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.
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