Genome-wide association study of partial resistance to bacterial canker of apricot

Abstract

Apricot, a highly valuable crop is threatened by the growing importance of bacterial canker caused by Pseudomonas syringae. Among the key factors able to control the disease, genetic improvement is a promising measure. The variability of susceptibility on branches and the characterization of genetic determinants through a genome wide association study were thus investigated on a core-collection.73 accessions were annually inoculated in the orchard with an aggressive strain of the bacterium for 4 years. Phenotypic data about the length of both external canker (lgc) and superficial browning (bs) of tissues were collected. The analysis displayed a highly environmental-dependent genetic variation with broad-sense heritabilities of lgc and bs reaching respectively 59% and 78% for the most severe year. Considering the two variance-maximizing years, genetic (G) and genetic x year (GxY) BLUP were predicted for each variable using a linear mixed model. Association analysis were performed with a 63,236 SNP set through both a multi-variate (GEMMA) and a multi-locus genome-wide analysis.By exploiting the between-years (multi-locus model on G and GxY terms) and between-phenotypes (multivariate model on lgc-bs G terms) correlations, 11 significant associations have been detected. Among them, two SNP impacting both lgc and bs expressions over the two studied years and explaining 41% and 31% of the total phenotypic variance were identified on chromosomes 5 and 6. A long-range linkage disequilibrium had been noticed between these two markers suggesting a co-selection effect. The associated SNP reported from this work will open up new opportunities for a Marker-assisted selection strategy