## 5 Mining 'Omics Data for Leads to Novel Defense Genes  
Whole genome sequencing (genomics), and global profiling of gene expression (transcriptomics) and protein expression (proteomics) are valuable in comparing both host and pathogen genotypes. Genome sequencing provides the ultimate genotyping data, and can aid in predicting whether an organism has the capacity to produce a phenotype based on the presence or absence of known genes. The transcriptome represents a collection of expressed genes in a selected group of cells from a selected genotype, at a given time, and under specific conditions. At best, it gives insight into the abundant genes and major molecular pathways associated with a biological response, such as a host resistance. However, it is not always clear how to select specific genes for further testing in the laboratory or field from global gene expression data. The size and quality of reference databases continue to be a critical aspect of gene identification (annotation) in 'omics studies. A comprehensive comparative genomics approach recently was used to discover pathogenicity genes of the root-knot nematode, _Meloidogyne incognita_[18]. The authors collated 15,952 genes common to plant-parasitic nematodes that were not found in other nematode genomes and identified 993 genes predicted to encode secreted nematode proteins with potential to interact with host proteins and result in disease. Sixteen genes that were present as single-copy in _M. incognita_ were targeted for gene silencing experiments. RNA-based gene silencing is discussed in more detail in Section 6. Of the 16 target genes, 12 resulted in reduction in nematode egg masses and/or gall counts in root infection assays when gene function was disrupted. This approach identified novel pathogenicity proteins and narrowed the candidate gene pool to a feasible number for further testing  
A transcriptome study of root responses to _M. graminicola_ infection was carried out using the resistant African rice, _Oryza glaberrima_, and a susceptible japonica cultivar of _O. sativa_[6]. In the resistant rice, nematode penetration was reduced, and females were smaller and laid fewer eggs compared to the susceptible rice. Over 3-fold more host genes were induced in root tips or whole roots at early infection in the resistant compared to susceptible rice, and about 5.5-fold fewer genes were repressed in the resistant compared to the susceptible genotype. The expression of genes encoding the antifungal protein thionin was high in root tips of the resistant rice without nematode challenge, whereas genes for the phenylpropanol pathway enzyme phenylalanine ammonia lyase (PAL), for lignin biosynthesis, and the pathogenesis-related proteins PR-2 (glucanase) and PR-10 (RNase-like) were strongly induced during infection. A gene for callose degradation was also induced upon infection in the resistant rice. These findings indicated that resistance involves the jasmonate and ethylene signal pathways, and changes in cell-wall composition. However, cultivar differences in lignin content were not supported by observations of autofluorescence around the giant cells. Finally, the authors examined 10 genes from their study that corresponded to _O. sativa_ candidate-resistant genes shown to be physically linked to QTL for _M. graminicola_ resistance [3]. These included genes for the phenylpropanol and lignin biosynthetic pathways, thionin and thuamatin-like antifungal genes, jasmonic acid biosynthesis, and a stripe rust resistance gene orthologique. Transcriptomic responses to _H. avenue_ were reported for roots of resistant and susceptible wheat genotypes [79]. The resistant wheat roots harbored fewer mature nematodes, which was attributed to slowed development of J3- and J4-stage nematodes. The roots of the resistant genotype also displayed a bi-phasic release of ROS, an early transient, and a later sustained burst, typical of many resistance responses in leaves [80; 81].