Diversity Of The Viruses Infecting Pepper In Hainan

Pepper production is a leading agricultural industry in winter of Hainan province, and it’s also a major source of economic income for local farmers. But in recent years, pepper viral diseases have widespread and caused a huge quality decreasing and quantity lossing on pepper in tropical and subtropical regions worldwide. The major viruses on pepper plants is from the genus Potyvirus which the characters of high mutation rates and the strain differentation. To make sure how many the virus species and strains of a specie on Hainan peppers, the investigation of peppr viral diseases, the virus species and the strain diversity of these viruses were conducted.Firstly, in order to fully understand the virus species around the Hainan island, we collected141pepper leaves which are viruses suspected infection between2013and2014. Many viruses were detected by RT-PCR method. The results showed that99pepper samples were infected by five virus species and the viral detection rate is70.2%. The five viruses species are Chilli ringspot virus (ChiRSV), Pepper veinal mottle virus(PVMV), Chilli veinal mottle virus (ChiVMV), Cucumber mosaic virus (CMV) and Pepper mild mottle virus(PMMoV). To data, PVMV was first detected and reported on Hainan peppers by RT-PCR method based on potyviruses degenerated primers.Secondly, in order to deepen insight into the virus species and their damages in Hainan island, the condition of viruses on peppers was further analyzed. The infection rates of ChiRSV, PVMV, ChiVMV, ChiRSV and PVMV is38.4%,36.4%,14.1%,40.4%and37.4%, respectively. Therefore, according to the infection rates, CMV is the dominant virus on Hainan pepper plants because of38.4%infection rate; ChiRSV, PVMV and ChiVMV are also important pathogens that have caused serious problem on pappers of Hainan, especially the PVMV. The co-infection of viruses on peppers were severe in Hainan. Among half of the99viruses infected samples were mix-infected with two viruses or more. The major mix-infected types were ChiRSV+PVMV and CMV+ChiRSV+PVMV.Thirdly, to clarify the strains of each virus specie and there genetic relationships on Hainan pepper plants, we cloned the cp genes of ChiRSV, PVMV and ChiVMV, and a phylogenetic tree of ChiVMV, ChiRSV and PVMV Hainan isolates with other isolates based on cp genes by Maximum Likelihood method were made. The results showed that all ChiVMV isolates can be grouped into four clades, named Group1, Group2, Group3and Group4. Among Hainan isolates, the CP protein nucleotide sequences of ChiVMV shared more than98%identity. All ChiVMVs of Hainan isolates can be defined to one strain and belonged to the Group1; The cp genes of Hainan ChiRSVs can be classified into two subtrees, namely ChiRSV I and ChiRSV II, they have some different cp gene sequnces, they shared high nucleotide identity amog themselves, but the nucleotide and amino acid sequences between the two subtrees shared91.6%to100%,92.9%to100%identity, respectively. So, ChiRSV Hainan isolates can be grouped into two strains,called ChiRSV I groups and ChiRSV II groups for now; The cp genes of PVMV Hainan isolates shared high nucleotide among themselves, more than98%identity. PVMV can be considered one strains in Hainan, named PVMV Asia Group.Fourthly, to clear the VPg gene differentiation of potyviruses, we cloned the VPg genes of ChiVMV, ChiRSV and PVMV, then a phylogenetic tree of ChiVMV, ChiRSV and PVMV Hainan isolates with other isolates based on VPg genes by Maximum Likelihood method were made by analysing the sequnces characteristics of VPg genes, respectively. The results show that the VPg nucleotide sequences of ChiVMV Hainan isolates shared more than98%identity, the VPg nucleotide sequences of PVMV Hainan isolates shared97.9%to100%identity, but the VPg genes of ChiRSV Hainan isolates can be classified into two subtrees which have some different VPg gene sequnces, named ChiRSV a group and ChiRSV b group, they shared high nucleotide identity amog themselves, but the nucleotide and amino acid sequences between ChiRSV a group and ChiRSV b group shared86.6%to100%,92.6%to100%identity, respectively. So, there just existed only one group VPg gene of ChiVMV Hainan isolates with highly conserved sequence, so did PVMV. And the VPg gene of ChiRSV Hainan isolates can be classified into two groups with distinct genetic sequences.This study conducted a research about virus species on Hainan pepper plants, their genetic variation and viral population genetic structures of potyviruses, these polymorphic analysis can help to acknowledge their emerge, epidemic and control characters. It’s also have a important theoretical foundation and significance on anti-virus breeding work.