Genome-wide association multi-locus and multi-variate linear mixed models reveal two linked loci with major effects on partial resistance of apricot to bacterial canker

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.Electronic supplementary materialThe online version of this article (10.1186/s12870-019-1631-3) contains supplementary material, which is available to authorized users.

Cherry picking by pseudomonads: After a century of research on canker, genomics provides insights into the evolution of pathogenicity towards stone fruits

“…This could be coupled with the identification of mutants deficient in growth and/or symptoms in the different tissues (Somlyai et al, 1986). A recent high-throughput approach called transposon insertion sequencing (TnSeq) involves inoculating pools of transposon mutants and using sequencing to determine mutant frequencies within this pool before and after exposure to a selective environment, such as within a plant (van Opijnen et al, 2009). This approach has proved powerful in identifying different genes important for bacterial fitness in the apoplast versus surface of leaves in the Pss-bean interaction (Helmann et al, 2019).…”

“…The use of plant genomic association techniques to identify genes for resistance is increasing. Recently, an association study (Omrani et al, 2019) mapped partial resistance towards Pss in apricot to several quantitative trait loci (QTLs), with two loci explaining 41% and 26% of phenotypic variation, respectively. The candidate loci contained genes annotated as producing products involved in phytohormone signalling, specifically abscisic acid, and may mediate crosstalk between different signalling pathways during immunity.…”

Identifying resistance in wild and ornamental cherry towards bacterial canker caused by Pseudomonas syringae

“…There is limited knowledge of resistance in Prunus towards bacterial canker pathogens. Cherry and apricot varieties with partial resistance to one or more of the pathogens have been identified using methods such as laboratory‐based shoot inoculations and field tree inoculations (Farhadfar et al, 2016 ; Hulin, Mansfield, et al, 2018 ; Omrani et al, 2019 ; Santi et al, 2004 ). In our previous study, we found that the partial resistance seen in woody tissue of certain cherry cultivars was not detected using detached leaf syringe‐infiltration assays (Hulin, Mansfield, et al, 2018 ).…”

“…In addition, it is arguably more durable than single resistance ( R ) gene‐based immunity, which is, theoretically, more frequently overcome during pathogen evolution (Pilet‐Nayel et al, 2017 ). Progress towards understanding the genetic factors involved in bacterial canker resistance has been made by Omrani et al ( 2019 ) who identified quantitative trait loci (QTLs) involved in partial resistance in apricot. These loci contain genes involved in phytohormone signalling, a process known to play a pivotal role during the plant immune response.…”

“…Bacterial canker, caused by members of the Pseudomonas syringae species complex, can be a major limiting factor in the cultivation of Prunus spp. (Omrani et al, 2019;Vicente et al, 2004). The disease is primarily characterized by necrosis, gummosis and/ or dieback of woody plant tissues.…”