, which is higher than dry season, 60% and 46%. Based on the results of nucleotide sequencing and phylogenetic analysis, detected virus isolates in Bantul were Shallot Yellow Stripe Virus (SYSV) and Onion Yellow Dwarf Virus (OYDV), under the genus of Potyvirus, and Shallot latent virus (SLV), under the genus of Carlavirus.