Abstract：Abstract：Differential Display Reverse Transcript Polymerize Chain Reaction (DDRT—PCR)was applied to study gene expression in submergence-tolerant rice FR13A and submergence sensitive rice IR39595-503-2-1-2 under submergence stress. The results showed that 1428 bands were amplified from 40 pairs of primers in the two varieties, 102 of them appear different obviously between the two varieties and which accounted for 7.1%, 42 of 102 bands which came from submergence-tolerant variety. The northern blot results showed that 7 fragments of the 42 were confirmed to express in submergence tolerant variety FR13A. Those fragments were then cloned into vectors for sequencing．Sequence analysis through Internet Blast searching showed that 4 of them related to response and biochemical changes under water logging, one of them showed high homogeneity to ATP binding protein,3 of them showed high homogeneity to partial sequence of Isocitrate dehydrogenase, NADH2 dehydrogenase and Terminal acetyltransferase .the other 3 fragments ware novel cDNA fragment.
