Aphanomyces root rot in pea : genomic insights into pathogen diversity and disease resistance

Abstract

The cultivation of vining pea (Pisum sativum) faces significant challenges due to root rot, primarily caused by Aphanomyces euteiches, a soil-borne oomycete pathogen. Pea cultivars resistant to aphanomyces root rot (ARR) are currently lacking and common mitigation methods include crop rotation and avoidance of highly infested fields. The thesis work integrates population genetic, transcriptomic, and comparative genomic analyses to enhance our understanding of aphanomyces root rot in pea, providing valuable knowledge for future breeding and disease management efforts. Genetic diversity analyses of A. euteiches in Europe revealed three distinct groups on a north to south gradient: a north-eastern (NE), central European (CE) and southern (S) group. Shared multilocus genotypes between geographically distant regions indicate genetic movement between countries. The S group differed in virulence and oospore size compared to NE and CE and displayed signs of genetic isolation, all of them indications to view group S as a separate Aphanomyces species. The use of partial resistance in the pea genotype PI180693 was assessed in crosses with the susceptible, commercial cultivar Linnea in controlled and field conditions. The new breeding lines displayed enhanced disease resistance to ARR compared to the susceptible parent. The results further highlighted the difficulties of predicting breeding line performance in the field based on trials in controlled conditions and of breaking the linkage between ARR resistance and unfavourable breeding traits in classical breeding. Characterization of the transcriptomic immune response in Linnea and PI180693 to A. euteiches infection showed to be time- and genotype-dependent, involving differential regulation of transcription factors and genes associated with hormone signalling. Cross-referencing with genes located in resistance quantitative trait loci led to the identification of 39 candidate disease resistance genes, including a putative immune receptor with NLR structure that was polymorphic between the pea genotypes.