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Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
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Estimating virus effective population size and selection without neutral markers.

Elsa Rousseau1,2,3, Benoît Moury3, Ludovic Mailleret1,2

  • 1Université Côte d'Azur, Inria, INRA, CNRS, UPMC Univ Paris 06, Biocore team, Sophia Antipolis, France.

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|November 21, 2017
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Summary

Researchers combined high-throughput sequencing and experimental evolution to study Potato virus Y (PVY) evolution in pepper plants. They found virus effective population size is a heritable trait, offering a new strategy for breeding plant varieties that slow virus adaptation.

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Area of Science:

  • Evolutionary biology
  • Plant pathology
  • Virology

Background:

  • High-throughput sequencing (HTS) and experimental evolution allow observation of pathogen variant dynamics within hosts.
  • Understanding virus evolution is crucial for managing plant diseases and agricultural productivity.

Purpose of the Study:

  • To investigate the evolutionary dynamics of Potato virus Y (PVY) variants within different pepper genotypes.
  • To develop and validate a method for estimating selection and genetic drift in multi-allelic pathogen populations.
  • To explore the heritability of virus effective population size and its implications for disease management.

Main Methods:

  • Experimental evolution of five PVY variants in 15 doubled-haploid pepper lines.
  • Variant frequency determination using HTS across multiple sampling dates and host genotypes.
  • Development and validation of a Wright-Fisher model to estimate selection and effective population size (Ne).

Main Results:

  • PVY variants experienced diverse selection and genetic drift regimes across different pepper host genotypes.
  • Variant dynamics were accurately modeled using Wright-Fisher models, with consistent variant fitness ranks across hosts.
  • Virus effective population size (Ne) dynamics varied significantly, often showing a bottleneck during systemic movement.
  • Virus effective population size was demonstrated to be a heritable trait in plants.

Conclusions:

  • Plant breeding strategies can be developed to manipulate virus effective population size, thereby slowing virus adaptation.
  • The developed method provides a robust framework for analyzing pathogen evolution under selection and drift.
  • Findings offer insights into host-pathogen interactions and potential avenues for durable disease resistance in crops.