Gene expression in incompatible Striga-host interactions
The mechanics of plant host response to attempted parasitism and the nature of the gene expression changes occurring during both compatible and incompatible interactions between S. gesnerioides and cowpea have been investigated using oligonucleotide-based microarrays. Up until now, only limited information was available on global changes in transcription taking place in hosts in response to Striga parasitism. Our data show that alterations, both positive and negative, in a wide range of processes occur as a consequence of Striga attack. In cultivars harboring resistance genes capable of interfacing with a defense signal transduction pathway, as in the case of cowpea cultivar B301 which contains multirace resistance to S. gesnerioides, a rapid and robust defense response is elicited in the form of hypersensitivity at the site of parasite attachment, under conditions where the invading parasite is recognized. We found that accompanying the visible hypersensitive response is the up-regulation of genes involved in signal transduction and biosynthetic processes associated with formation barriers to prevent parasite ingress. These include activation of gene expression associated with cell wall biogenesis and strengthening (e.g., lignifications), as well as processes leading to programmed cell death at the host-parasite interface.
In a study of the interaction of S. hermonthica with its host plant sorghum, Hiraoka and Sugimoto  observed that attempted parasitism induced JA-responsive genes and suppressed SA-responsive genes in the roots of a highly susceptible cultivar, and suggested that susceptible hosts recognize Striga parasitism as wounding stress rather than microbial stress. In contrast, they found that in the roots of a moderately resistant sorghum cultivar, both SA- and JA-responsive genes were induced suggesting that resistance involved pathways associated with both wounding and pathogen challenge. Pretreatment of the roots of the moderately resistant sorghum cultivar with SA led to an inhibition of Striga development suggesting that the SA-responsive genes are directly involved in host resistance mechanism. In a subsequent study, subtractive hybridization was used to examine the interaction of Lotus japonicus with P. aegyptiaca (a compatible interaction) and S. hermonthica (incompatible) . These investigations found little or no overlap among the Phelipanche and Striga-induced transcripts, suggesting that L. japonicus roots are able to distinguish the compatible parasite from the incompatible one. Among the genes specifically induced by P. aegyptiaca were those encoding components of JA biosynthesis, whereas S. hermonthica parasitism induced genes in phytoalexin biosynthesis.
Examination of the differential expression of genes encoding candidate disease resistance and signal transduction components during the interactions of S. gesnerioides with various cowpea cultivars revealed that PR-5 transcript levels were dramatically elevated in the roots of cowpea genotypes resistant to Striga compared to uninfected roots and roots challenged with a race of Striga to which it was susceptible or adapted to another host species . In contrast, transcript levels of COI1 and EDS1 increased during susceptible and non-host interactions but were unchanged during resistance response. The COI1 gene product plays a pivotal role in activation of JA-mediated response cascades and, in some cases, serves as an inhibitor of SA signaling. EDS1 encodes lipase-like proteins that control defense activation and programmed cell death in plants. Induction of COI1 gene expression in the compatible Striga-cowpea interaction suggests that COI1 may down-regulate or suppress the resistance response and block SA signaling pathway in cowpea plants, thus allowing Striga attachment and further development.
Swarbrick et al.  characterized gene expression changes in the roots of the S. hermonthica resistant and susceptible rice cultivars Nipponbare and IAC 165 using a rice microarray. These investigators found that the levels of a large number of transcripts in rice roots were either positively (up-regulated) or negatively (down-regulated) affected by parasitism. Among the genes up-regulated in the Striga-resistant cultivar Nipponbare were ones encoding HR protein homologs; PR-proteins associated with microbial pathogenesis including endochitinases (PR-3), glucanases (PR-2), and thaumatin-like proteins (PR-5); pleiotropic drug resistance ABC transporters; and enzymes in phenylpropanoid metabolism. In addition, transcripts encoding several WRKY transcription factors (TFs), previously implicated in other SA-dependent resistance responses , were observed to be more abundant in parasitized roots. Large-scale down-regulation of gene expression was observed in the susceptible cultivar IAC 165, particularly transcripts whose encoded products annotate to Gene Ontology (GO) functional categories of plant growth regulator signaling and metabolism, biogenesis of cellular components, and cell division. Interestingly, a majority of the genes down-regulated following attempted Striga parasitism in both IAC165 and Nipponbare roots encodes products that annotate as proteins of unknown function.
