19. Construction of an RFLP/RAPD linkage map by using recombinant inbred lines

Faculty of Agriculture, Kyushu University, Fukuoka, 812 Japan

We developed the recombinant inbred (RI) lines as a permanent mapping population for RFLP/RAPD (random amplified polymorphic DNA) markers and used them for construction of RFLP/RAPD map.

The RI lines were developed by inbreeding the progeny of an F\2\ population derived from the cross of Japonica variety "Asominori" with Indica variety "IR24" by the single-seed descent method. A set of 165 F\6\ lines were obtained from original 227 F\2\ individuals. Among them, we randomly selected 84 lines and used a single plant per line for mapping. RFLP markers previously mapped by Saito et al. (1991) and new genomic clones from IR24 were used and RAPD fragments amplified by 20 kinds of 10 nucleotide primers (Operon Technologies, INC.) were also used for mapping. The map distances were estimated by using the formula of Haldane and Waddington (1931). The RFLP/RAPD map constructed in this study (Fig. 1) covered approximately 1090 cM containing 114

Fig. 1. Rice RFLP/RAPD linkage map by using RI lines. The RFLP markers (Saito et al. 1991) are designated only number without prefix XNpb. The number with prefix Q shows an RFLP marker newly mapped. The RAPD markers are shown with primer names and the size of polymorphic fragment (e.g. for V17\1760\, V17 shows primer name and 1760 shows the size of the polymorphic fragment (bp)).

RFLP loci and 26 RAPD loci. Ten linkage groups were assigned to their respective chromosomes, although there were gaps in linkage groups for chromosomes 3 and 6. This RI population showed distorted segregation of markers for chromosomes 3, 6 and 12, and heterozygous loci (3.6% of average frequency of heterozygosity per line) still remained. The map, however, corresponded well to the previous map constructed by using F\2\ population (Saito et al. 1991). This landmark map and the RI population established in this study will be useful for further accumulation of molecular markers and model analysis of quantitative trait loci.

References

Haldane, J.B.S. and C.H. Waddington, 1931. Inbreeding and linkage. Genetics 16: 357-374.

Saito, A., M. Yano, N. Kishimoto, M. Nakagahra, A. Yoshimura, K. Saito, S. Kuhara, Y. Ukai, M. Kawase, T. Nagamine, S. Yoshimura, O. Ideta, R. Osawa, Y. Hayano, N. Iwata and M. Sugiura, 1991. Linkage map of restriction fragment length polymorphism loci in rice. Japan. J. Breed. 41: 665-670.