Identification of race-specific QTL and candidate genes for Aphanomyces root rot resistance in alfalfa (Medicago sativa L.)

Aphanomyces root rot (ARR), caused by the oomycete Aphanomyces euteiches, is one of the most devastating diseases of alfalfa in the United States. Two pathogenic races of A. euteiches have been identified, with most commercial cultivars resistant to race 1. However, there are limited commercial cultivars resistant to race 2, which is the predominant race in North America. To dissect the genetic control of race-specific resistance, we developed two F1 mapping populations from paired reciprocal crosses of resistant and susceptible plants derived from the commercial cultivar 53V52 and the check cultivar WAPH-5. Using cloned plants, 184 F1 plants were phenotyped from the 53V52-derived population and 372 plants from the WAPH-5 population with one or more strains of A. euteiches race 1 and race 2. Using DArTag genotyping and quantitative trait loci (QTL) mapping, genomic regions for race 1 resistance were identified on chromosome 1 in the 53V52-derived population and on chromosomes 1 and 4 in the WAPH-5-derived population, whereas race 2 resistance QTL were mapped to chromosome 2 in the 53V52-derived population and chromosome 4 in the WAPH-5-derived population. Candidate resistance genes were prioritized for three major-effect QTL by integrating gene functional annotations and putative causal mutations identified using the DNA language model-based framework PlantCaduceus, representing the first implementation of PlantCaduceus in an autotetraploid species. These markers and candidate genes provide valuable resources for marker-assisted introgression of race-specific ARR resistance into elite alfalfa breeding germplasm.