39. Molecular tagging of a recessive gene, xa-5, for resistance to bacterial blight of rice


International Rice Research Institute, PO Box 933, Manila, Philippines and Cornell University, Ithaca, NY 14853, USA

Bacterial blight (BB) is a serious rice disease in irrigated and rainfed lowland ecologies throughout Asia. lt is caused by Xanthomonas oryzae cv. oryzae (Xoo) and its prevalence is associated with the widespread cultivation of high-yielding but susceptible rice cultivars (Mew 1987). The most effective form of disease control is host plant resistance, and 19 genes have been identified that confer resistance to specific races or clusters of races of the pathogen (Kinoshita, 1989; Khush et al. 1990). lt is of interest to tag these genes using molecular markers to facilitate breeding efforts aimed at developing more durable forms of resistance to BB.

A set of 12 internationally accepted differential lines has been produced in the background of the susceptible variety, IR24 (Ogawa et al. 1988; Ogawa et al. 1990). Each isoline contains an individual gene for BB resistance. The focus of this study is the recessive gene, xa-5, which confers resistance to 4 of the 6 races of Xoo found in the Philippines (Taura et al. 1987).

A subset of mapped RFLP markers was used to survey the genomes of IRBB- 5 (the resistant isoline), IR1545-339 (the resistant donor), and IR24 (the susceptible recurrent parent), in an attempt to locate chromosomal regions that had been introgressed from the donor into the resistant isoline. A small F2 population (n = 36) was then used to confirm which of the putative positive regions contained the resistance gene of interest. Resistance or susceptibility was determined based on evaluation of lesion length following inoculation with Race 1via the clipping method (Kauffman et al. 1973).

In this study, we report that the recessive gene, xa-5, is closely linked to RG207 (Fig. 1) at the top of linkage group 5 (McCouch et al. 1988). Previous work established that this gene belonged to linkage group 5 based on trisomic analysis (Yoshimura et al. 1984) and was linked to the morphological mutant marker, spl-7, at a distance of 6.1 cM (R. Ikeda, pers. comm., IRRI, Philippines). This suggests that RG207 and spl-7 are linked, clarifying the relative orientation of the classical genetic map and the RFLP map with regard to this linkage group.

Markers in 8 chromosomal segments introgressed from the donor were tested for cosegregation with resistant and susceptible phenotypes in the F2, but only those in the vicinity of RG207 demonstrated linkage to the xa-5 gene. Larger F2 populations are being examined to accurately establish map distance between the marker and the resistance gene. Markers in introgressed segments unlinked to the resistance gene will be useful in eliminating extraneous donor-derived chromosomal segments from the BC4 isolines.

Identifying molecular markers which are closely linked to genes of agronomic importance represents an important step forward in efforts to increase the efficiency of selection in breeding. This is especially true for recessive genes, such as xa-5, where the presence of the gene in the heterozygous condition cannot be detected through traditional approaches without a generation of progeny testing. It also provides the foundation for cloning such genes where the protein product is unknown.

Fig. 1. Autoradiogram showing confirmation of linkage between RG207 and xa-5 resistant phenotype. Lanes 1 and 24= Lambda/HindIII size marker, lane 2=IR24, the susceptible recurrent parent, lane 3=IR-BB 5, the resistant isoline containing xa-5, lane 4=:IR1545-339, the resistant donor, lanes 5-14= resistant phenotypes, lanes 15-23=susceptible phenotypes-from an F2 popuulation derived from a cross between IR24 and IR-BB 5.



Kaufmann, H., A.P.K. Reddy, S.P.Y. Hsieh and S. D. Merca. 1973. An improved technique for evaluating resistance of rice varieties to Xanthomonas oryzae. Plant Dis. Report 57: 537- 541.

Kinoshita, T., 1989. Report of the committee on gene symbolization, nomenclature and linkage groups. RGN 6: 2-29.

Khush, G. S., E. Bacalangco, and T. Ogawa, 1990. A new gene for resistance to bacterial blight from O. longistaminata. RGN 7: 121-122.

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.

Mew, T.W., 1987. Current status and future prospects of research on bacterial blight of rice. Ann. Rev. Phytopathol. 25: 359-382.

Ogawa, T., T. Yamamoto, G. S. Khush, T.W. Mew, and H. Kaku, 1988. Near-isogenic lines as international differentials for resistance to bacterial blight of rice. RGN 5: 106-107.

Ogawa, T., R. E. Tabien, T. Yamamoto, G. A. Busto, and R. Ikeda, 1900. Breeding for near-isogenic lines for resistance to bacterial blight in rice. RGN 7:10.

Taura, S., T. Ogawa, R. E. Tabien, G. S. Khush, A. Yoshimura and T. Omura, 1987. The specific reaction of Taichung Native 1 to Philippine races of bacterial blight and inheritance of resistance to race 5 (PX0112). RGN 4: 101-102.

Yoshimura, A., T.W. Mew, G. S. Khush, and T. Omura, 1984. Genetics of bacterial blight resistance in a breeding line of rice. Phytopathology 74(7): 773-777.