Two genomic regions duplicated in distal ends of the short arms of chromoso
mes 11 and 12 in rice (Oryza sativa L.) were characterized by YAC ordering
with 46 genetic markers. Physical maps covering most of the duplicated regi
ons were generated. Thirty-five markers, including 21 rice cDNA clones, sho
wed the duplicated loci arrayed strictly in the same order along the two sp
ecific genomic regions. Regardless of their different genetic distances, th
e two duplicated segments may have a similar and minimum physical size with
an expected length of about 2.5 Mb. However, differences of RFLP frequency
for the duplicated DNA copies and recombination frequency for a given homo
eologous area between the two regions were observed, indicating that these
changes in genome organization occurred after the duplication. Our results
establish a good model system for resolving the relationships between gene
duplication, expression of duplicated genes, and the frequency of meiotic r
ecombination in small chromosomal regions.