Allele mining of eukaryotic translation initiation factor genes in Prunus for the identification of new sources of resistance to sharka

Abstract

Members of the eukaryotic translation initiation complex are co-opted in viral infection, leading to susceptibility in many crop species, including stone fruit trees (Prunus spp.). Therefore, modification of one of those eukaryotic translation initiation factors or changes in their gene expression may result in resistance. We searched the crop and wild Prunus germplasm from the Armeniaca and Amygdalus taxonomic sections for allelic variants in the eIF4E and eIFiso4E genes, to identify alleles potentially linked to resistance to Plum pox virus (PPV). Over one thousand stone fruit accessions (1397) were screened for variation in eIF4E and eIFiso4E transcript sequences which are in single copy within the diploid Prunus genome. We identified new alleles for both genes differing from haplotypes associated with PPV susceptible accessions. Overall, analyses showed that eIFiso4E is genetically more constrained since it displayed less polymorphism than eIF4E. We also demonstrated more variations at both loci in the related wild species than in crop species. As the eIFiso4E translation initiation factor was identified as indispensable for PPV infection, a selection of ten different eIFiso4E haplotypes along 13 accessions were tested by infection with PPV and eight of them displayed a range of reduced susceptibility to resistance, indicating new potential sources of resistance to sharka.

Figure 1

Taxonomy and geographic distribution of Prunus accessions. (A) Taxonomy and schematic phylogeny of the accessions used in this study. Classification follows previous classifications of Bortiri et al. linked with Rehder and Mason. Black squares localize the three main groups of this work in the Prunus genus: the Armeniaca, the Amygdalus and the Persica groups representing accessions related to apricots, almonds and peaches identified by triangles, squares and circles respectively. Green, red and blue colors refer to crop species, wild related species and wild/undomesticated apricots respectively. (B) Geographic distribution of the accessions used in this study according to their country of initial sampling (see Table S1). The world map can be downloaded under free license at https://www.vecteezy.com/vector-art/10961532-world-map-vector-illustration-isolated-on-grey-background-flat-earth-globe-or-world-map.

Figure 2

Stacked diagrams with cumulative frequencies of variations in eIF4E (A) and eIFiso4E (B) amino acid sequences within main groups and subgroups compared to their own main group reference sequence. Diagrams categorize frequencies following accessions; with identical sequences to the reference in grey, with at least one nucleotide substitution resulting in a synonymous variation in blue, with at least one amino acid variation (occurrence of presence > 5%) in orange and, with at least one rare amino acid variation (occurrence of presence < 5%) in green.

Figure 3

Frequency of rare amino acid variations (occurrence of presence < 5%) along eIFiso4E (A) and eIF4E (B) sequences. The interaction domains with the virus -Domain I and Domain II- are localized with their positions (pos.) on the sequences inside dotted grey rectangles. Each circle represents one amino acid variation retrieved at one specific position; each color refers to one subgroup as apricot crop species (blue), wild/undomesticated apricots (orange), apricot wild related species (red), almond crop species (yellow), almond wild related species (purple), peach crop species (green) and peach wild related species (grey).

Figure 4

Average PPV infection score after successive cycles of phenotypic evaluation for the selected accessions (see Table 4). Resistance to PPV and the negative control are characterized by a null score (0). Three levels of susceptibility are categorized from a weak (0 < score < 0.200), then a moderate (0.200 ≤ score < 0.500) to a high susceptibility score (0.500 ≤ score ≤ 1). The positive control is set to 1.