Sequence analysis of a rice BAC covering the syntenous barley Rpg1 region

In the course of map-based cloning of the barley stem rust resistance gene Rpg1, we identified a rice bacterial artificial chromosome (BAC) containing the Rpg1 flanking markers. Based on the excellent gene order colinearity b etween barley and rice in this region, we expected that this rice BAC would contain the barley Rpg1 homologue. In order to identify the putative rice homologue, we sequenced ca. 35 kb of the rice BAC at random and then an add itional 33 kb of contiguous sequence between the two most closely spaced Rp g1 flanking markers. Sequence analysis revealed a total of 15 putative gene s, 5 within the 33-kb contiguous region. A rice Rpg1 homologue was not iden tified, although a gene encoding a hypothetical polypeptide with similarity to a membrane protein could not be eliminated as a candidate. Surprisingly , four of the genes identified in the 33-kb contiguous rice sequence showed a high degree of similarity with genes on Arabidopsis chromosome 4. The ge nome regions harboring these genes showed some relatedness, but many rearra ngements were also evident. These data suggest that some genes have remaine d linked even over the long evolutionary separation of Arabidopsis and rice , as has also been reported for mammals and invertebrates.