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Thèse débutée le 1er novembre 2013 - defended in november 23^th 2016

Direction: Eric Grenier et Josselin Montarry

Found: Contrat INRA/Région Bretagne

"Genomics of Globodera pallida adaptation to potato resistances and consequences on life-history traits of the nematode."

Abstract:

The use of resistant cultivar is an ideal to be achieved in the objective of a sustainable agriculture, which is nevertheless limited by the capability of pathogens to breakdown host plant resistances. Improving resistance durability involves to be able to predict the adaptation speed of pathogen populations. Studying their evolutionary potential and assessing the eventuality of adaptation costs are a first step towards this objective, but the identification of the genetic bases of adaptation represents a crucial step to better understand and anticipate resistance breakdown. The cyst nematode Globodera pallida is an important pest of potato crops, for which a major resistance QTL, GpaVvrn, has been identified in Solanum vernei. However, the capability of G. pallida populations to adapt to this resistance in only few generations has been highlighted through experimental evolution. Improvement of knowledge about G. pallida population dynamics and genetics allows to infer their global evolutionary potential, however notions allowing to predict their adaptation speed to GpaVvrn in natural conditions remain limited. The purpose of this study was to improve that knowledge, by exploring two complementary areas in the objective of predicting resistance durability. On the one hand, we studied life-history traits impacted by adaptation in order to test for potential existence of a virulence cost. Unexpectedly, we highlighted that adaptation to resistance from S. vernei leads to an increase of virulent individual’s fitness on susceptible host, thus reinforcing the risk of a weak durability of resistance in field. On the other hand, we have sought to identify genomic regions involved in adaptation, through an original approach combining experimental evolution and genome scans on virulent and avirulent lineages. We were thus able to pinpoint candidate genomic regions to adaptation to host plant resistance, containing genes putatively encoding effectors, and especially SPRYSECs, known in cyst nematodes to be involved in suppression of host defense but also in nematode virulence. Results achieved in this PhD project will ultimately allow to improve knowledge on the genetic determinants of the virulence and to devise molecular tools to follow the frequencies of virulence alleles in G. pallida populations, in the aim of conceiving efficient strategies of use of potato resistant cultivars maximizing their durability.