Genetic Diversity Of Different Reed Ecotypes And Bioinformatic Analysis Of PcTGD

Phragmites communis Trin. is a kind of herbage plant living for several years. The representative environment is freshwater or salk marshland. However reed plants can adapt themselves to adverse terrestrial habitats and evolve various ecotypes. There are four ecotypes of reed plants growing widely in Hexi zoulang GanSu province(china).According to the characteristic of their different terrestrial habitats,the reeds were named as: swamp reed(SR),heavy salt meadow reed(HR),light salt meadow reed(LR)and dune reed(DR).Long-term investigations have been done with physiological, biochemistry and molecular biology of the four reed ecotypes. This study investigated the genetic diversity of the four reed ecotypes with PARD and allozyme metheds on the base of previous studies. Sequences analysis and Structure Prediction for Phragmites communis dTDP-D-glucose dehydratase(PcTGD) by bioinformatics are also been done. The main results are as follows:1. The mean percentage of polymorphic loci(P) of four reed ecotypes was 34.1%, and mean expected heterozygosity(He) 0.158.They are all higher than the mean values of plant at the population level so manifest the four reed ecotypes have higher genetic diversity. The values of HR and LR is low than the mean values and the values of SR and DR is high than the mean values. It implies that HR and LR had evolved out from SR or DR.2. The investigation on genetic distance implies that the most closely related two ecotypes are HR and DR, while the most distantly related two are LR and SR. The results of RAPD analysis and allozyme assay were consistent with each other.3. The inbreeding coefficient(F) of the four reed ecotypes are all low than zero and they all have a low outcrossing rate. This implies that the breeding pattern of the four reed ecotypes doesn't be controled by asexual reproduction pattern in a long term, although the breeding pattern of reeds is vegetative reproduction.4. Sequences analysis for Phragmites communis dTDP-D-glucose dehydratase(PcTGD).Using the Chou-Fasmanand GOR methods, we have predicted the secondary structure of the deduced amino acid sequences of previouely cloned Phragmites communis Trin TGD gene. Its hydrophobicity has also been determined by ProtScale method. PcTGD is mainly hydrophobicity on its primary structure. The percentage of helices, strands and coil is separately 26.9%, 23.4% and 49.7%.5. Using PSORT-II methods, we have predicted subcellular location of PcTGD. The results implies that the subcellular location most likely is cytoplasmic.6. Using BLASTP and CLUSTAL W methods, we conducted sequence similarity searching and alignment. We have predicted the three dimensional structure by MODELLER and conducted an rational checking by PROCHECK method.7. PcTGD has a highly conserved active site Tyr***Lys and a Gly*Gly**Gly motif at the N terminus which are belong to a short-chain dehydrogenase/reductase extended family(SDR), and the sequence of its nucleic acid and protein has a highly similarity with SDR(90% and 27%) It characterise PcTGD as a member of SDR.