Evaluation of a novel method of RNA fingerprinting based on AFLP to compare between avirulent L19 and virulent L22 of potato cyst nematode Globodera rostochiensis

Cyst nematodes have a single infective stage-the preparasitic second stage juvenile- and the pathogenicity factors related to early events in the infection process will exclusively or predominantly be present in this life stage and they will be functional outside the nematode. Therefore, the most interesting TDFs (transcribed derived fragments), are expected in H stage only or S & H stages of the avirulent L19 strain and not present in the virulent L22 strain. Pools of mRNAs of three distinct developmental stages (D, S and H) in the avirulent L19 and the virulent L22 of G. rostochiensis were used for preparation of cDNA of each stage. cDNA-AFLP involves three steps (i) the resulting cDNAs were digested by two kinds of restriction enzymes EcoR I (being rare cutter) and Taq I (being frequent cutter) and ligation of oligonucleotide adapters, (ii) selective amplification of sets of restriction fragments and (iii) gel analysis of the amplified fragments. In this work, the expression levels of 3197 TDFs in three developmental stages of L19 and L22 were monitored. Certainly, a small number of transcripts will be represented by more than one TDFs. Our results, show no obvious difference between avirulent L19 and virulent L22 because the total TDFs bands observed on AFLP polyacrylamide gels of avirulent L19 and virulent L22 in three distinct stages and about 43 EcoR I and TaqI primer combinations about 3197 TDFs. In L19 about 50 TDFs (1.56 %) but in case of L22 about 67 TDFs (2.10 %) were observed in S and H stages or H stage only. However 9 TDFs (0,20 %) were observed in S and H stages or H stage only of avirulent L19 and not present in virulent L22.