title: A new eIF4E1 allele characterized by RNAseq data mining is associated with resistance to potato virus Y in tomato albeit with a low durability.
abstract: Allele mining on susceptibility factors offers opportunities to find new sources of resistance among crop wild relatives for breeding purposes. As a proof of concept, we used available RNAseq data to investigate polymorphisms among the four tomato genes encoding translation initiation factors [eIF4E1 and eIF4E2, eIFiso4E and the related gene new cap-binding protein(nCBP)] to look for new potential resistance alleles to potyviruses. By analysing polymorphism among RNAseq data obtained for 20 tomato accessions, 10 belonging to the cultivated type Solanum lycopersicum and 10 belonging to the closest related wild species Solanum pimpinellifolium, we isolated one new eIF4E1 allele, in the S. pimpinellifolium LA0411 accession, which encodes a potential new resistance allele, mainly due to a polymorphism associated with an amino acid change within eIF4E1 region II. We confirmed that this new allele, pot12, is indeed associated with resistance to potato virus Y, although with a restricted resistance spectrum and a very low durability potential. This suggests that mutations occurring in eIF4E region II only may not be sufficient to provide efficient and durable resistance in plants. However, our study emphasizes the opportunity brought by RNAseq data to mine for new resistance alleles. Moreover, this approach could be extended to seek for putative new resistance alleles by screening for variant forms of susceptibility genes encoding plant host proteins known to interact with viral proteins.
authors.affiliation: GAFL, INRA, 84140 Montfavet, France.
authors.forename: Caroline
authors.initials: C
authors.lastname: Lebaron
authors.affiliation: GAFL, INRA, 84140 Montfavet, France.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Rosado
authors.affiliation: GAFL, INRA, 84140 Montfavet, France.
authors.forename: Christopher
authors.initials: C
authors.lastname: Sauvage
authors.affiliation: GAFL, INRA, 84140 Montfavet, France.
authors.forename: Camille
authors.initials: C
authors.lastname: Gauffier
authors.affiliation: BFP, INRA, Université Bordeaux, 33882 Villenave d'Ornon, France.
authors.forename: Sylvie
authors.initials: S
authors.lastname: German-Retana
authors.affiliation: Pathologie Végétale, INRA, 84140 Montfavet, France.
authors.forename: Benoît
authors.initials: B
authors.lastname: Moury
authors.affiliation: GAFL, INRA, 84140 Montfavet, France.
authors.forename: Jean-Luc
authors.initials: JL
authors.lastname: Gallois
mesh_terms: D000483:Alleles; D060467:Disease Resistance; D039561:Eukaryotic Initiation Factor-4E / Q000235:genetics* / Q000276:immunology*; D018506:Gene Expression Regulation, Plant; D018551:Solanum lycopersicum / Q000145:classification / Q000235:genetics* / Q000276:immunology / Q000821:virology; D010935:Plant Diseases / Q000235:genetics / Q000276:immunology / Q000821:virology*; D010940:Plant Proteins / Q000235:genetics* / Q000276:immunology*; D017800:Potyvirus / Q000276:immunology / Q000502:physiology*
chemical_list: D039561:Eukaryotic Initiation Factor-4E; D010940:Plant Proteins