Modern Applied Science; Vol. 10, No. 4; 2016 ISSN 1913-1844 E-ISSN 1913-1852 Published by Canadian Center of Science and Education 137 Characterization and Genetic Variation of Sugarcane Streak Mosaic Virus, a Poacevirus Infecting Sugarcane in Thailand Paweena Kasemsin 1,2 , Pissawan Chiemsombat 3 & Ratchanee Hongprayoon 1,2,3 1 Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140 Thailand 2 Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok, Thailand 3 Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, Thailand Correspondence: Pissawan Chiemsombat, Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand. Tel: 6681-4132-222. E-mail: agrpwc@ku.ac.th Received: October 23, 2015 Accepted: December 23, 2015 Online Published: February 2, 2016 doi:10.5539/mas.v10n4p137 URL: http://dx.doi.org/10.5539/mas.v10n4p137 Abstract Sugarcane leaves showing yellow streak mosaic symptoms were observed in farmers’ fields in Kamphaeng Saen, Nakhon Pathom province, during disease surveys conducted in 2010. Diagnosis of symptomatic leaf samples by RT-PCR for Sugarcane mosaic potyvirus failed, but it revealed the presence of Sugarcane streak mosaic virus (SCSMV). SCSMV-infected sugarcane, designated as THA-NP3, was subjected to RNA extraction and RT-PCR-based viral gene cloning and sequencing. The complete genome of THA-NP3 (JN163911) contained 9,781 nucleotides, excluding 3′ poly (A) tail which encoded a polyprotein of 3,130 amino acid residues. Protein sequence analysis indicated nine putative cleavage sites that yielded ten functional proteins namely P1, HC-Pro, P3, 6K1, CI, 6K2, NIa-VPg, NIa-Pro, NIb and CP, and an additional frameshifted PIPO protein. Sequence alignment revealed that THA-NP3 shared 97.84% nucleotide identity with JP2 from China and 81.39-97.78% identities to other recorded SCSMV sequences. Surveys for streak mosaic disease were conducted from 2010 to 2014 at major sugarcane growing areas in five provinces, Nakhon Pathom, Kanchanaburi, Nakhon Ratchasima, Khon Kaen and Udon Thani, and among germplasm collections. The percentages of the infected samples ranged from 43.48-90.91% and 54.17-100% in collected farmers and germplasm fields, respectively. Genetic diversity based on coat protein (CP) coding sequences of 58 Thai SCSMV isolates showed 86.17-100% nucleotide identities among them and 85.70-99.29% identities to isolates from other countries. Phylogenetic analysis of CP sequences indicated two major clusters of virus variants, one in cropping fields and another in germplasm fields. Genetic variations of SCSMV isolates were consistently indicated according to recombination events detected in CP coding regions. These findings represent essential knowledge and should be utilized to improve the SCSMV resistance of sugarcane varieties. Keywords: Sugarcane streak mosaic virus, Potyviridae, Poacevirus, polyprotein, coat protein sequence 1. Introduction Sugarcane (Saccharum officinarum L.) is a valuable crop for the sugar industry and is widely cultivated in Brazil, India, China, Thailand and Pakistan. In Thailand, it is largely cultivated in central, western and northeastern areas such as Nakhon Sawan, Kanchanaburi, Nakon Ratchasima, Khon Kaen and Udon Thani provinces. The major commercial sugarcane varieties cultivated in Thailand include LK92-11, K76-4, K84-200, UT1, UT3, UT8, SP50 and KK3 (Thongpaiyai, Wongpraneekul, & Chatwachirawong, 2012). Major constraints of sugarcane production in Thailand are sugarcane white leaf disease caused by phytoplasma, sugarcane red rot disease caused by Colletotrichum falcatum, and mosaic disease caused by Sugarcane mosaic virus (SCMV). During surveys conducted from 2002 to 2004, the diagnosis of symptomatic sugarcane plants showing mosaic, yellow streak, chlorotic or necrotic streak, chlorotic mild mottle or mild mosaic revealed the presence of SCMV in many sugarcane production fields (Gemechu, 2004). In 2005, a distinct virus species, namely Sugarcane streak mosaic virus (SCSMV) was detected in sugarcane and sorghum plants which showed typical mosaic symptoms as those caused by SCMV but failed to react with the antisera against SCMV, SrMV and JGMV (Chatenet et al., 2005).