Variability in Fusarium species Causing Wilt Disease in Crops: A Transcriptomic Approach to Characterize Dialogue Between Host and Pathogen - Crop Improvement: New Approaches and Modern Techniques - page 282

the necrotrophic pathogens are benefitted from any kind of physical damage to cells
and JA provides defense against these and further JA is also associated with induced
systemic resistance (ISR), which is a priming reaction against subsequent infections
(Pieterse et al. 2009 ; Matilla et al. 2010 ). Henceforth these recent advanced techni-
cal studies of microbial communities on metagenomics and metatranscriptomics
(Morales and Holben 2011 ; Kakirde et al. 2010 ) could be applied to pathogens
and then conjoining with plant transcriptomics, shall provide deeper insights into
multiple interactions. In the plant rhizospere 33,000 archeal and bacterial species
were found when grown on disease-suppressive soil, by combining a high-density
16S ribosomal DNA oligonucleotide microarray (PhyloChip metagenomics) of the
rhizosphere microbiome with culture dependent functional analyses (Mendes et al.
2011 ). The disease caused by Rhizoctonia solani (fungal root-infecting pathogen)
was found to be suppressed by the Proteobacteria, Firmicutes and Actinobacteria
species, which led to the proposal or conclusion that plants interaction with multiple
microbe species can contribute to suppression of the disease (Schenk et al. 2012 ).
Future Prospects
The prime concerns are related to with the understanding of host-pathogen interac-
tions including plant defense responses. To monitor fungal colonization the system-
atic re-isolation procedures are required in host-pathogen combinations (compatible
and incompatible). This is a challenging issue, which will lead to developing new
strategies to control disease. In order to identify the genes required for the hyper-
sensitive response, studies shall focus on performing expression profiling of crop
plants. The cDNA-AFLP analysis shall provide expression profiling of both normal
and Fusarium infected plants, (identification of plant/pathogen genes associated
with the infection process). The focus on variability of Fusarium sp. infecting Crops
is the need of hour and will help to understand the host-pathogen relationship for
disease management. The crop colonization by Fusarium sp. shall be studied and
the samples collected from definite time points irrespective of speed and extent
of colonization among the strains. The molecular biology advancements have led
to the use of DNA based markers in place of morphological markers. Initially, the
RNA samples of (healthy/infected plants) shall be put to cDNA-AFLP analysis for
identifying transcripts differentially expressed, which are associated with resistance
response and infection process.
Further, the RNA samples from in vitro grown fungal strains shall help in iden-
tifying in planta expressed fungal transcripts and also in identifying in vitro differ-
entially expressed fungal genes among the strains. The infected plants samples col-
lected for analysis by cDNA-AFLP at different time intervals will determine early
to late stages of infection and will also allow detection of the pathogen transcripts.
The expression patterns of the transcripts shall be monitored with several different
primer combinations for amplification in a selective manner and for every primer
combination; the TDFs (transcript derived fragments) can be viewed as bands on