Three genes identified by genome wide association mapping of root-knot nematode susceptibility in Arabidopsis

Root-knot nematodes are devastating plant-pathogens affecting the agricultural productivity of major food crops world-wide. The major control strategy nowadays is through incorporating major-effect resistance-genes in food-crops. However, the supply of nematode resistance genes available for breeding is very limited. Hence, there is need for alternative control strategies. Here, we show that more subtle quantitative trait loci could be used as an additional genetic resource for nematode control.We mapped the genetic architecture of susceptibility of the model plant Arabidopsis thaliana to Meloidogyne incognitia using a set of 340 natural isolates. These isolates represent the world-wide genetic variation in this plant. Each of these isolates was tested in at least four technical replicates, the average number of egg-masses per plant ranged from five to 45. We found ample genetic variation in M. incognita reproduction on these plants, with a narrow-sense heritability of 0.52. Subsequently, we mapped quantitative trait loci by genome wide association, explaining genetic variation in nematode reproduction. At a permissive significance threshold of LOD > 4, we identified 19 associated loci. We investigated three loci by characterizing nine T-DNA knock-out mutants of candidate genes. This way, three genes that function as (co-)regulators of nematode susceptibility in Arabidopsis were identified: BRASSINAZOLE RESISTANT1, an F-box familiy protein, and ETHYLENE RESPONSE FACTOR 6. Our results show that there is quantitative genetic variation in the host-plant affecting nematode reproduction. Furthermore, our results suggest that allelic variation in these susceptibility genes could be used to improve the resistance of crops to root-knot nematodes. Our results pave the way to investigate these traits in food-crops.