Genomic analysis reveals MATH gene(s) as candidate(s) for P lum pox virus ( PPV ) resistance in apricot ( P runus armeniaca L .)

Summary Sharka disease, caused by P lum pox virus ( PPV ), is the most important viral disease affecting P runus species. A major PPV resistance locus ( PPV res ) has been mapped to the upper part of apricot ( P runus armeniaca ) linkage group 1. In this study, a physical map of the PPV res locus in the PPV ‐resistant cultivar ‘Goldrich’ was constructed. Bacterial artificial chromosome ( BAC ) clones belonging to the resistant haplotype contig were sequenced using 454/ GS‐FLX Titanium technology. Concurrently, the whole genome of seven apricot varieties (three PPV ‐resistant and four PPV ‐susceptible) and two PPV ‐susceptible apricot relatives ( P . sibirica var. davidiana and P . mume ) were obtained using the I llumina‐ H i S eq2000 platform. Single nucleotide polymorphisms ( SNP s) within the mapped interval, recorded from alignments against the peach genome, allowed us to narrow down the PPV res locus to a region of ∼196 kb. Searches for polymorphisms linked in coupling with the resistance led to the identification of 68 variants within 23 predicted transcripts according to peach genome annotation. Candidate resistance genes were ranked combining data from variant calling and predicted functions inferred from sequence homology. Together, the results suggest that members of a cluster of meprin and TRAF‐C homology domain ( MATHd )‐containing proteins are the most likely candidate genes for PPV resistance in apricot. Interestingly, MATHd proteins are hypothesized to control long‐distance movement ( LDM ) of potyviruses in A rabidopsis , and restriction for LDM is also a major component of PPV resistance in apricot. Although the PPV resistance gene(s) remains to be unambiguously identified, these results pave the way to the determination of the underlying mechanism and to the development of more accurate breeding strategies.