Physical mapping of unique nucleotide sequences on identified rice chromosomes

A physical mapping method for unique nucleotide sequences on specific chrom osomal regions was developed combining objective chromosome identification and highly sensitive fluorescence in situ hybridisation (FISH). Four unique nucleotide sequences cloned from rice genomic DNAs, varying in size from 1 .3 to 400 kb, were mapped on a rice chromosome map. A yeast artificial chro mosome (YAC) clone with a 399 kb insert of rice genomic DNA was localised a t the distal end of the long arm of rice chromosome (1q2.1) and a bacterial artificial chromosome (BAC) clone (180 kb) containing the rice leaf blast- resistant gene (Pi-b) was shown to occur at the distal end of the long arm of chromosome 2 (2q2.1). A cosmid (35 kb) with the resistance gene (Xa-21) against bacterial leaf blight was mapped on the interstitial region of the long arm on chromosome 11 (11q1.3). Furthermore a single RFLP marker, 1.29 kb in size, was mapped successfully to the distal region of the long arm of rice chromosome 3 (4q2.1). For precise localisation of the nucleotide sequ ences within the chromosome region, image analyses were effective. The BAC clone was localised to the specific region, 2q2.1:96.16, by image analysis. The result was compared with the known location of the BAC clone on the ge netic map and the consistency was confirmed. The effectiveness and reliabil ity in physically mapping nucleotide sequences on small plant chromosomes a chieved by the FISH method using a variety of probes was unequivocally demo nstrated.