To clone a rice yield QTL,a comparative analysis on the region of the physical maps derived from rice varieties Zhenshan 97 and Minghui 63,the two parents for mapping the QTL,was performed.Physical gaps in this region of the two physical maps were closed.Putative SNPs of this region between Zhenshan 97 BAC end sequences and Nipponbare reference sequence,and that between Minghui 63 BAC end sequences and Nipponbare reference sequence were validated.Results showed that most putative SNPs are correct but some are from errors of BAC end sequence.The confirmed SNPs will be used as important markers in the positional cloning of gene or QTL.Furthermore,representative putative Zhonghua 11 specific repetitive sequences found in our laboratory through Zhonghua 11 BES analysis were comparatively analyzed via Southern hybridization.The results will be helpful in cloning of the rice yield QTL and realizing the evolution of rice repetitive sequences among different rice varieties.