47. Progress in intearation of the molecular maps of rice

1) Dept. of Plant Breed. & Biometry, 252 Emerson Hall, Cornell University, Ithaca, N.Y. 14853, U.S.A.

2) Dept. of Mol. Biol., National Institute of Aerobiological Resources, 2-1-2 Kannondai, Tsukuba City, 305 Japan

3) Dept. of Aerobiology, Faculty of Agriculture, Univ. of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113 Japan

In an effort to integrate the molecular maps of rice developed by Dr. Tanksley's lab at Cornell and Dr. Saito's lab at Tsukuba, about 70 RFLP markers distributed along in the chromosomes were exchanged between the two groups. To date, 29 of the Tsukuba markers have been mapped onto the inter-specific BC population maintained at Cornell, and 25 of the Cornell markers have been mapped onto the inter-subspecific F2 population maintained at Tsukuba. The results of this work suggest that the linear order of markers along all 12 chromosomes is in good agreement. The alignment of the two molecular maps serves to increase the number of RFLP markers to rice researchers and should facilitate efforts to map characters of agronomic importance.

The Cornell map is based on a backcross population derived from an inter-specific cross between O. sativa (indica) and a wild species of rice, O. longistaminata, while the Tsukuba map is based on an F2 population derived from an inter- subspecies cross between the two major subspecies within O. sativa (indica and japonica). There are over 600 markers on the Cornell map and 350 on the Tsukuba map. The advantage of mapping based on an inter-subspecific cross is that there

Fig. 1. Summary of reciprocal mapping efforts between Cornell and Tsukuba groups and correspondence of RFLP and classical linkage maps of rice. Comparative mapping was conducted by Jinhua Xiao at Cornell University and Naoki Kishimoto at Tsukuba. Vertical lines represent chromosomes mapped with morphological markers (stippled bar) over the last 40 years, and with DNA markers since 1988 by the Cornell (open bar) and Tsukuba (solid bar) groups. RFLP locus names exchanged by Cornell and Tsukuba researchers appear to the right of bars representing chromosomes; numbers on the Tsukuba map indicate clones derived from the Nipponbare genomic library (XNpb); marker numbers on the Cornell map are prefaced to indicate different libraries of orgin of the cloned sequences: RG=rice genomic, RZ=rice cDNA and CDO-oat cDNA; cloned genes on both maps are listed according to standard nomenclature. Morphological markers appear to the left of the chromosome on all maps. The horizontal bars along the chromosomes represent clones there are mapped but not exchanged on the two RFLP map (see section an individual maps included in this issue for more details). Right arrows from Tsukuba to Cornell maps=relative position of Tsukuba markers on Cornell map; left arrow from Cornell to Tsukuba maps=relative position of Cornell markers on Tsukuba map.

is a high rate of recombination, providing increased mapping resolution for markers lying near each other on a chromosome. The greater efficiency of the inter-specific cross may enable to place any previously unmapped markers on a chromosome with great ease. All the RFLP markers on the Tsukuba maps and most of the rice genomic markers (coded RG) on the Cornell map have been screened on Indica/Japonica crosses and provide a reservoir of such clones likely to be polymorphic oli other inter-subspecific crosses.

Until recently, these two maps had been constructed independently, and because there were few common RFLP markers in both maps (e.g. ribosomal gene and waxy gene), it was difficult to align or compare them. This collaborative work by exchanginc, RFLP markers from all 12 chromosomes however, has clarified the alignment. Moreover, thirteen genes controlling morphological, biochemical, or pest resistant phenotypes have been newly mapped in the Cornell map.

One noteworthy exception to the basic concordance of the rice maps is the case of chromosome 4. The three markers (CDO244, XNpb151 and XNpb271) that have been reciprocally mapped on this chromosome suggest that approximately half of the chromosome represented on the Tsukuba map is compressed into the central portion of the chromosome as mapped at Cornell. Further, both the Tsukuba and the Cornell maps place the morphological marker Ph (phenol reaction) near the top of chromosome 4, while this marker appears near the middle of the chromosome on the classical map. Alignment of the two maps with the classical map indicates that a large segment on chromosome 4 defined by morphological mutant markers on the classical map might not be represented on either of the RFLP maps. Thus, either there is an entire arm of chromosome 4 that is not represented on either of the molecular maps, or conversely, this large segment containing many morphological markers has been mistakenly assigned to chromosome 4, and really belongs on another chromosome. Linkage analyses with molecular and morphological markers in this region will help clearify this situation.

The total number of map units in the inter-subspecific maps developed by Saito et al. (1991) and McCouch et al. (1988) are 1,836cM (350 markers) and 1,389cM (135 markers), respectively. The classical map (Kinoshita 1990), which is also based on inter-subspecific or intra-specific crosses is 1,306 cM (162 markers) (not including chromosome 8). A repression of recombination is evident on the inter-specific map developed at Cornell, which measures 1,222 cM (600 markers). There is an overall reduction of approximately 30% in map units when the same markers are mapped onto an inter-specific compared to an inter-subspecific population (see Tanksley et al, this volume). This variation in recombination frequency is evident despite that the genome coverage may be roughly equivalent in physical terms, as is sugoested by the reciprocal mapping for the distal markers from many of the chromosomes. This is consistent with observations by other workers that the recombination frequency tends to be less in crosses involving more genetically divergent parents (Rick, 1969). Further, it is known that recombination frequency is not uniform throughout a chromosome (Ganal et al., 1989), being suppressed in regions near the centromere and expanded in subtelomeric regions (Broun et al., 1922), nor it is uniform on genomewide basis when crosses are compared. A greater understanding of what physical and genetic factors regulate recombination would be used to advantage where fine mapping loosely linked loci is of interest. With the current availability of almost 1,000 genetically m markers in rice, high density mapping as well as physical mapping and map-based cloning become feasible.

References

Broun, P., M.W. Ganal and S.D. Tanksley, 1992. Telomeric arrays display high levels of heritable polymorphism among closely related plant varieties. Proc. Natl. Acad. U.S.A. 1354-1357.

Ganal, M.W., N.D. Young and S.D. Tanksley, 1989. Pulsed field gel electrophoresis and physical mapping of large DNA fragment in the Tm-2a region of chromosome 9 in tomato. Mol. Gen. Genet. 215: 395-400.

Ideta, O., A. Yoshimura, H. Tsunematsu, T. Matsumoto and N. Iwata, 1992. Integration of RFLP and conventional linkage maps in rice. In C.B. You and Z.L. Chen (eds.), Agricultural Biotechnology (Proc. of Asia-Pacific Conference on Agricultural Biotechnology), p. 163-166, China Science and Technology Press, Beijing.

Kinoshita, T., 1990. Report of the committee on gene symbolization, nomenclature and linkage groups. RGN 7: 16-50.

Kishimoto, N., Majid R. Foolad, Shimosaka E., Seiji Matsuura and Saito A. 1993. Alignment of molecular and classical linkage maps of rice, Oryza sativa L., Plant Cell Reports (submitted)

McCouch, S.R., G. Kochert, Z.H. Yu, Z.Y. Wang, G.S. Khush, W.R. Coffman and S.D. Tanksley, 1988. Molecular mapping of rice chromosomes. Theor Appl Genet 76: 815-829.

Rick, C.M. 1969. Controlled introgression of Solanum pennellii into Lycopersicon esculentum: segregation and recombination. Genetics 62: 753-768.

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. Ohsawa, Y. Hayano, N. Iwata and M. Sugiura, 1991. Linkage map of restriction fragment length polymorphism loci in rice. Jpn. J. Breed. 41: 665-670.