Predicting Success of IndicalJaponica Crosses in Rice, Based on a PCR Marker for the S-5n Allele at a Hybrid-Sterility Locus

Exploitation of crosses between the japonica and indica subspecies of rice (Oryza sativa L.) is hindered by hybrid sterility. However, germplasm containing the S-5" wide compatibility allele, derived from tropical japonica (javanica), can be used as an intermediate in the transfer of traits. A PCR-based DNA marker, STS213, was used to identify the fraction of an F3 population, segregating for S-5" and the japonica allele S-5j, that was most likely to yield fertile progeny from crosses with indica rice. Plants carrying the STS213 allele associated with wide compatibility, had significantly higher fertility than plants containing the japonica allele. The ability to detect seedlings bearing S-5", the wide-compatibility allele, will facilitate the introgression of this allele into temperate japonica cultivars while eliminating the need to test cross, self and score for ferlility a majority of the individuals during introgression. R~CE CULTIVARS are classified into two major subspecies, indica and japonica. The japonica subspecies is composed of two groups, the temperate japonicas and the tropical japonicas (sometimes referred to as javanicas). For clarity, the temperate and tropical types are here referred to as japonica and javanica, respectively. Because of genes that cause semi-sterility of F1 hybrids, exchange of desirable traits is limited in wide crosses involving the indica and japonica subspecies (Kato, 1930; Yanagihara et al., 1992). The hybrid-sterility locus S-5 on chromosome 6 (Ikehashi and Araki, 1986), is associated with antagonism between the heterozygous indica/japonica maternal tissue (S-Y/S-Y) and female gametes carrying the S-Y allele. As a result, S-Y-bearing spikelets tend to be sterile. However, germplasm carrying a third allele of Indonesian origin, S-5n or the javanica wide-compatibility allele, can cross readily with both S-5 i and S-Y homozygotes without significant reduction in fertility of the F1 hybrid (Terao and Mizushima, 1939; Ikehashi and Araki, 1986). Widecompatibility varieties have been used successfully in rice breeding to produce fertile hybrid progeny (Ikehashi, 1991; Yuan 1994). At present, the transfer of the S-5n allele into improved indica or temperate japonica breeding lines is laborious. The presence of this allele can be detected only by first performing testcrosses (for example to an indica line if the S-5n allele is being transferred into a japonica cultivar) followed by selfing the TC1 progeny C.E. Williams, USDA-ARS and Dep. of Entomology, Purdue Univ., West Lafayette, IN 47907; D.J. Mackill, USDA-ARS and Dep. of Agronomy, Univ. of California, Davis, CA 95616; P.C. Ronald, Dep. of Plant Pathology, Univ. of California, Davis, CA 95616; S. Yanagihara and S. McCouch, Dep. of Plant Breeding and Biometry, Cornell Univ., Ithaca, NY 14853. Contribution from USDA-ARS and Purdue Univ. Agric. Res. Programs, West Lafayette, IN 47907. Journal Series no. 15352. The research was supported in part by the California Rice Research Board. Received 26 Feb. 1997. *Corresponding author ([email protected]). Published in Crop Sci. 37:191