The orientation of RFLP linkage map and the assignment of RFLP markers to the restricted chromosomal segment were determined on seven pachytene chromosomes (1, 3, 4, 5, 8, 9 and 12) of rice. A total of 24 interchange breakpoints were detected by pachytene analysis of reciprocal translocation (RT) heterozygotes derived from crosses between 12 RT lines and normal diploid varieties. Further, 19 strains of japonica-indica hybrid tertiary trisomics were developed and provided for RFLP gene dosage analysis, resulting in locating 32 breakpoints of the extra tertiary chromosomes within genetic linkage segments defined by RFLP markers. From these results, the orientation of RFLP linkage groups on pachytene chromosomes and the assignment of 113 RFLP markers and four cloned rice genes to chromosome arms were conducted, together with the delimitation of centromeres on 6 RFLP linkage groups (1, 3, 4, 8, 9 and 12). Meanwhile, 15 groups of RFLP markers were incorporated with the restricted segments of pachytene chromosome. Compared with RFLP map, the physical distance of a part of the long arm of chromosome 1 was 5.4 to 8.8 cM/μm at the pachytene stage.
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