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Title: GWAS powered by a local score approach unravels the genomic bases of Medicago truncatula quantitative disease resistance to multiple Aphanomyces euteiches strains

Author
item BONHOMME, MAXIME - University Of Toulouse
item NAVIER, HELENE - University Of Rennes, France
item HAJRI, AHMED - University Of Rennes, France
item BADIS, YACINE - University Of Toulouse
item MITEUL, HENRI - University Of Rennes, France
item FARIELLO, MARIA INES - Universidad De La República
item Samac, Deborah - Debby
item DUMAS, BERNARD - University Of Toulouse
item BARANGER, ALAIN - University Of Rennes, France
item JACQUET, CHRISTOPHE - University Of Toulouse
item PILET-NAYEL, MARIE-LAURE - University Of Rennes, France

Submitted to: Heredity
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/8/2019
Publication Date: 5/28/2019
Citation: Bonhomme, M., Navier, H., Hajri, A., Badis, Y., Miteul, H., Fariello, M., Samac, D.A., Dumas, B., Baranger, A., Jacquet, C., Pilet-Nayel, M. 2019. GWAS powered by a local score approach unravels the genomic bases of Medicago truncatula quantitative disease resistance to multiple Aphanomyces euteiches strains. Heredity. 2019(5):1-15. https://doi.org/10.1038/s41437-019-0235-x.
DOI: https://doi.org/10.1038/s41437-019-0235-x

Interpretive Summary: Immunity or resistance is the most effective means of controlling plant diseases. Identifying the genes responsible for resistance is needed to accelerate the development of plant varieties with durable disease resistance. However, resistance to many plant diseases is the result of action of a number of genes with small additive effects, which are difficult or impossible to detect using standard methods of data analysis. A new method for identifying resistance genes with small effects in the legume plant barrel medic to the pathogen causing Aphanomyces root rot was developed and compared to a standard method. This method was much more efficient at detecting the presence of these genes, but had less precision for identifying the specific genes than standard methods. Several new candidate genes were identified that are likely involved in resistance to diverse strains of the pathogen. This method has broad application for identifying resistance genes in crop plants and the candidate genes identified may be useful in breeding for diseases resistance in legume crops such as pea and alfalfa.

Technical Abstract: Quantitative Trait Loci (QTL) with small effects, which are pervasive in quantitative phenotypic variation, are difficult to detect in Genome-Wide Association Studies (GWAS). To improve their detection, we proposed a local score approach, which accounts for linkage disequilibrium by accumulating association signals from single markers. Simulations revealed that the local score approach outperformed single SNP p-value – based tests for detecting small-effect QTL (heritability of 0.05 to 0.1) in a GWAS context with high marker density. Using more than 5 million SNPs, the local score approach was applied to identify loci involved in Quantitative Disease Resistance (QDR) to multiple strains of the plant root rot pathogen Aphanomyces euteiches, determined by a GWAS using a collection of 174 accessions of the model legume Medicago truncatula. Strong heritability of QDR was found in response to two closely related A. euteiches strains (ATCC 201684 and RB84), naturally infecting a wide range of legume crops, for which a large-effect QTL on chromosome 3 containing a Resistance Gene Analog (RGA) dominated the resistance response. Conversely, lower heritability of QDR was detected in response to three other strains (Ae109, MF-1, NC-1) belonging to the A. euteiches pathotype infecting only pea and alfalfa. The local score approach, but not p-value – based tests, successfully identified new candidate genes underlying small-effect loci associated with QDR to these strains. RGA as well as F-box gene families were significantly over-represented in the candidate gene list, suggesting key roles for genes involved in pathogen effector recognition and the plant proteasome in resistance to A. euteiches in M. truncatula