Experimentally evolved populations of the potato cyst nematode Globodera pallida allow the targeting of genomic footprints of selection due to host adaptation

Abstract

In the current agronomical context of pesticide use reduction, deciphering the genetic bases of pathogen adaptation to plant defences is of major importance to improve durability of resistance. Indeed, knowledge of virulence gene frequencies in pathogen populations could allow the prediction of resistance durability before deployment. Globodera pallida is a major pest of potato crops for which a promising resistance QTL, GpaVvrn, has been identified in Solanum vernei. An experimental evolution study, in which G. pallida lineages evolved on resistant or susceptible potato genotypes for up to eight generations, previously showed that G. pallida was able to rapidly overcome GpaVvrn resistance. However, it was not known if enough genetic mixing occurred in these lineages to be able to detect islands of differentiation in a genome scan approach. Here, this question was investigated using 53 polymorphic microsatellite markers distributed along the genome and three different tests based on genetic differentiation and heterozygosity. Eight outlier loci were identified, indicative of genomic regions putatively involved in host adaptation. Several loci were identified by multiple detection methods and/or in two independent adapted lineages. Some candidate genomic regions identified also seemed to be involved in overcoming resistance to nematodes in a plant genotype harbouring the same resistance QTL in a different genetic background. These results validate the feasibility of a genome scan approach on biological material coming from short experimental evolution, and encourage the use of a high coverage genome scan by whole genome resequencing.