Application of restriction fragment fingerprinting with a rice microsatellite sequence to assembling rice YAC clones

To refine the current physical map of rice, we have established a restricti on fragment fingerprinting method for identifying overlap between pairs of rice yeast artificial chromosome (YAC) clones and defining the physical arr angement of YACs within contiguous fragments (contigs). In this method, Sou thern blots of rice YAC DNAs digested with a restriction endonuclease are p robed with a rice microsatellite probe, (GGC)(5). The probe produces a uniq ue fingerprint profile characteristic of each YAC clone. The profile is the n digitized, processed in a computer, and a statistic that represents the d egree of overlap between two YACs is calculated. The statistics have been u sed to detect overlaps among YAC clones, thereby idling a gap between two n eighbouring contigs and organizing overlapping rice YAC clones into contigu ous fragments. We applied this method to rearranging YACs that had previous ly been assigned to rice chromosome 6 by anchoring with RFLP markers.