Narrowing down the apricot Plum pox virus resistance locus and comparative analysis with the peach genome syntenic region

Abstract

Sharka disease, caused by the Plum pox virus (PPV), is one of the main limiting factors for stone fruit crops worldwide. Only a few resistance sources have been found in apricot (Prunus armeniaca L.), and most studies have located a major PPV resistance locus (PPVres) on linkage group 1 (LG1). However, the mapping accuracy was not sufficiently reliable and PPVres was predicted within a low confidence interval. In this study, we have constructed two high-density simple sequence repeat (SSR) improved maps with 0.70 and 0.68 markers/cm, corresponding to LG1 of 'Lito' and 'Goldrich' PPV-resistant cultivars, respectively. Using these maps, and excluding genotype-phenotype incongruent individuals, a new binary trait locus (BTL) analysis for PPV resistance was performed, narrowing down the PPVres support intervals to 7.3 and 5.9 cm in 'Lito' and 'Goldrich', respectively. Subsequently, 71 overlapping oligonucleotides (overgo) probes were hybridized against an apricot bacterial artificial chromosome (BAC) library, identifying 870 single BACs from which 340 were anchored onto a map region of approximately 30-40 cm encompassing PPVres. Partial BAC contigs assigned to the two allelic haplotypes (resistant/susceptible) of the PPVres locus were built by high-information content fingerprinting (HICF). In addition, a total of 300 BAC-derived sequences were obtained, and 257 showed significant homology with the peach genome scaffold_1 corresponding to LG1. According to the peach syntenic genome sequence, PPVres was predicted within a region of 2.16 Mb in which a few candidate resistance genes were identified.

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

“…Several molecular markers were placed close to the major locus (Dondini et al, 2011;Vera-Ruiz et al, 2011;Soriano et al, 2012). The SSRs close to PPVres loci does not guarantee the resistance behavior of the apricot cultivar although they are located close to the PPVres loci.…”

“…Twelve of these are described as located close to the PPVres on LG1 (Vera-Ruiz et al, 2011 andSoriano et al, 2008). The remaining eight markers (ssrPaCITA16, ssrPaCITA19, ssrPaCITA4, UDAp-404, ssrPaCITA21, pchgms2, UDP98-412, and ssrPaCITA15) were selected from different linkage groups (Table 1.) Later, the primers Gol029 and ssrPaCITA15 in LG8 were excluded due to the difficulties associated with allele coding.…”

“…Due to the difficulties associated with woody plant breeding, the development of resistance-related molecular markers to be used in marker-assisted selection (MAS) has become of vital importance. Genetics maps of apricots have been developed for PPV resistance (Hurtado et al, 2002;Lambert et al, 2007;Soriano et al, 2008;Lalli et al, 2008;Marandel et al, 2009;Pilarová et al, 2010;Dondini et al, 2011;Vera Ruiz et al, 2011) and resistance-related molecular markers were searched. A http://dx.doi.org/10.1016/j.scienta.2015.07.012 0304-4238/© 2015 Elsevier B.V. All rights reserved.…”

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

“…; Vera Ruiz et al . ). Markers linked to this locus in the North American apricot cultivars have been developed (Soriano et al .…”

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

“…More recently, Vera‐Ruiz et al . () developed high‐density simple sequence repeat (SSR) linkage maps and narrowed down the PPVres support intervals to 7.3 and 5.9 cM in ‘Lito’ and ‘Goldrich’ maps, respectively, with an estimated size according to the peach genome sequence of 2.16 Mb (Arús et al ., ; Jung et al ., ). From this point, Soriano et al .…”