Genetic Bottlenecks Reduce Population Variation in an Experimental RNA Virus Population

Abstract

Genetic bottlenecks are stochastic events that limit genetic variation in a population and result in founding populations that can lead to genetic drift. Evidence of past genetic bottlenecks in numerous biological systems, from mammals to viruses, has been described. In this study, we used an artificial population of Cucumber mosaic virus consisting of 12 restriction enzyme marker-bearing mutants. This population was inoculated onto young leaves of tobacco plants and monitored throughout the course of systemic infection. We show here that the genetic variation in a defined population of an RNA virus is significantly, stochastically, and reproducibly reduced during the systemic infection process, providing clear evidence of a genetic bottleneck.Populations generate genetic variation over time, which can be specifically reduced by selection or stochastically reduced by genetic bottlenecks. After a bottleneck, a limited number of randomly selected individuals create a founding population, resulting in genetic drift. The occurrence of bottlenecks in nature has been inferred from the low genetic diversity of extant populations and extrapolation of an historical event (reviewed in reference 1).Genetic bottlenecks may occur frequently during the natural life cycles of RNA viruses. Transmission events, both horizontal and vertical, and systemic infections represent events in the virus life cycle that may impose a bottleneck. A few studies of plant viruses have attempted to estimate the effect of bottlenecks by examining diversity in populations from systemically infected tissues (18,40). In addition, a number of studies of animal and bacterial viruses have examined changes in the population structure after passage through artificial bottlenecks (4, 7, 32, 49), but naturally occurring bottlenecks have been poorly studied.RNA viruses are characterized by the potential for a high degree of variability due to short generation times and errorprone replication (reviewed in reference 11), leading to populations known as quasispecies (14,15). In spite of this potential, quasispecies variation in experimental evolution studies with plant viruses was significantly lower than what might be predicted (42).Low genetic diversity may result from low mutation rates. However, a rough estimation of the mutation rate of Tobacco mosaic virus suggested that plant viruses were not significantly different from animal RNA viruses (27). Selection (predominantly negative) for maintaining a functional encoded protein or functional RNA structure is believed to play an important role in the elimination of deleterious variants (20,34,36). Population bottlenecks during transmission might also be an important factor for limiting the variation in a population. This phenomenon was implicated in some laboratory passage experiments (2, 23, 25) as well as some analyses of natural plant virus populations (3, 6, 17). However, there hasn't been any direct experimental evidence showing that naturally occurring bottlenecks play a role in the genetic structure o...

Estimation of the number of virus particles transmitted by an insect vector

“…The decrease of the number of CMV variants detected in inoculated plants evidenced the bottleneck effect of aphids during virus transmission. However, it seems difficult from these experiments to untangle the bottleneck effect of aphids during transmission from the bottleneck effect during plant invasion, which was shown to be quite severe (15)(16)(17). In contrast, our analysis of the bottleneck effect exerted by aphids was not based on the loss of richness of virus populations between the inoculum and the inoculated plants, but on the competition between two virus variants, one of them being noninfectious (avirulent).…”

Evaluation of potential risks associated with recombination in transgenic plants expressing viral sequences

“…In any case, in addition to exclusion from the transgene of the 39 NCR, there is an additional feature of the virus cycle that would further reduce the likelihood of emergence of rare recombinants, even if their intrinsic fitness were high. This is the presence of at least two narrow population bottlenecks, one at the stage of systemic movement of the virus and the other at vector transmission, which will strongly favour the most abundant RNAs (Ali et al, 2006;Li & Roossinck, 2004).…”

Inhibition of Tobacco Mosaic Virus Movement by Expression of an Actin-Binding Protein

“…These effects of LatB on ER-mediated transport have the potential to reduce the number of virus genomes that spread between cells over time. However, because the number of transported genomes is usually not a limiting factor in the spread of infection (Sacristan et al, 2003;Li and Roossinck, 2004), the effects of LatB do not necessarily translate into an obvious effect at the level of infection sites. Thus, even though we did not observe an effect of LatB treatment on the spread of infection in N. benthamiana leaf tissues under our conditions, we do not exclude the possibility that a potential reduction in the number of transported virus genomes may represent a critical factor for infection in other hosts or tissues.…”