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

Abstract

Sharka disease, caused by Plum pox virus (PPV), is the most important viral disease affecting Prunus species. A major PPV resistance locus (PPVres) has been mapped to the upper part of apricot (Prunus armeniaca) linkage group 1. In this study, a physical map of the PPVres 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 Illumina-HiSeq2000 platform. Single nucleotide polymorphisms (SNPs) within the mapped interval, recorded from alignments against the peach genome, allowed us to narrow down the PPVres 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 Arabidopsis, 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.

Evaluation of Turkish apricot germplasm using SSR markers: Genetic diversity assessment and search for Plum pox virus resistance alleles

“…Therefore researches have focused on these three loci. Zuriaga et al (2013) sequenced and analyzed BAC clones corresponding to the ∼196-kbp PPVres loci and confirmed the presence of these three markers in the sequenced region. The potential of these three markers for MAS studies was investigated in several studies.…”

New insights into the history of domesticated and wild apricots and its contribution to Plum pox virus resistance

“…We also used the SSLP marker ZP002, designed within the best candidate gene for the PPVres locus (Zuriaga et al . ; Decroocq et al . ).…”

Recessive Resistance to Plant Viruses: Potential Resistance Genes Beyond Translation Initiation Factors

“…Simultaneously, genomics-based crop breeding using NGS technologies is expected to overcome the challenge of feeding an increasing world population. As suggested by Varshney et al (2014), NGS technologies, which have rarely been applied to antiviral breeding using natural variants (Zuriaga et al, 2013; Mariette et al, 2016), would be quite useful for identifying loci in naturally resistant variants and also for breeding to introduce resistant loci into specific cultivars. Several studies have identified loci of interest from Arabidopsis mutants using whole-genome sequencing of pooled mutant F2 populations (Schneeberger et al, 2009; Austin et al, 2011; Uchida et al, 2011).…”