Identification of novel genetic regions associated with resistance to European canker in apple

Abstract

Background European canker, caused by the fungal pathogen Neonectria ditissima, is an economically damaging disease in apple producing regions of the world – especially in areas with moderate temperatures and high rainfall. The pathogen has a wide host range of hardwood perennial species, causing trunk cankers, dieback and branch lesions in its hosts. Although apple scion germplasm carrying partial resistance to the disease has been described, little is still known of the genetic basis for this quantitative resistance. Results Resistance to Neonectria ditissima was studied in a multiparental population of apple scions using several phenotyping methods. The studied population consists of individuals from multiple families connected through a common pedigree. The degree of disease of each individual in the population was assessed in three experiments: artificial inoculations of detached dormant shoots, potted trees in a glasshouse and in a replicated field experiment. The genetic basis of the differences in disease was studied using a pedigree-based analysis (PBA). Three quantitative trait loci (QTL), on linkage groups (LG) 6, 8 and 10 were identified in more than one of the phenotyping strategies. An additional four QTL, on LG 2, 5, 15 and 16 were only identified in the field experiment. The QTL on LG2 and 16 were further validated in a biparental population. QTL effect sizes were small to moderate with 4.3 to 19% of variance explained by a single QTL. A subsequent analysis of QTL haplotypes revealed a dynamic response to this disease, in which the estimated effect of a haplotype varied over the field time-points. Conclusions This study describes the first identified QTL associated with resistance to N. ditissima in apple scion germplasm. The results from this study show that QTL present in germplasm commonly used in apple breeding have a low to medium effect on resistance to N. ditissima. Hence, multiple QTL will need to be considered to improve resistance through breeding.

Quantitative trait loci associated with apple endophytes during pathogen infection

“…OTU3169 (Rhodospirillales) and the bacterial PC2 had two QTL hits colocalizing with canker QTLs (on LG5 and 15), whereas the other OTUs/PCs with overlapping hits were specific to one of the canker QTL regions. Only a subset of the endophyte QTL with significant correlation to canker traits had QTL hits that co-localised with previously reported resistance QTL (bacteria: OTU8, OTU38, OTU59, OTU100, OTU159, fungi: PC3, OTU19, OTU71, OTU143) However, the canker disease QTL reported by Karlström et al (2022) had small to moderate effect sizes (4-19%). The effect sizes of QTL associated with the bacterial traits that were correlated with canker traits were comparably larger.…”

“…The linkage map used in our study based on the 'Aroma' x 'Golden Delicious' population was highly inflated compared to the iGL consensus map from which the marker orders were derived (di Pierro et al, 2016). This is likely due to a higher number of cosegregating markers in the biparental population as there is a limited number of recombination events compared to the multiple populations used to produce the consensus map (N'Diaye et al, 2017) Co-localisation of endophyte QTL and genetic regions associated with susceptibility to European canker Several QTL regions (on LG 5, 8, 15 and 16) associated with endophyte abundance and composition colocalize with previously identified QTLs for resistance to N. ditissima (Karlström et al, 2022). OTU3169 (Rhodospirillales) and the bacterial PC2 had two QTL hits colocalizing with canker QTLs (on LG5 and 15), whereas the other OTUs/PCs with overlapping hits were specific to one of the canker QTL regions.…”

“…Genotypic data for the apple biparental population and linkage map DNA from the biparental population and the two parental cultivars were extracted as per Karlström et al (2022). The population was genotyped on the Illumina Infinium ® 20k SNP array.…”

“…The correlation in the abundance of endophyte and canker disease traits are shown in Supplementary Figure 2 to indicate the degree of correlation among these phenotypic traits. Further descriptions of trait data from the same experiment is detailed in Karlström et al (2022) and Papp-Rupar et al (2022) for disease and endophyte abundance results, respectively. Disease results for standard reference cultivars from the field experiment is detailed in Karlström et al (2022).…”

“…Further descriptions of trait data from the same experiment is detailed in Karlström et al (2022) and Papp-Rupar et al (2022) for disease and endophyte abundance results, respectively. Disease results for standard reference cultivars from the field experiment is detailed in Karlström et al (2022).…”