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 272

RAPD, SCARs, RT-PCR, SNPs, microarrays, pyrosequencing, DNA barcoding and
many more and this has led to gene function determination in fungi (Nayaka et al.
2011 ). The DNA microarrays and next-generation sequencing techniques have
helped greatly in genome-wide expression, but in these cases known collection of
transcript sequences must be readily available (Roh et al. 2010 ). However, in com-
parison with above tools, the method of choice for gene discovery (identifying tran-
scripts) in plant-microbe interaction remains to be cDNA-AFLP (Vuylsteke et al.
2007 ; Gupta et al. 2009 ). The cDNA-AFLP technique has been used to study the
interaction between the Fusarium pathogens and the plant hosts, e.g. Fusarium in-
teraction with host Cucumis melo through the analysis of differentially expressed
genes in the vascular colonization by using the approach of cDNA-AFLP (Szafran-
ska et al. 2008 ; Sestili et al. 2011 ). In the species other than model species the utili-
zation of cDNA-AFLP techniques for expression studies is appropriate as it helps in
identification of genes in two species during infection and is also important for
identifying factors of pathogenesis and virulence and thus would help in developing
strategies in controlled manner (Durrant et al. 2000 ; Guo et al. 2006 ; Polesani et al.
2008 ; Wang et al. 2009 ; Gupta et al. 2010 ; Zvirin et al. 2010 ). Under the evolution-
ary pressure the species of Fusarium have modified for better adaptability and thus
have colonized in differing ecological systems (Desjardins et al. 1993 ). These spe-
cies produce a variety of compounds (bioactive secondary metabolites), which are
show toxicity towards plants (Munkvold et al. 1997 ). These toxins also find their
way to animals and humans through the plant products consumed as fodder or food.
The Fusaria have different strains belonging to many groups which are identical
morphologically and thus are difficult to study such as endophytes (Bacon and Hin-
ton 1996 ), saprophytes (Fracchia et al. 2000 ), and plant pathogens (Chandra et al.
2008 ) and thus is the reason for difficulty in establishing taxonomy systems for
Fusarium species. So, it is required to utilize molecular based methods in differen-
tiating taxa. In this context, in recent times the application of phylogenetic species
concept to Fusarium systematic has helped in resolving the difficulties in taxono-
my. This concept requires several characters such as morphology of species cross-
ing between species and molecular markers in species for it to be statistically pow-
erful (Yli-Mattila et al. 2002 ). However, the molecular markers (DNA sequence
data) are preferred because they provide relevant characters. The molecular data in
combination with other morphological characters within Fusarium have helped to
differentiate species, which were otherwise placed differently (Zeller et al. 2003 ). It
has been noted, based on the DNA sequences that often the strains of Fusarium
placed in a forma specialis differ significantly and these need not be monophyletic
in origin (Baayen et al. 2000 ). Inferring from this the traits of plant pathogenicity,
which have high economic importance, need not to have characters that are evolu-
tionary conserved and thus is part in Fusarium species description. Since the arrival
of DNA sequencing at the scene it has become an important criterion in diagnostics
and distinguishing species. The most commonly used sequences to distinguish Fu-
sarium sp. are calmodulin (O'Donnell et al. 2000 ), TEF (translocation elongation
factor 1-α) (Wulff et al. 2010 ), ITS1 and ITS2 (internally transcribed spacer regions
in the ribosomal repeat region) (O'Donnell and Cigelnik 1997 ), tub2 (β-tubulin)