A study of the strain evolution and recombination of South African isolates of Potato virus Y

[摘要] ENGLISH ABSTRACT:Potato virus Y (PVY) is responsible for considerable yield losses in the South African potato industry.The incidence of this virus has greatly increased over the past 20 years. In previous studies nonrecombinantstrains of PVY, PVY N and PVY O, were detected in South African potatoes. In a recent studythe occurrence of non-recombinant strains of PVY in South African potatoes was shown to havedecreased while infection by more virulent recombinant strains, PVY NTN and PVY N-W, had increaseddramatically. Infection of potato plants with PVY may cause stunted growth and mosaic or necrotic leafsymptoms which in turn can lead to a significant reduction in yield. Highly virulent recombinant PVYisolates as well as some of the non-recombinant strains may cause potato tuber necrotic ringspot disease(PTNRD) which may result in losses of 10% to total crop failure. For this reason investigation ofinfection by local recombinant isolates on local cultivars was important. To this end a representativenumber of isolates were selected for whole genome sequencing based on the relative occurrence of thevarious isolates in South Africa. A number of these sequenced isolates were subsequently used to infectlocal cultivars of potato in order to investigate the influence of genetic variation within the viral genomeon symptom expression.In this study 27 South African isolates of PVY were sequenced through overlapping RT-PCR fragments.Seven of these isolates, six PVY NTN and one PVY N-W, were used to mechanically infect four localcultivars of potatoes under greenhouse conditions. The infected plants were monitored to establish therate of systemic spread using a highly sensitive qRT-PCR and resulting tubers were visually screened forPTNRD. Highly variable recombinant isolates appear to be less virulent than the more conservedrecombinant isolates possibly indicating molecular determinants for pathogenicity. For this reason theamino acid sequences of the South African isolates were compared to those of international isolates andscrutinized for variation and substitutions. Some South African isolates displayed amino acidsubstitutions unique to the specific isolate, making them unlike those found internationally. Substitutionrates throughout the amino acid sequences differed greatly, with some isolates displaying hardly anychanges whilst others varied a great deal from overseas isolates. Certain regions, many of which hadspecific functions, were more conserved than others.This study further investigated the recombination events within the PVY genome using reticulatephylogenetic analysis, molecular dating and network construction techniques. Unlike existing approaches,the one described in this study neither assumes an underlying strictly bifurcating species tree nor assumesprior knowledge of processes underlying deviations between individual gene trees. Through the use of theresulting robust time calibrated phylogeny, the patterns of diversification and recombination in PVY maybe placed in the historical context of human cultivation of potatoes. Through the use of these techniquesthe study aimed to test whether diversification of the major strains of PVY and recombination betweenthem occurred within the time frame of the domestication and modern cultivation of potatoes. From theseanalyses it can be deduced that recombinant strains of PVY were imported into South Africa.

[发布机构] Stellenbosch University