A recent study that used whole genome oligonucleotide arrays to examine the transcriptome of A. thaliana roots after inoculation with pre-germinated S. hermonthica seeds found that large numbers of genes involved in cell wall synthesis, defense signaling, regulation of transcription and protein synthesis, oxidative stress, and primary and secondary metabolism were up-regulated at the earliest stages of parasite infection . This included up-regulation of many genes (EDS1, EDS5, PAD3, NPR1, NIMIN1, PR2) involved in the SA signaling pathway, as well as the up-regulation of a key WRKY transcription factor (AtWRKY70) that regulates the expression of genes involved in the SA signaling pathway and is thought to have a role in determining the balance between SA and JA signaling. In addition, there was evidence for the activation of genes involved in the JA and ethylene biosynthetic pathways.
In the present study of cowpea-S. gesnerioides interactions, among the most highly induced genes in the early resistance response (6 dpi) of B301 to SG3 are those involved in response to biotic stimuli, abiotic stimuli, wounding, oxidative stress and HR, and components of the JA and ETH signaling pathways. Among the genes most highly induced were a number of chitinases and chitinase homologs including narbonin, a protein with glycosyl hydrolase activity  whose biological function has yet to be elucidated . Narbonin has been previously suggested as interfering with parasite growth in the root by altering cell wall extensibility .
Lignifications and callused deposition have been previously observed at the interface of host plant cells with invading Orobanche haustorium  and is thought to be correlated with levels of host resistance to Orobanche. We similarly observed an increased expression of genes involved in cell wall biogenesis suggesting that lignifications may be part the mechanism of defense employed by cowpea against S. gesnerioides ingress.
A number of cytochrome P450s, previously implicated in various cellular detoxification pathways in plants, were also found to be induced during the resistance response of B301. Increased cytochrome P450 gene expression has been previously reported during the resistance reaction of rice infected by S. hermonthica.
The only other global study of cowpea transcriptional profiling published thus far is the work by Das et al.  who investigated differences in gene expression in resistant and susceptible cowpea genotypes elicited by feeding of the root-nematode, Meloidogyne incognita, using a soybean Affymetrix Gene Chip expression array. At 3 dpi in both compatible and incompatible interactions, more genes were down-regulated than up-regulated. When expression between infected resistant and susceptible genotypes was compared, a greater number and proportion of genes were down-regulated in the resistant than in the susceptible genotype, whereas more genes were up-regulated in the susceptible than in the resistant genotype in response to nematode infection. Gene ontology based functional categorization revealed that the typical defense response was partially suppressed in resistant roots, allowing nematode juvenile development. Das et al.  suggests that suppression of genes in ROS formation and other defense related responses might be important negative resistance mechanism. Our findings contrast with this, since we see activation of a wide range of processes as a consequence of Striga attack. Direct comparisons of gene lists suggest that in both early stages (3 dpi) of incompatible and compatible interactions there are many induced genes common in both host-parasite interactions suggesting that these may be part of a basal defense response. Among these were genes involved in lignifications and cross-linking. This response leads to heavy lignifications of cell walls and creates a mechanical barrier for the pathogen. In the incompatible cowpea-nematode interaction, expansin, thought to be important for maintaining the specialized feeding structures in hosts, was highly down-regulated. This was not observed in the cowpea-Striga interaction but down-regulation of expansins were observed in the response of a resistant rice cultivar to attack by S. hermonthica.
Gene expression in compatible Striga-host interactions
We know that root parasitic angiosperms secrete pectin methylesterases, polygalacturonase, and other cell wall softening enzymes during attempted penetration of the host root cortex, and that such secretions may in fact assist in overcoming the cell wall reinforcement that occurs in the host root in response to parasite parasitism [30–33]. It is now evident that many different phytopathogens have also evolved specific effectors and virulence factors that are capable of entering the host cell and suppressing the host resistance machinery or bypassing surveillance [34–36]. Among the most highly down-regulated genes in B301 roots during a susceptible interaction with SG4z were genes in the phenylpropanoid and lignin biosynthesis pathways, primary and secondary cell wall biogenesis, and components of the SA and JA signal transduction pathways.
S. gesnerioides-infected cowpea often demonstrated severe reduction in the growth rate and reduction of the host biomass . This was due to two major factors: direct carbon transfer from the host to S. gesnerioides, and reduction of photosynthetic capacity . One of the noticeable changes in gene expression during the susceptible response in B301 was the suppression of plant growth regulators, particularly auxin and gibberellins. Some genes, such as cellulose synthase, known to be involved in cell wall development  were also observed to be down-regulated.
One of the keys to the success of a parasitic plant-host interaction is the translocation of water and nutrients (including nitrates, amino acids, carbohydrates and minerals) from host to parasite through the haustoria . The identification of differentially up-regulated transcripts for transporters responsible for nitrogen, sulfur and amino acids in B301 roots during susceptible interactions with invading SG4z suggests that, in addition to suppressing some host functions to facilitate entry, the parasite is also modifying others to provide a source of nutrition. This is clearly an area that warrants additional study.