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Background   Plum pox  virus (PPV), causing Sharka disease, is one of the main limiting factors for  Prunus  production worldwide. In apricot ( Prunus armeniaca  L.) the major PPV resistance locus ( PPVres ), comprising ~ 196 kb, has been mapped to the upper part of linkage group 1. Within the  PPVres , 68 genomic variants linked in coupling to PPV resistance were identified within 23 predicted transcripts according to peach genome annotation. Taking into account the predicted functions inferred from sequence homology, some members of a cluster of meprin and TRAF-C homology domain (MATHd)-containing genes were pointed as PPV resistance candidate genes.    Results  Here, we have characterized the global apricot transcriptome response to PPV-D infection identifying six  PPVres  locus genes ( ParP-1  to  ParP-6 ) differentially expressed in resistant/susceptible cultivars. Two of them ( ParP-3  and  ParP-4 ), that encode MATHd proteins, appear clearly down-regulated in resistant cultivars, as confirmed by qRT-PCR. Concurrently, variant calling was performed using whole-genome sequencing data of 24 apricot cultivars (10 PPV-resistant and 14 PPV-susceptible) and 2 wild relatives (PPV-susceptible).  ParP-3  and  ParP-4 , named as   P   runus    ar   meniaca    P   PVres   M ATHd- c ontaining genes ( ParPMC ), are the only 2 genes having allelic variants linked in coupling to PPV resistance.  ParPMC1  has 1 nsSNP, while  ParPMC2  has 15 variants, including a 5-bp deletion within the second exon that produces a frameshift mutation.  ParPMC1  and  ParPMC2  are adjacent and highly homologous (87.5% identity) suggesting they are paralogs originated from a tandem duplication. Cultivars carrying the  ParPMC2  resistant (mutated) allele show lack of expression in both  ParPMC2  and especially  ParPMC1 .    Conclusions  Accordingly, we hypothesize that  ParPMC2  is a pseudogene that mediates down-regulation of its functional paralog  ParPMC1  by silencing. As a whole, results strongly support  ParPMC1  and/or  ParPMC2  as host susceptibility genes required for PPV infection which silencing may confer PPV resistance trait. This finding may facilitate resistance breeding by marker-assisted selection and pave the way for gene edition approaches in  Prunus .    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1237-1) contains supplementary material, which is available to authorized users.

Resistance to Plum Pox Virus (PPV) in apricot (Prunus armeniaca L.) is associated with down-regulation of two MATHd genes