44. A high density molecular map of the rice genome

Dept. of Plant Breeding and Biometry, Cornell University, Ithaca, N.Y., 14853-1901, U.S.A.

In 1986 development of a molecular linkage map for rice was initiatied at Cornell University through the support of the Rockefeller Foundation. The purpose of the project was to develop a complete molecular linkage map (based mainly on RFLPS) that could be used by rice scientists throughout the world for a variety of applications in breeding and genetics. Currently, more than 600

Fig. 1. Molecular linkage map of the rice genome. Markers by horizontal tick marks ordered with LOD>2 (using Mapmaker computer software (Lander et al., 1987)). The markers in parentheses have been located in intervals with LOD<2. Clone designation indicate clone source: RG=rice genomic, RZ=rice cDNA, CDO=oat (Avena) cDNA, BCD = barley (Hordeum) cDNA, UMC = maize (Zea mays) genomic. Underlined marker positions have been approximated from previously published maps. Markers listed underneath chromosomes belong on the linkage group but are not placed to intervals. Asterisks indicate markers located to chromosome using trisomic analysis. Bold type indicates known genes. Bold and italics indicate isozymes or morphological markers. Loci separated by commas cosegregate. Kosambi cM are to the left of the chromosomes.

markers have localized on this rice map with an average spacing of approximately 1 marker every 2 cM (approximately every 1 million base pairs) (Fig. 1). The markers localized on the map are derived from both genomic and cDNA libraries from several sources: from the indica rice variety, IR36 (both genomic and cDNA clones), from oat (Avena), barley (Hordeum) (cDNA's only), and maize (Zea mays) (genomic clones) (Maize clones are ftom the publically available library developed by Burr and Burr (1991)). All of the clones can be used for studies with any of the species within the genus Oryza. In addition, the cDNA clones (which correspond to actual genes) can also be used in mapping studies with other monocot species. This feature has implications for future studies of rice and other grass species. Recently, it has been possible to use these clones to compare the homoeologous relationships between rice and two other grain species (maize and wheat) (Ahn and Tanksley, in preparation). We have discovered that a large number of linkage groups are conserved among these species. The development of integrated maps for these species will allow cross access to probes among them. As a result, it is likely that several thousand new probes (from maize and wheat) will be available for rice research in the near future.

The map presented in Fig. 1 was based on a backcross population derived from the interspecific cross O. sativa X O. longistaminata. O. longistaminata is a wild rice ftom Africa which possesses the same genome (AA) as O. sativa. The high level of restriction fragment length polymorphism between the two species allows for great efficiency in genetic mapping. A total of 1222 map units was measured in this cross; however, the overall rate of recombination appears to be approximately 70% of that found in intraspecific crosses (Causse et al, in preparation). Total map units in intraspecific crosses would thus be expected to be approximately 1950 cM. This correspond to a DNA: cM ratio of approximately 250 kb/cM which is significantly less than most crop species and very close to the value for Arabidopsis thaliana. This feature, combined with the ability to transform rice, makes this crop a likely target for the use of map-based cloning to isolate eenes that have been localized on the RFLP map.

A number of morphological markers have also been mapped relative to RFLP markers and are shown on the map in Fig. 1. The mapping of morphological markers onto the molecular map as well as analysis with primary trisomics confirms the linkage group assignments of the molecular map. Of highest priority for rice breeders has been the mapping of genes important in rice production especially disease and insect resistance genes. Rice blast (caused by the fungal pathogen Pyricularia oryzae) and bacterial leaf blight (caused by Xanthomonas oryzae pv. oryzae) represent two of the most serious disease problems in rice worldwide and several major genes conferring resistance to these pathogens have been mapped with respect to RFLPs (Yu et al. 1991; Ronald et al. 1992; Tohme, CIAT, Cali, Colombia, pers. comm.; Yoshimura et al, 1992). Ge..le3 for photoperiod sensitivity and rice grain aroma have also been localized on the RELP map (Mackill et al. 1992, Ahn et al. 1992).

Currently, a number of studies are in progress to use the rice RFLP map to identify quantitative trait loci (QTL) important in rice breeding. Some of the primary targets are traits that limit rice production in areas of high pathogen pressure or which experience climatic or edaphic extremes. High priorities include identification of QTLs for horizontal (or multigenic) disease resistance (Wang et al, submitted) and for drought and salt tolerance. In addition, studies are currently underway to determine the genetic basis of intersubspecific hybrid vigor (e.g. indica x japonica) (Xiao, Cornell University, Ithaca, NY., personal comm.). Heterotic yield increases in inter-subspecific crosses are often double that found in intra-subspecific crosses (Yuan, Hunan Hybrid Rice Research Institute; Changsha, Hunan, China, pers. comm). Identification of the QTLs responsible for this response might lead to the development of even higher yielding rice varieties.

Probes corresponding to the Cornell rice map are freely available. Requests for RG, RZ, CDO, and BCD clones should be sent to Theresa Fulton, Department of Plant Breeding and Biometry, 252 Emerson Hall, Cornell University, Ithaca, New York 14853, FAX (607) 255-6683 or to Dr. Ning Huang, Division of Plant Breeding and Genetics, IRRI, PO Box 933, 1099 Manila, Philippines, FAX (632- 818-2087).

Ahn, N. and S.D. Tanksley, 1992. RFLP tagging of a gene for aroma in rice. Theor Appl Genet (in press)

Burr, B. and F.A. Burr, 1991. Recombinant inbreds for molecular mapping in maize: theoretical and practical considerations. Trends in Genetics 7: 55-60.

Lander, E.S., P. Green, J.Abrahamson, A. Barlow, M.J. Daly, S.E. Lincoln and L., Newburg, 1987. MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1: 174-181.

Mackill, D.J., M.A. Salam, Z.Y. Wang and S.D. Tanksley, 1992. A major photoperiod-sensitivity gene tagged with RFLP and isozyme markers in rice. Theor Appl Genet (in press)

Ronald, P.C., B. Albano, R. Tabien, L. Abenes, K. Wu, S. McCouch and S.D. Tanksley, 1992. Genetic and physical analysis of the rice bacterial blight disease resistance locus, Xa-21. MGG (in press).

Wang, G., D.J. Mackill, J.M. Bonman, S.R. McCouch and R.J. Nelson, 1992. RFLP mapping of qualitative and quantitative genes for blast resistance in a durably resistant rice cultivar. (submitted)

Yoshimura, S., A. Yoshimura, A. Saito, N. Kishimoto, M. Kawase, M. Yano, M. Nakagahra, T. Ogawa and N. Iwata, 1992. RFLP analysis of introgressed chromosomal segments in three near-isogenic lines of rice for bacterial blight resistance genes, Xa-1, Xa-3, and Xa-4. Jpn. J. Genet 67: (in press).

Yu, Y.H., D.J. Mackill, J.M. Bonman and S.D. Tanksley, 1991. Tagging genes for blast resistance in rice via linkage to RFLP markers. Theor Appl Genet 81: 471-476.