## 3 Discussion
### Desperately Seeking to Settle  
Of the 36,121 _M. graminicola_ transcripts surveyed in this study, only 367 genes were differentially expressed between resistant and susceptible plants datasets (DEGs-RvS). Globally, we did not observe expression of specific nematode genes but rather a different dynamic of gene expression associated to nematode infection in the resistant rice genotype. For instance, whether entering resistant or susceptible host roots, the nematode (pre-J2s) produce a large set of degrading enzymes, including CWDEs, peptidases as well as a series of other proteinaceous effectors (Figure 3). However, expression of the enzyme-coding genes sharply decreases in the susceptible host after 2 days when _M. graminicola_ initiate their feeding sites in the vascular cylinder. On the contrary, expression of the same genes in the resistant host lasts longer and is still sustained after 8 days when only a limited number of feeding sites are initiated. The same expression pattern applies for nematode genes encoding neuropeptides, some might be involved in chemotaxis and movement. Conversely, RKN genes involved in development are poorly expressed when the nematodes try to infect the resistant host but are activated after 4 to 8 days in the susceptible plants where the nematodes successfully settle and start to develop into J3 (Figure 3). Escaping these general trends in expression patterns are several effector genes that are expressed at different time points (Figure 4) and a few genes with unknown function that might deserve interest (Table S3). To our knowledge, only two studies finely described the RKN genes regulation during the interaction with resistant hosts, namely in the resistant African horned melon _Cucumis metuliferis_[16] and in tomato [17]. [PERSON] et al. [16] focused on the secretome of _M. incognita_ in _C. metuliferis_ when [PERSON] et al. [17] performed a comprehensive comparative analysis of gene expression of _M. incognita_ infecting either susceptible tomato (_Solanum Lycopersicum_) lines or a resistant transgenic tomato line  
Figure 6: Effect of _Mg-VAP_ genes silencing on nematode colonization. Number of nematodes observed in susceptible Nipponbare rice roots 8 days after plant inoculation with 100 J2s soaked in siRNAs targeting either _Mg-VAP1_ or _Mg-VAP2_. As control treatments, nematodes were soaked in water (C) or in siRNAs targeting GFP. Boxplots represent data of one experiment (\(n\geq 8\) per treatment). Data were statistically tested for significance with ANOVA with post-hoc Tukey HSD (\({}^{*}p<0.05\)). The experiment was repeated twice with the same results. expressing the _Mi_ resistance gene. Our observations of RKN gene regulation in resistant rice are similar to the conclusions of [PERSON] et al. [17], who indicated over-expression of _M. incognita_ genes encoding glucosyl hydrolases, pectate lyases, and peptidases in the resistant tomato as opposed to RKN genes involved in host parasitism, development and defence in the susceptible host. Thus, a global view of the nematode behavior emerges, indicating that while J2s settle in susceptible plants and cease the production of CWDE, peptidases and neuropeptides transcripts, the nematodes still require synthesizing such compounds in resistant plants. To facilitate root penetration and migration in host tissues, plant-parasitic nematodes produce cell-wall modifying enzymes, including CWDEs able to degrade cellulose, hemicellulose and pectin polysaccharides and other enzymes to soften the cell-wall structure (see [7] for review). These genes were likely inherited through lateral genetic transfer from soil bacteria or fungi [49] enabling nematodes to successfully invade plant tissues. For sedentary nematodes, expression of CWDE genes generally ends once the nematodes settle and enter in the sedentary phase [7]. In rice- (this study) and tomato-resistant [17] plants, gene expression is sustained, suggesting that the nematode have more difficulties to migrate in the resistant roots and/or to settle to establish a feeding site.