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Developing genetic resistance to pathogens is a major goal for plant breeding. In many crops, the translation initiation factors eIF4E are susceptibility factors to many RNA viruses, including PVY –Potato virus Y- and allelic variants from those genes are a source of genetic resistances. Natural variability issued from the crop wild relatives constitutes a large reservoir of such resistances but methods have yet to be developed in order to efficiently tap for alleles of interest.

In this work, we show that transcriptomic data can be mined for resistance alleles of a target gene. Using RNAseq data collected in the ARCAD project we isolated a new eIF4E resistance allele from an accession close to the cultivated tomato. Moreover, the analysis of this new allele, that is associated with a resistance easily overcome by PVY, allows us to better characterize the amino acid substitutions in eIF4E associated with an efficient resistance to PVY in crops.

This work stems from the collaboration between several INRA unit (Génétique et Amélioration des Fruits et Légumes-AVIGNON, Pathologie Végétale-AVIGNON, Biologie du Fruit et Pathologie-BORDEAUX). It can be extended to mine for new resistances, in a cross-crop manner, by looking at the many susceptibility host genes on which the virus rely to successfully infect plants.