## 4 Genes Associated with Disease Resistance against Soilborne Pathogens  
Molecular markers are of value to breeders and pre-breeders, but identification of the genes underlying genetic resistance should be identified in order to determine resistance mechanisms. Such knowledge can be applied to other host genotypes, pathogen isolates and, possibly, to other environments. Proceeding from a trait or locus to a gene of interest is now more feasible with whole genome sequencing, sequencing of coding portions of the genome [65], and global sequencing of expressed genes (transcriptomics). Data for multiple individuals can be obtained and analyzed simultaneously due to lower costs of next-generation sequencing and more sophisticated software for assigning function to candidate genes. In a screen for _M. graminicola_ resistance in _O. sativa_, [PERSON] et al. [3] focused on 493 candidate resistance genes in the regions of 11 QTL associated with reduced gall numbers. Genes most likely to have defense-related functions were identified using a variety of software. Sixteen of the genes were differentially expressed in rice roots during nematode infection [66], and 51 were differentially expressed in giant cells [67], discussed further in Section 5. Genes that were predicted to encode lectin domain proteins or other lectin-associated proteins were well represented in the candidate gene pool. The candidate pool also contained orthologues of the barley _Mla_ gene for powdery mildew resistance, and genes encoding peroxidase, enzymes for ROS generation. In a study of _H. filipjevi_ resistance in wheat, [PERSON] et al. [57] reported 11 resistance QTL and 9 candidate protein-coding genes in the regions of the QTL. The candidate proteins included transcription factors that control the expression of specific genes, and regulators of cellular processes. Alternatively, molecular genetics and biochemical approaches have been used to discover the roles of specific genes for defense functions in the host. For instance, the _Cre3_ genes from wheat, _Tritcium turgidum_, and its wild wheat relative, _Aegilops tauschiii_, encode resistance gene analogs, a subset of a large and complex family of nucleotide binding site leucine-rich repeat (NBS LRR) proteins [68; 69]. The NBS-LRR proteins have a role in early pathogen recognition leading to resistance. A majority of plant genes required for qualitative (race-specific) resistance contain NBS and LRR motifs. The _H. avenue_ resistance genes _Cre3_, _Cre 5_, and _Cre 7_ in wheat acted through a cytosolic ascorbate peroxidase gene [70]. The ascorbate peroxidase gene was induced earlier and to a greater extent in resistant genotypes compared to susceptible ones, and its expression was high around the nematode feeding site. This finding indicated that ROS were contributing to resistance in the case of these _Cre_ genes. Clues to defense pathways in the host can be obtained from studies of single genes. The wild grass, _Aegilops variabilis_, carries CreX- and CreY-mediated resistance to _H. avenue_, which has been deployed in wheat [71]. A gene encoding tryptophan decarboxylase1 was strongly induced in _Ae. variabilis_ roots during early stages of nematode infection compared to non-infected controls, but when silenced using the barley striped mosaic virus gene silencing system, the plant roots showed enhanced susceptibility to infection [72]. Tryptophan decarboxylase converts tryptophan to tryptamine, a precursor for the synthesis of secondary metabolites and the phytohormone IAA. Subsequent studies with the _Ae. variabilis_ gene were done in tobacco, a more tractable host for gene disruption and overexpression experiments. These studies showed that overexpression of the _tryptophan decarboxylase1_ gene bolstered resistance, and confirmed that gene disruption or inhibition of its protein reduced resistance [72].