Genetic Structure Of Sugarcane Mosaic Virus Populations

Sugarcane mosaic virus (SCMV) is the most prevalent virus causing maize dwarf mosaic disease in northern China. In this study, we made a three years follow-up survey of maize dwarf mosaic disease from2009to2011. The virus strains causing maize dwarf mosaic in China were classified and their genetic structure was analyzed.A SCMV isolate, BD8, was obtained from the maize showing dwarf and mosaic symptoms in Baoding, China. The complete genomic sequence of BD8is9576nucleotides (nt) excluding the poly(A) tail. It contains one single open reading frame of9,192nt and encodes a large polyprotein of3,063amino acids (aa), flanked by a5’-untranslated region (UTR) of148nt and a3’-UTR of236nt. The entire genomic sequence of BD8shares identities of79.1%～80.8%with those of other13SCMV isolates available in the GenBank at nt level, while their CP genes share identities of76.9%～82.6%and82.8%～86.9%at nt and aa levels, respectively. Phylogenetic analysis of the complete genomic sequences reveals that SCMV can be clustered to four groups:group Ⅰ includes isolates from maize, group Ⅱ consists of isolates from sugarcane or maize, groups Ⅲ and Ⅳ contain single isolate of AU-A (AJ278405) and BD8, respectively. Thus, BD8represents a new strain of SCMV. Furthermore analysis of the CP gene sequences of more isolates shows that BD8is clustered to a group with the isolates from Thailand and Vietnam, which implies that isolates of this strain have been distributed in South Asia. In the greenhouse, BD8can cause severe symptom in all the20maize varieties tested with high incidence, indicating that BD8is highly virulent.In the year2010and2011, we collected51SCMV isolates from Hebei, He’nan, Shandong, Shanxi and Shaanxi and subsequently sequenced and determined their full length genomic sequences.1) Recombination analysis shows that25isolates were significant recombinants, of which,12recombinants are recombined between groups, and the other13recombinants are recombined within groups.2) Phylogenetic analysis of65complete genomic sequences reveals that SCMV can be clustered to four groups as previous:Ⅰ (maize), Ⅱ (sugarcane/maize), Ⅲ (sugarcane) and Ⅳ (maize), the isolates obtained in this research are mainly clustered into Group Ⅰ and Ⅳ. Furthermore analysis in another phylogenetic tree, constructed based on145CP gene sequences, implies that all the isolates are divided into five groups also as previous:A (MZ group), B (NSCE group), C (MZ/SCE group), D (SCE group) and E (SO group). The group A is the most widespread, but the group C is only found in China and South Asia. In China, all the five groups have existed. Our isolates are mainly clustered into groups A and C.3) Among the eleven genes of SCMV, only the gene NIb is under positive (or diversifing) selection pressure.4) Gene flow among the isolates from Hebei, Shandong and Shanxi is frequent, but that between the isolates respectively from Hebei-Shandong and Shaanxi is not frequent, and significant genetic differences exist between them. There exists frequent gene flow in part of the genomic sequences between the isolates from Shandong and Shaanxi, respectively. In addition, within group C, gene flow between the isolates respectively from China and South Asia is frequent, but not between the isolates respectively from China and abroad China within group A.5) Isolates from China in the group A are in a state of expansion, but those in the group C are in a state of dynamic equilibrium, and have a trend of expansion.