Efficiency of IRAP and ITS-RFLP marker systems in accessing genetic variation of Pyrenophora graminea

Abstract

The usefulness of IRAP (inter-retrotransposon amplified polymorphism) and ITS-RFLP (restriction of PCR-amplified internal transcribed spacers of the rDNA) markers in the analysis of 39 Pyrenophora graminea isolates was determined. Each marker system could discriminate between all of the isolates in detecting polymorphism, albeit with variable efficiency. IRAP and ITS-RFLP produced 85% and 77% polymorphic bands, respectively, with a corresponding mean polymorphic information content (PIC) of 0.38 and 0.36. The IRAP marker index ratio (2.41) was higher than ITS-RFLP (1.50). On one hand, the quality nature of data (QND) was higher for ITS-RFLP (0.169) than IRAP (0.093). However, correlation between both marker similarity matrices was significant (r = 0.34, p < 0.05). These findings suggest their combined use in phylogenetic analysis. To our knowledge, this is the first report of a comparison involving these two advanced DNA marker systems.

Distribution of mating-type alleles and M13 PCR markers in the black leaf spot fungus Mycosphaerella fijiensis of bananas in Brazil

“…The genetic variability of pathogenic populations has been analyzed using several different molecular markers (Zein et al, 2010;Nusaibah et al, 2011). The most commonly used marker techniques include inter-simple sequence repeat (ISSR) analysis, which has been widely used to study fungal variability (Neal et al, 2011), and the analysis of inter-retrotransposon amplified polymorphisms (IRAPs), which is a readily accessible method owed to the availability of sequencing databases and the abundance of retrotransposons in the genomes of many organisms (Zein et al, 2010).…”

Pyrenophora tritici-repentis, Causal Agent of Tan Spot: A Review of Intraspecific Genetic Diversity

“…Arabi and Jawhar (2007) observed high genetic diversity in Syrian population of P. graminea with ITS region. Zein et al, (2010) observed fingerprints generated www.intechopen.com from the five restriction digestions of the nrDNA ITS region denoted high levels of intraspecific variation within the P. graminea population. Bakri et al, (2011) observed high levels of intraspecific variation within the P. graminea population.…”

“…Isolates of different species of have been characterized used this methodology (Arabi & Jawhar, 2007;Wu et al, 2003;Zein et al, 2010). This procedure was developed by Botstein et al, www.intechopen.com (1980).…”

“…However, the same isolates showed a broader spectrum and a higher level of virulence on the host differentials (Wu et al, 2003). Recently, Zein et al, (2010), analyzed isolates of P. graminea, the causal agent of leaf stripe disease obtained from Syria, using ITS-RFLP. They observed the fingerprints generated from the six restriction digestions of the DNA ITS region showed high levels of intraspecific variation within the P. graminea population.…”

“…They observed the fingerprints generated from the six restriction digestions of the DNA ITS region showed high levels of intraspecific variation within the P. graminea population. Zein et al, (2010), used IRAP (inter-retrotransposon amplified polymorphism) and ITS-RFLP, each marker system could discriminate between all of the isolates in detecting polymorphism. Similar studies with a global collection of P. tritici-repentis could be developed to provide information for future selection of isolates to develop durable wheat tan spot resistance.…”