No unintended changes in the proteome and metabolome of the cisgenic fire blight resistant apple line C44.4.146

Cisgenesis can be used to amend susceptible apple cultivars with disease resistance genes, thus reducing the current dependency on plant protection products for fruit production. The introgression of the same genes by conventional breeding would require a long backcrossing and selection process. However, the cisgenic approach is of interest only if the advantages of the added trait predominate potential unintended effects introduced through the transformation process, which include tissue culture, gene transfer and plant regeneration. Here we investigated the first cisgenic fire blight resistant apple line C44.4.146 carrying the FB_MR5 resistance gene from Malus × robusta 5 for potential unintended effects. The leaf proteome and metabolome of field-grown plants of C44.4.146 were compared with its wild type ‘Gala Galaxy’ and placed into the context of natural variation found in selected mutants of ‘Gala’. For this, pooled leaf material of the same genotypes was used for protein and metabolite extractions and analysis using chromatography-coupled mass spectrometry. The abundance of 3762 proteins and 827 metabolite features were compared. Between C44.4.146 and the untransformed wild type, the abundance of seven proteins and four metabolite features showed statistically significant differences. However, none of these abundances were statistically different between C44.4.146 and at least one of the other genotypes. We conclude that the cisgenic approach did not cause detectable unintended effects. The data generated and the results presented here contribute to the assessment of risks associated with cisgenesis.