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.

BMC Plant Biol 2019 Jan 21;19(1):31. Epub 2019 Jan 21.

INRA, UR1052 Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, Montfavet, France.

Background: 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 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.

Results: We 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.

Conclusions: Our 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.

Download full-text PDF

Source Listing
January 2019
28 Reads

Publication Analysis

Top Keywords

partial resistance
bacterial canker
mixed models
candidate loci
superficial browning
linear mixed
genome-wide association
multi-locus multi-variate
plant-pathogen interactionsconclusions
study best
best linear
interactionsconclusions study
allelic depending
association study
resistance performed
performed genome-wide
predictors genetic

Altmetric Statistics


(Supplied by CrossRef)

DA St Clair et al.
Annu Rev Phytopathol 2010

CC Mundt et al.
Euphytica 2002

CC Mundt et al.
Infect Genet Evol 2014

L Gardan et al.
Revue de Zoologie Agricole et de Pathologie Végétale 1973

JE Crosse et al.
Trans Br Mycol Soc 1953

O Berge et al.
PLoS One 2014

M Scortichini et al.
J Plant Pathol 2010

JR Lamichhane et al.
Adv Agron 2014

MM Kennelly et al.
Plant Dis 2007

A Vigouroux et al.
Plant Dis 1989

Similar Publications