Poncirus trifoliata, a close relative of Citrus species, has been widely used as a cold hardy rootstock for citrus production in low-temperature environments. cDNA Amplified Fragment Length Polymorphism (cDNA-AFLP) and Relative Quantification (RQ-PCR) were used to study gene expression of P. trifoliata in response to 10, 24 and 55 h of low temperature (4°C) treatment and a gradual 3 weeks long cold-acclimation regime. Thirteen differentially expressed cDNA fragments were chosen for further study. These fragments show high similarities to genes with the following known functions: signal transduction and regulation of gene expression, osmotic stress response, cell skeleton reorganization, vesicle trafficking and senescence. Expression levels of genes implicated in signal transduction and regulation of gene expression (MAPK3 and bZIP TF) increased with prolonged exposure to low temperature, but were not upregulated following cold-acclimation. Others were induced following cold-acclimation, but not upon exposure to 4°C. Only the auxin-ethylene GH3-like protein showed dramatic increases during all cold treatments. These comparisons provide information on the dynamic changes in gene expression levels during different cold response regimes. [ABSTRACT FROM AUTHOR]