Identification of differentially expressed genes in Alternanthera philoxeroides under drought stress using suppression subtractive hybridization

The current study was conducted by using suppression subtractive hybridization (SSH) to identify the differentially expressed genes in Alternanthera philoxeroides under drought stress and thus to explore the molecular mechanisms of drought tolerance. The mRNA was extracted from the roots of drought-treated and well-watered A. philoxeroides to construct SSH cDNA library. Positive clones were selected for sequencing and further analyzed by BLAST for screening non-redundant and homologous expressed sequence tags (ESTs). Then these ESTs were put into the Gene Ontology database for functional annotation and Kyoto Encylopedia of Genes and Genomes (KEGG) for metabolic pathways analysis. Four cDNA fragments, ZFP (zinc finger protein), HSP70 (heat shock protein 70), CAT (catalase), and TPS (trehalose-6-phosphate synthase), were randomly chosen for RT-PCR analysis. In the SSH cDNA library, 286 positive clones picked up randomly were sequenced and finally 269 sequences were available. After cluster analysis of the ESTs, 82 unigenes were obtained, in which 63 genes displayed a high homology to known sequences. KEGG analysis found that these genes were involved in 14 metabolic pathways, such as the pathways of plant hormone signal transduction and biosynthesis of secondary metabolites. The expressions of the above four cDNA fragments were all up-regulated in A. philoxeroides under drought stress. This study presented a basis forbstudying the drought tolerance mechanism of A. philoxeroides, which provided a theoretical basis for managing the spread of this plant.