PHÂN TÍCH TRÌNH TỰ PHÂN ĐOẠN S10 CỦA CÁC CHỦNG VIRUS GÂY BỆNH LÚA LÙN SỌC ĐEN Ở VIỆT NAM

A total of 13 typical black-streaked dwarf rice disease samples representing ecological zones in Vietnam were subjected for viral total dsRNA isolation using cellulose CF11 column. Analysis of extracted dsRNAs revealed 7 linear segments, which were similar to the electrophoretic profile of Southern black-streaked dwarf virus (SRBSDV). RT-PCR using primer pairs matched to both 3’ and 5’ ends sequence of S10 segment of China isolates (EU523360, EU784840) resulted in amplification of S10 segment cDNA products. RT-PCR products were cloned into pJET1.2 vector using CloneJET™ PCR Cloning Kit and the complete nucleotide sequence of S10 segments were obtained by automatic sequencer. Blast searches indicated that these S10 segments shares 98 - 99% nucleotide identities with S10 sequence of SRBSDV in Genebank (EU784840.1). Using BioEdit, Blast, Clustal2.1, MEGA5.1 softwares for phylogenetic trees based on Vietnam and China S10 nucleotide sequences showed that the viral isolates of Vietnam and China are divided at least into three distinct groups with boostrap value of 99%. Among Vietnamese isolates, group 1 consists of 4 samples collected in the Red River Delta (Nam Dinh, Ninh Binh, Thai Binh) and 2 samples collected in the northern mountainous provinces (Son La, Lao Cai); group 2 consists of 4 samples collected in central region (Quang Tri, Hue), 1 sample collected in Son La and 1 sample collected in the Thai Binh; Group 3 consists of only one sample collected in Nghe An.