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Abstract
Root-knot nematodes (RKN, Meloidogyne spp.) are the most economically dangerous pathogens affecting soybean production in the southeastern U.S., causing an estimated $166 million (2.4%) in losses in 2023. The toxicity and regulation of available nematicides makes them problematic as a standard defense against RKN. The extensive host range of RKN makes devising a crop rotation pattern that gives sufficient time between compatible hosts difficult. Genetic resistance is the ideal control mechanism against RKN. Rmi1 (Resistance to M. incognita 1) is an additive gene for M. incognita resistance identified from the soybean cv. Forrest. Rmi1 resides in a major QTL on chromosome 10 that has been identified in multiple mapping studies for M. incognita resistance in soybean in differing genetic backgrounds, but its identity remained unknown. First, a survey of plant-parasitic nematodes (PPN) in Georgia soybean fields was conducted to determine PPN and RKN species distribution. RKN was identified in nearly half of tested soil samples. M. incognita was by far the most common RKN species. Next, gene expression after M. incognita infection in Forrest-derived recombinant inbred lines (RILs) either with or without Rmi1 was analyzed using RNAseq, identifying differential expression of several genes relating to RKN feeding cell development and plant defense pathways in the resistant line. To characterize the causal gene(s), Rmi1 was fine mapped to two candidate genes – a β-1,4-endoglucancase (EG) and pectin methylesterase (PME1). Both genes contain multiple polymorphisms in the promoter and gene sequences, including three missense SNPs in EG and five missense SNPs and one nonsense SNP in PME1. EG shows higher expression in susceptible lines than in Rmi1 resistant lines regardless of infection status, suggesting a possible role in host susceptibility. Using promoter:GUS constructs created using either the resistant or susceptible EG promoter, expression was observed in giant cells. A composite plant assay using CRISPR/Cas9 editing to knockout EG in a resistant RIL did not alter resistance, but a decrease in susceptibility after EG knockout was observed in a susceptible RIL, demonstrating the potential involvement of the β-1,4 endoglucanase as a susceptibility factor for soybean resistance to M. incognita.