Occurrence,Distribution,and Population Genetic Evolution Analysis Of Viruses Causing Sugarcane Mosaic Diseases In China

Mosaic is one of the most important diseases of sugarcane,which is caused by single or compound pathogenesis of sugarcane mosaic virus(SCMV;genus Potyviruses),sorghum mosaic virus(Sr MV;genus Potyviruses),sugarcane streak mosaic virus(SCSMV;genus Poacevirus)under the family Potyviridae,and maize yellow mosaic virus(Ma YMV;genus Polerovirus)under the family Solemovirida).In this study,a total of 901 sugarcane leaf samples exhibiting diverse mosaic symptoms were collected from 24 counties and cities in eight provinces of China.Four sets of specific primers were used to detect the four viruses by RT-PCR.In addition,RT-PCR fragment sequences of four virus samples were cloned,including 132 SCMV-CP,265 Sr MV-CP fragments,86SCSMV-CP fragments,and 38 ORF2-3 fragments of Ma YMV.Moreover,three full-length genome sequences(5642 bp)of Ma YMV were also cloned.Based on sequences obtained in this study and reference sequences downloaded from Gen Bank database,the genetic diversity and population genetic evolution of the four viruses were systematically analyzed.The results are obtained as below:Among 901 samples,viral detection rates revealed by RT-PCR were:81.1% for either of four viruses,70.1% for Sr MV,33.4% for SCMV,30.3%for SCSMV,and 5.1% for Ma YMV.The mixed infection rate of two or more than two viruses was up to 52.2%.Sr MV was dominant in Saccharum spp.hybrid with the infection rate of 72.3%,while SCMV was dominant in S.officinarum with the infection rate of 77.4%.Sequence analysis showed that the nucleotide sequence identities were66.2-100% for SCMV CP,71.3-100% for Sr MV CP,88.3-100% for SCSMV CP,and 94.1-100% for Ma YMV genomic sequences,suggesting high genetic variation in each viruses.Recombination analysis showed that potential recombination events occurred in SCMV(2),Sr MV(1),and Ma YMV(7).Phylogenetic analysis showed that 217 SCMV isolates were divided into five evolutionary groups;306 Sr MV isolates were divided into twelve evolutionary groups;119 SCSMV isolates were divided into six evolutionary groups.In addition,based on 82 fragments or 46full-length genome sequences,Ma YMV isolates were divided into three evolutionary groups,i.e.,Chinese group,African group,and South American group.Neutral test analysis showed that the four virus populations were the neutral evolution model.Selection pressure analysis demonstrated that SCMV,Sr MV,and SCSMV underwent the negative selection,and Ma YMV were under the negative selection for all genes except for MP.Genetic differentiation and gene flow analysis showed that host isolation was main evolutionary factors for forming SCMV population structure,while geographical isolation were the main evolutionary factors for Sr MV and Ma YMV population structures.However,the two evolutionary factors were not associated with SCSMV population structure.Among 46 full-length Ma YMV genome sequences,low diversity was found in ORF0,ORF3,and ORF4 sequences,while high variation was observed in ORF1 and ORF5 sequences.In conclusion,this study systematically demonstrated that occurrence and distribution of four viruses causing sugarcane mosaic diseases in China,and furthermore analyzed the molecular variation and evolution mechanism of the four viruses,which enriched the genetic evolution information of them in the world,and provided reference for the prevention and control of sugarcane mosaic disease in China.