Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida.

Delphine Eoche-Bosy 1 Matthieu Gautier 2, 3 Magali Esquibet 1 Fabrice Legeai 4, 1 Anthony Bretaudeau 5, 1 Olivier Bouchez 6 Sylvain Fournet 1 Eric Grenier 1 Josselin Montarry 1
4 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
5 Plateforme bioinformatique GenOuest [Rennes]
UR1 - Université de Rennes 1, Plateforme Génomique Santé Biogenouest®, Inria Rennes – Bretagne Atlantique , IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires
Abstract : Improving resistance durability involves to be able to predict the adaptation speed of pathogen populations. Identifying the genetic bases of pathogen adaptation to plant resistances is a useful step to better understand and anticipate this phenomenon. Globodera pallida is a major pest of potato crop for which a resistance QTL, GpaVvrn , has been identified in Solanum vernei. However, its durability is threatened as G. pallida populations are able to adapt to the resistance in few generations. The aim of the present study was to investigate the genomic regions involved in the resistance breakdown by coupling experimental evolution and high-density genome scan. We performed a whole genome resequencing of pools of individuals (Pool-Seq) belonging to G. pallida lineages derived from two independent populations having experimentally evolved on susceptible and resistant potato cultivars. About 1.6 million SNPs were used to perform the genome scan using a recent model testing for adaptive differentiation and association to population-specific covariables. We identified 275 outliers and 31 of them, which also showed a significant reduction of diversity in adapted lineages, were investigated for their genic environment. Some candidate genomic regions contained genes putatively encoding effectors and were enriched in SPRYSECs, known in cyst nematodes to be involved in pathogenicity and in (a)virulence. Validated candidate SNPs will provide a useful molecular tool to follow frequencies of virulence alleles in natural G. pallida populations and define efficient strategies of use of potato resistances maximizing their durability. This article is protected by copyright. All rights reserved.
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Molecular Ecology, Wiley, 2017, 26 (18), pp.4700-4711 〈10.1111/mec.14240〉
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Delphine Eoche-Bosy, Matthieu Gautier, Magali Esquibet, Fabrice Legeai, Anthony Bretaudeau, et al.. Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida.. Molecular Ecology, Wiley, 2017, 26 (18), pp.4700-4711 〈10.1111/mec.14240〉. 〈hal-01605681v2〉



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