Wheat-rye translocation lines are widely used in wheat breeding programmes by reason of biotic stress tolerances. Though there have been a number of researches regarding abiotic stress tolerance, the tolerance of the lines depends on wheat genetic background, not on rye chromosome. Here, we investigated wheat-rye translocation specific transcripts derived from cDNA-AFLP under drought stress, which may help to elucidate the reaction under the stress. ‘OK91G117’ (1BL.1RS translocation) and ‘OK91G144’ (non-translocation) were used as materials, which are near-isolines for 1RS. 25% PEG 6000 was added in culture solution to simulate drought condition and root tissues were sampled at each 0 h, 3 h, 6 h, 12 h, 24 h, and 48 h after PEG treatment for RNA extraction. As a result of cDNA-AFLP, TDFs (transcript derived fragments) that were specific to OK91G117 were sequenced. GO functions of each sequenced TDF were annotated by Blast2GO using standard parameter with cut-off level 3 and mapped to the GO term (i.e. biological process; BP, molecular function; MF, cellular component; CC). The term with “organic substance metabolic process”, “primary metabolic process”, and “cellular metabolic process” account for almost 50 % of BP. The most represented terms among probes classified to MF were “transferase activity” and most of TDF were annotated in “cell part” of CC. In addition, rye-chromatin specific markers were developed by BLAST comparing sequence of TDF with wheat and rye genome data. RT-PCR was conducted to validate expression patterns of selected TDF. Further studies will be needed to elucidate functions of the highly expressed genes under drought stress.

Hamlet (PI549276) possessing 2RL was obtained by cross between a wheat cultivar ND7532 (Froid/Centurk) and a rye cultivar Chaupon. Chaupon was known to have resistant gene to biotype L of Hessian fly [Mayetiola destructor (Say)] larvae. The wheat-rye translocation line (Coker797*4/Hamlet) was also known to be resistant to biotype L of Hessian fly larvae. We analysed a set of 96 ESTs from the wheat-rye translocation line (2BS/2RL). ESTs were classified by various physiological processings, such as primary metabolism, secondary metabolism, transcription, translation, transport, signal transduction, defense, transposable element, and others. Three sequences encoding thioredoxin peroxidase, 26S rRNA, and rubisco small subunits were homologous to registered genes in rye. Although limited number of clones were used to develop ESTs, these clones and their sequence information may be useful for researchers studying general physiology and molecular biology on the translocation line.