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

Authors: LIN, MENG - Breeding Insight; TANG, XUEMEI - Breeding Insight; ZHAO, DONGYAN - Breeding Insight; MEDINA, CESAR - University Of Minnesota; Dornbusch, Melinda; BEIL, CRAIG - Breeding Insight; SHEEHAN, MOIRA - Breeding Insight; Samac, Deborah

Submitted to: G3: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/7/2026
Publication Date: 5/14/2026
Citation: Lin, M., Tang, X., Zhao, D., Medina, C.A., Dornbusch, M.R., Beil, C.T., Sheehan, M.J., Samac, D.A. 2026. Identification of race-specific QTL and candidate genes for Aphanomyces root rot resistance in alfalfa (Medicago sativa L.). G3: Genes, Genomes, Genetics. Article: jkag131. https://doi.org/10.1093/g3journal/jkag131.
DOI: https://doi.org/10.1093/g3journal/jkag131

Interpretive Summary: Aphanomyces root rot (ARR) is one of the most devastating diseases of alfalfa in the United States. The disease causes root rot of seedlings and mature plants leading to reduced nitrogen fixation, yield loss, and shortened stand life. Breeding for disease resistance has been slow because resistance is a rare trait and plant breeders rely on inoculating individual plants with the pathogen to identify plants with resistance. In this study, alfalfa populations were developed with a range of resistance to two physiological races of the pathogen, and a set of 3,000 DNA markers were used to identify regions of the alfalfa chromosomes containing genes for resistance to ARR. Populations developed from a commercial alfalfa cultivar and populations developed from a highly resistant check cultivar had distinctly different locations for disease resistance genes indicating that resistance came from different sources. Comparing the locations of markers to the genes in the chromosome, several genes potentially responsible for disease resistance were identified. The DNA markers near these genes can be used to rapidly identify plants with resistance and combine the two sources of resistance. These markers will accelerate the development of new disease resistant alfalfa cultivars with stronger resistance responses. Such cultivars will have enhanced performance in locations with high disease pressure and enable US farmers to have more productive and profitable crops.

Technical Abstract: Aphanomyces root rot (ARR), caused by the oomycete Aphanomyces euteiches, is one of the most devastating diseases of alfalfa in the United States. Infected seedlings are stunted with chlorotic cotyledons that become necrotic as the disease progresses while established plants develop a sublethal rot of fibrous and lateral roots under wet soil conditions, leading to reduced nodulation, yield loss, and shortened stand life. 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 resistant and susceptible parents identified from the commercial cultivar 53V52 and the check cultivar WAPH-5. Plants in both populations were phenotyped with one or more strains of race 1 and race 2. Genomic regions significantly associated with race 1 resistance was identified on chromosome 1.1 in the 53V52-derived lines and on chromosomes 1.1 and 4.1 in the WAPH-5-derived lines, whereas race 2 resistance were mapped to chromosome 2.1 in the 53V52-derived lines and chromosome 4.1 in the WAPH-5-derived lines. Candidate resistance genes were prioritized for three major-effect quantitative trait loci 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.