For this purpose, we develop genetic mapping approaches in F1 progenies and association genetics to specify the location of resistance genes/QTLs on apple or pear chromosomes.
In apple, this approach is now greatly enriched by the monitoring of the resistant haplotypes along the pedigrees recently reconstructed over old apple varieties (Fig1). The identification of recombination points in the vicinity of the target QTLs throughout the pedigree makes it possible to specify the location or even the effect of certain QTLs, or to plan controlled crosses to better characterize them in dedicated progenies. Moreover, pedigrees allow us to predict the presence of favorable resistance alleles in genotypes that have not been mapped until now.
For some QTLs/major genes, we are trying to identify (clone) the underlying genes: this is the case for the fire blight resistance QTL FB_E of the ornamental variety Evereste, for the scab resistance QTL qT1 which colocalizes with the major R gene Rvi6, and for the major rosy apple aphid tolerance gene Dp-fl, with the goal to understand the mechanisms involved. The scab resistance QTLs qF11 and qF17, whose functions are complementary (epistasis), are also gene targets to be characterized in the near future. Thanks to the complete annotated apple genome sequence, positional and functional candidate genes are identified under the QTLs and characterized in terms of allelic diversity and expression. In connection with functional genomics studies, we are also looking for expression QTLs (eQTLs) for certain defense genes highlighted in transcriptomic studies.
In collaboration with the LAE unit of INRAE, Nancy, we now seek to identify metabolites whose variation is controlled by these scab resistance QTLs, in order to identify candidate metabolites that could be direct effectors of the observed resistance.
Furthermore, we explored the interaction between genetic and PRI-induced resistance in a mapped F1 progeny previously treated or not with the PRI ASM (acibenzolar-S-methyl) and then inoculated with scab or fire blight under controlled conditions (greenhouse). In our study, ASM modulates the expression of resistance QTLs only moderately, but the combination of both resistance sources significantly enhances the overall resistance level. In the framework of the project CapZeroPhyto, the efficacy of this combination will be evaluated in an experimental orchard (managed by the Experimental Horticultural unit of INRAE at Angers UE-Horti) planted with genotypes of different classes of presence/absence of QTLs qT1, qF11 and qF17, treated or not with ASM.
The selection pressures exerted by apple scab resistance genes/QTLs on populations of the fungus Venturia inaequalis have been the subject of strong collaborations with the EcoFun team, which is continuing its work on the potential adaptation of pathogen populations to ASM. The durability of the combination of intrinsic (genetic) and ASM-induced resistance will be studied in the above orchard still within the framework of the project CapZeroPhyto.
In collaboration with the VaDiPom team, we strongly contribute to the marker-assisted selection (MAS) of genotypes combining major genes and QTLs for resistance to these different pathogens and pests, both in apple and pear (Fig2). A major step is the identification and validation of SNP markers having a sufficiently specific association with the resistance alleles for the targeted QTLs and that correctly cover the confidence interval of each QTL. Once again, the reconstructed pedigrees and shared haplotypes are very useful on the one hand to orientate controlled crosses aiming at pyramiding a maximum of favorable alleles for the targeted QTLs (resistance, fruit quality, etc.), and on the other hand to evaluate a priori the specificity of the SNPs to efficiently identify the individuals to be selected in the created progenies.
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Lasserre-Zuber, P., Caffier, V., Stievenard, R., Lemarquand, A., Le Cam, B., Durel, C.-E., 2018. Pyramiding quantitative resistance with a major resistance gene in apple: from ephemeral to enduring effectiveness in controlling scab. Plant Disease 102, 2220–2223. https://doi.org/10.1094/PDIS-11-17-1759-RE
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Pagliarani, G., Dapena, E., Miñarro, M., Denancé, C., Lespinasse, Y., Rat-Morris, E., Troggio, M., Durel, C.-E., Tartarini, S., 2016. Fine mapping of the rosy apple aphid resistance locus Dp-fl on linkage group 8 of the apple cultivar ‘Florina’’.’ Tree Genetics and Genomes 12, 56. https://doi.org/10.1007/s11295-016-1015-x
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