Susceptibility genes, a novel strategy to improve resistance against the root-knot nematode Meloidogyne incognita

The root-knot nematode Meloidogyne incognita is the most invasive plant disease-causing agent threatening global agricultural productivity. The lifecycle of M. incognita mainly takes place inside host roots where it forms a permanent feeding site. The formation of the feeding site is damaging to the plant as it is forced to allocate significant amounts of assimilates to the feeding nematode. To control nematode infections, crops can be made more resistant by introgressing major resistance genes (R-genes). So far, only the R-gene Mi-1.2 is widely used in cultivated crops in the defence against M. incognita. Resistance based on Mi-1.2 is currently losing efficacy in the field due to rising temperatures as Mi-1.2 is temperature sensitive and because of natural selection of virulent nematode populations. This has prompted a search for alternative strategies to develop durable nematode resistant crops. To this end, the research described in this thesis focused on identifying less conducive allelic variants of genes that critically determine susceptibility of plants to M. incognita (i.e. S-genes). In Chapter 2, we used genome-wide association (GWA) mapping to unravel the genetic architecture of susceptibility of Arabidopsis to M. incognita. For the GWA mapping, we quantified the susceptibility of 340 natural Arabidopsis inbred lines which were thought to lack major R-genes against M. incognita. This led to the identification of four QTLS significantly associated with the reproductive rate of M. incognita as a measure of susceptibility of Arabidopsis. Functional characterization of two quantitative trait loci (QTL) revealed a role for BRASSINAZOLE RESISTANT1 (BZR1) and a novel F-box family protein (FRNI1) in the susceptibility of Arabidopsis to M. incognita. However, our first GWA study could only explain 50% of the additive heritable variation within the population of Arabidopsis lines. Therefore, we reanalysed the data using less stringent thresholds in the statistical analysis in Chapter 3. This resulted in the identification of 15 additional QTLs collectively explaining 100% of the additive heritable variation in reproductive rate of M. incognita in Arabidopsis. To test if we had not merely identified false positives, we functionally characterized one novel QTL with the lowest statistical support and smallest effect size. This resulted in the identification of ETHYLENE RESPONSE FACTOR 6 (ERF6) as co-regulator of susceptibility to M. incognita in Arabidopsis. Previously, ERF6 had been linked to mediating abiotic stress responses in Arabidopsis, which suggests that susceptibility to root-knot nematodes involves mitigation of abiotic stress. In Chapter 4, we describe a QTL harbouring two genes encoding TIR-NLR-type immune receptors typically associated with major resistance in plants, named DOMINANT SUPPRESSOR OF Camta 3 NUMBER 1 (DSC1) and TIR-NB-LRR-WRKY-MAPx protein (WRKY19). After functional characterization with T-DNA mutant lines, we discovered that both genes do not confer major resistance, but play a role in susceptibility to M. incognita through other mechanisms. Given the head-to-head orientation of DSC1 and WRKY19 in the Arabidopsis genome, we suggest that both genes may function as a TIR-NLR immune receptor pair regulating basal levels of immunity to root-knot nematodes. In Chapter 5, we describe a QTL on chromosome 5 harbouring three genes which contribute to the quantitative variation in susceptibility of Arabidopsis to M. incognita. The three genes encode a RING-variant domain-containing protein RU-BOX1 and two novel F-box proteins, FFBD1 and FRNI1. Further investigation showed that the mechanisms underlying the effects of RU-BOX1 and FRNI1 on susceptibility of Arabidopsis to M. incognita may involve gibberellic acid and auxin-mediated signalling and responses. In conclusion, this thesis demonstrates that Arabidopsis harbours significant quantitative variation in susceptibility to M. incognita. This quantitative variation in susceptibility to M. incognita gives evidence for the complex genetic architecture of this trait in Arabidopsis, which most likely does not involve segregating major R genes. Instead, Arabidopsis harbours allelic variation in genes that critically determine susceptibility independent of effector triggered immunity and that are therefore designated as S-genes. This knowledge can be used to identify loss-of-susceptibility alleles of homologous S-genes in other plant species for the development of durable resistance against M. incognita in crops.