Comparative genomic analysis of QTL for resistance to Aphanomyces euteiches between pea, lentil, faba bean and the model species Medicago truncatula

Aphanomyces root rot, caused by Aphanomyces euteiches , is a damaging disease affecting various legume species. Quantitative trait loci (QTL) for partial resistance were previously identified mainly in pea, and also in lentil and Medicago truncatula . This study aimed to identify novel resistance loci from available populations in lentil and faba bean and examine genomic conservation of resistance QTL across legume host species. QTL mapping in the Pop2 faba bean recombinant inbred line (RIL) population and genome-wide association study (GWAS) in the AGILE lentil diversity panel were performed for resistance to A. euteiches under controlled conditions, using genotyping data previously reported. A previous QTL mapping in the LR3 M. truncatula RIL population was updated using 1,536 new SNPs (single nucleotide polymorphisms). Synteny between resistance QTL to A. euteiches was analyzed based on gene orthology in the QTL regions projected onto genomes, using the OrthoLegKB graph database. Four loci, including a major-effect QTL on chromosome 3, Ae-Vf3.1 , were associated with resistance in faba bean. In lentil, six minor-effect GWAS-SNPs and two favorable haplotypes at Ae-Lc1.1 and Ae-Lc2.1 loci were identified. Updated analyses in M. truncatula narrowed to 8 Kb, including three candidate genes, the interval at the major-effect locus AER1 . Synteny analysis identified 65 resistance QTL to A. euteiches overlapping 24 syntenic blocks defined between legume genomes. No synteny was highlighted between two major-effect QTL. These results pave the way for translational genomics approaches facilitating resistance gene discovery and for resistance QTL deployment strategies in legume rotations to preserve their durability.