Genetic evolutionary analysis of soybean mosaic virus populationsfrom three geographic locations in China based on the P1 and CPgenes

AbstractSoybean mosaic virus (SMV) is one of the major pathogens causing serious soybean losses. Little is known about thegenetic structure and evolutionary biology of the SMV population in southwestern China. In this study, 29 SMV isolateswere obtained from Sichuan Province, and the genomic regions encoding the first protein (P1) and coat protein (CP)were sequenced. Combined with SMV isolates from the southeastern and northeastern regions of China, the genetic andmolecular evolution of SMV was studied. Recombination analysis revealed that intraspecific and interspecific recombinationhad occurred in the SMV population. A phylogenetic tree based on the P1 gene reflected the geographic origin of thenon-interspecific recombinant SMV (SMV-NI), while a tree based on the CP gene did not. Though frequent gene flow ofthe SMV-NI populations was found between the southeastern and northeastern populations, the southwestern populationwas relatively independent. Genetic differentiation was significant between the SMV interspecific recombinant (SMV-RI)and the non-interspecific recombinant (SMV-NI) populations. It was interesting to note that there was an almost identicalrecombination breakpoint in SMV-RI and Watermelon mosaic virus (WMV). Population dynamics showed that SMV-RImight be in an expanding state, while the SMV-NI population is relatively stable