cDNA-AFLP analysis reveals differential gene expression in response to salt stress in Brachypodium distachyon

Environmental stresses such as drought, salinity, cold, and heat negatively affect the growth of plants and productivity of crops. The mechanism of salt tolerance is one of the most important fields in plant science, and our understanding of this process must be improved in order to increase agricultural crop production. In our study, we identified salt stress-responsive transcripts using the cDNA-AFLP technique. The obtained transcripts were further analyzed by semi-quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) under various abiotic stresses and hormone treatments. Among 87 transcript-derived fragments (TDFs) that were classified based on their presence or absence (qualitative variants) or differential expression (quantitative variants), we identified 32 TDFs that corresponded to Brachypodium genes with locus name. These clones are involved in various molecular functions and have transferase, protein binding, nucleotide binding, transporter, protein kinase, catalytic, hydrolase, RNA binding, and enzyme regulation activities. Further, the expression patterns of up-regulated 9 salt stress-response genes in cDNA-AFLP experiments were evaluated through semi-quantitative RT-PCR. Those genes were involved in signaling cascades [the casein kinase I (CKI)-like protein], regulation of enzyme activity [protein phosphatase 2C (PP2C) gene], phospholipid asymmetry [aminophospholipid ATPase (ALA)], cellular ion homeostasis [calcium-transporting ATPase, potassium transporter, calcium-binding protein (CBP)], and plant growth and development [pentatricopeptide repeat-containing protein (PPRP), 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenases] and the putative roles of the identified TDFs involved in salt stress mechanisms are discussed. A better understanding of the mechanisms of salt stress tolerance and salt stress response genes in Brachypodium would be very useful for the breeding and genetic engineering of salt tolerance varieties in other Poaceae families, including wheat, barley, and rice.