Abstract
BackgroundDiseases caused by Pseudomonas syringae (Ps) are recognized as the most damaging factors in fruit trees with a significant economic and sanitary impact on crops. Among them, bacterial canker of apricot is exceedingly difficult to control due to a lack of efficient prophylactic measures. Several sources of partial resistance have been identified among genetic resources but the underlying genetic pattern has not been elucidated thus far. In this study, we phenotyped bacterial canker susceptibility in an apricot core-collection of 73 accessions over 4 years by measuring canker and superficial browning lengths issued from artificial inoculations in the orchard.In order to investigate the genetic architecture of partial resistance, we performed a genome-wide association study using best linear unbiased predictors on genetic (G) and genetic x year (G × Y) interaction effects extracted from linear mixed models.Using a set of 63,236 single-nucleotide polymorphism markers genotyped in the germplasm over the whole genome, multi-locus and multi-variate mixed models aimed at mapping the resistance while controlling for relatedness between individuals.ResultsWe detected 11 significant associations over 7 candidate loci linked to disease resistance under the two most severe years. Colocalizations between G and G × Y terms indicated a modulation on allelic effect depending on environmental conditions. Among the candidate loci, two loci on chromosomes 5 and 6 had a high impact on both canker length and superficial browning, explaining 41 and 26% of the total phenotypic variance, respectively. We found unexpected long-range linkage disequilibrium (LD) between these two markers revealing an inter-chromosomal LD block linking the two underlying genes. This result supports the hypothesis of a co-adaptation effect due to selection through population demography. Candidate genes annotations suggest a functional pathway involving abscisic acid, a hormone mainly known for mediating abiotic stress responses but also reported as a potential factor in plant-pathogen interactions.ConclusionsOur study contributed to the first detailed characterization of the genetic determinants of partial resistance to bacterial canker in a Rosaceae species. It provided tools for fruit tree breeding by identifying progenitors with favorable haplotypes and by providing major-effect markers for a marker-assisted selection strategy.
Highlights
Diseases caused by Pseudomonas syringae (Ps) are recognized as the most damaging factors in fruit trees with a significant economic and sanitary impact on crops
Considering all years, part of the total phenotypic variation was attributed in order of significance to year (p < 2.2E-16, 36% lgc and 25% bs), genotype, genotype x year interaction and operator effects (Fig. 1)
99th percentile of the r2vs distribution are displayed appeared to be located in a low linkage disequilibrium (LD) region with no specific genomic structure. As these two main Single-nucleotide polymorphism (SNP) were detected by the two mapping approaches, we focused on the effect of the haplotype, constituted by the genotypes on
Summary
Diseases caused by Pseudomonas syringae (Ps) are recognized as the most damaging factors in fruit trees with a significant economic and sanitary impact on crops. Among the biotic stresses affecting apricot crop durability and in a broader way stone fruit species, bacterial canker, caused by ubiquitous bacteria in the species complex Pseudomonas syringae (Ps), is one of the most damaging This disease could potentially lead to the death of trees in the orchard, especially young trees within their five first years after planting. Cold winter temperatures and especially high frequency of frost-defrost episodes have been highlighted as major factors favoring bacterial canker [11, 12] Integrated management practices such as the use of resistant and soil-adapted rootstock material and grafting at a tall height could lower bacterial canker incidence in orchards [13, 14]. These cultural recommendations are technically challenging for orchard management and provide only a partial protection in orchards
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