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Rusts are among the most important foliar biotrophic fungal diseases in legumes.  Lathyrus cicera  crop can be severely damaged by  Uromyces pisi , to which partial resistance has been identified. Nevertheless, the underlying genetic basis and molecular mechanisms of this resistance are poorly understood in  L. cicera . To prioritise the causative variants controlling partial resistance to rust in  L. cicera , a recombinant inbred line (RIL) population, segregating for response to this pathogen, was used to combine the detection of related phenotypic- and expression-quantitative trait loci (pQTLs and eQTLs, respectively). RILs’  U. pisi  disease severity (DS) was recorded in three independent screenings at seedling (growth chamber) and in one season of exploratory screening at adult plant stage (semi-controlled field conditions). A continuous DS range was observed in both conditions and used for pQTL mapping. Different pQTLs were identified under the growth chamber and semi-controlled field conditions, indicating a distinct genetic basis depending on the plant developmental stage and/or the environment. Additionally, the expression of nine genes related to  U. pisi  resistance in  L. cicera  was quantified for each RIL individual and used for eQTL mapping. One  cis -eQTL and one trans-eQTL were identified controlling the expression variation of one gene related to rust resistance – a member of glycosyl hydrolase family 17. Integrating phenotyping, gene expression and linkage mapping allowed prioritising four candidate genes relevant for disease-resistance precision breeding involved in adaptation to biotic stress, cellular, and organelle homeostasis, and proteins directly involved in plant defence.

Integrating Phenotypic and Gene Expression Linkage Mapping to Dissect Rust Resistance in Chickling Pea