## 5 Mining 'Omics Data for Leads to Novel Defense Genes
Resistance was associated with induction of genes for phenylpropanol biosynthesis, a chitin elicitor receptor kinase, the brassinosteroid insensitive1-associated kinase, peroxididases, and lipoxygenases. The latter two genes were thought to be involved in the ROS bursts. Induction of genes involved in oligo- and monosaccharide transport, RNA methylation, DNA repair, and sulfite metabolism were also observed. In a related study, [PERSON] et al. [82] examined genes induced by _H. avenue_ in the roots of the susceptible wheat at early- to mid-stage infection. The genes encoded cell-wall degrading enzymes, peptide transporters, auxin biosynthesis and signaling, peroxididases, glutathione S-transferases, and UDP-glycostransferases (for glycosylation of secondary stress metabolites and phytohormones). The antifungal lipid transfer proteins, 1,3-\(\beta\)-glucanases, and chitinases also were induced. Additional experiments could be done to demonstrate a genetic or physiological correlation between susceptibility and candidate gene induction, as some of the genes might be involved in the non-specific root immunity response to biotic stress [83]. Twelve of 16 NBS-LRR genes were repressed during nematode challenge, indicating that susceptibility was associated with damping early pathogen recognition mediated by NBS-LRR resistance proteins. The same susceptible wheat cultivar used in the above two studies was challenged with mobile J2 _H. avenue_ to characterize root interactions with the pre-penetration stage of the nematode [84]. Wheat roots produced 27 induced genes and 66 repressed genes, and the nematodes showed 867 induced genes and 12 repressed genes. The repressed wheat genes were enriched for ROS metabolism, whereas over 40% of the induced nematode genes were orthologues of known candidate parasitism genes; genes for primary metabolism and nematode body wall development were also observed. One nematode-expressed gene of interest encoded a chitinase-like protein that suppressed the host cell death resistance response in the tobacco assay. There is a void of information about how the roots of small-grain cereals respond to _R. solani_ or _F. culmorum_ on a global gene expression scale. However, the resistance response to _R. solani_ AG-8 was examined in the model Brassica _A. thaliana_ using the Affymetrix ATH1 Genome array, a DNA hybridization-based platform [85]. The study revealed that _R. solani_ AG-8 induced root genes for ROS metabolism, including peroxididases, an alternative oxidase, the respiratory burst homolog subunit RbohD of the NADPH oxidase complex, FAD-binding proteins, and glutathione S-transferases. Genes for heat shock proteins, expansins, and modification of xyloglucan, pectin, polygalacturonic acid, and other cell wall-associated proteins components were also induced. The authors generated mutations in two _Rboh_ subunit genes NADPH oxidase that resulted in an enhanced degree of susceptibility to _R. solani_ AG-8. In general, the data indicated that Arabidopsis roots responded to a fungal necrotroph in ways reported for small-grain cereal roots after nematode challenge. One exception was the lack of evidence for the jasmonate signal pathway. Specifically, though, the study pointed to the importance of a functional NADPH oxidase in disease resistance. A proteomics approach was used to identify _R. solani_ AG-8 genes induced in the presence of wheat seedlings [12]. This interaction represented the susceptibility response of the host, and the pathogenic response for _R. solani_. Protein fractions were obtained from cultured mycelium and mycelium growing on nitrocellulose membranes laid over wheat seedlings in a system. Among the secreted proteins found only in mycelium exposed to the host, cell-wall-degrading enzymes and proteins associated with ROS metabolism were well-represented. Culture filtrates constitutively expressed proteins for lignin breakdown. In the process of mapping the peptide fragments to the genome of _R.