Potato virus Y (PVY) is one of the most damaging viruses on tobacco worldwide.

This virus is responsible for mosaic or necrotic symptoms depending on the PVY strain. Aggressive PVY necrotic strains can lead to considerable yield losses.

A large deletion conferring resistance to PVY, the “va” gene, has been recently characterised in tobacco (Julio et al., 2014). It has been shown that the loss of a eukaryotic translation initiation factor 4E copy (eIF4E) results in recessive resistance to PVY. However, PVY isolates overcoming the va gene have been observed in several countries. These resistance-breaking PVY isolates induce necrotic symptoms in the Virgin A mutant (VAM) resistant cultivar, the main source used to transfer the va resistance into tobacco varieties.

Phenotyping tests were conducted on a large collection of 162 varieties from the Imperial Tobacco collection. The absence of a functional eIF4E was characterised by Polymerase Chain Reaction (PCR) and PVY resistance was estimated by symptom survey and ELISA tests. The screening was performed with different PVY necrotic strains, including one able to overcome the va gene.

Ten cultivars displaying resistance to PVY while expressing a functional eIF4E-Va gene were identified, suggesting that the resistance observed does not rely on va in these cultivars. ELISA assays showed that PVY isolates can infect the ten cultivars, although they do not induce necrotic symptoms. Therefore, a different mechanism, involving tolerance to necrosis, appeared to be involved.

Fine mapping on a F2 segregating population confirmed that this tolerance trait is inherited as a single recessive gene on chromosome 13. Anchoring the linkage map to the tobacco genome physical map allowed the identification of a candidate gene with a Single Nucleotide Polymorphism (SNP) in eight of these cultivars. This gene could be used in future breeding programmes to minimise the impact of PVY resistance-breaking strains able to overcome the va mediated-resistance and to limit crop losses.