| Potato virus S is one of the important viruses that infect potatoes,usually showing no symptoms,but it often infects with other viruses and causes serious losses to potato production.In order to understand the distribution and evolution of PVS strains in two potato cropping regions in China(north one cropping region and southwest mixed cropping region),as well as the population genetic characteristics of PVS in the world,in this research,universal primers were designed based on the sequence of the PVS coat protein(CP)published in Gen Bank and a general RT-q PCR system for PVS detection was established;707 field potato samples collected from 11 provinces(municipalities and autonomous regions)from the north one cropping region and southwest mixed cropping region were tested with the established RT-q PCR method,and 250 PVS positive samples were screened out,which were identified for their strains using dual RT-PCR;the CP gene sequences of 82 PVS isolates were determined,and using 40 PVS sequences as reference which were downloaded from Gen Bank,phylogenetic analysis was carried out together with the sequences obtained by sequencing;and 166 PVS sequences from 22 countries in 5 continents in Gen Bank were download,and together with the measured sequences,it was divided into five groups(Asia,Europe,North America,South America,and Oceania)by region,and population genetic analysis was made,including genetic diversity and genetic differentiation,population structure,and the effects of genetic recombination,natural selection,gene flow and genetic drift on population genetics were explored.Results are as follows:(1)A universal system of RT-q PCR for PVS detection was established.There was a good linear relationship between the average cycle number(Cyclethreshold,Ct value)of the standard curve fluorescence signal baseline of the two strains(PVS~O and PVS~A)and the logarithm of PVS virion copy number(determination coefficient R~2=0.9942 and 0.9912).The sensitivity is 100 times higher than that of conventional RT-PCR.The accuracy and practicability were verified by 90 field samples.(2)The two strains of PVS,PVS~Oand PVS~A,occur in the two main potato production regions(north one cropping region and southwest mixed cropping region),with a total detection rate of PVS~A 48.80%,PVS~O 30.80%,and compound infection rate 20.40%.The detection rate of PVS~O in the north one cropping region was high(46.21%),while the detection rate of PVS~A in the southwest mixed cropping region was high(77.14%).The mixed infection rate in the northern one cropping region(25.52%)was higher than that in the southwest mixed cropping region(13.33%).The distribution of PVS~O and PVS~A is different in the two cropping regions.(3)Phylogenetic analysis showed that there were subgroups in PVS~O and PVS~A,and PVS~A and most of PVS~A sequences from China were independent of the reported subgroups.The clustering of PVS isolates from China was,to some extent,related to their geographical sources.(4)The genetic diversity within the five populations was higher(Hd>0.5,Pi>0.005),and there was obvious genetic differentiation among different populations(P<0.005).The analysis of population structure showed that the populations in Asia,Europe and North America were closer in genetic relationship,while South America and Oceania were farther away from them.The recombination analysis showed that there were two recombinant isolates in China,with parents both in China and worldwide,but they were more similar to those from China.The results of natural selection analysis showed that the five populations were mainly negatively selected,but there were positive selection sites,indicating that most of the variation was harmful,but there were also favorable variations accumulated slowly in the process of natural selection.Except for Asia vs South America,and Europe vs Oceania,there are genetic drifts between other eight pairs of populations. |
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