30. Linkage between a RFLP probe and photoperiod sensitivity

2) Department of Plant Breeding & Biometry, Cornell University, Ithaca, NY 14853-1902, U. S. A.

Photoperiod sensitivity is an important trait of rice, being present in most traditional lowland (indica) varieties. Developing improved rices with strong photoperiod sensitivity is a major breeding objective for both rainfed lowland and deepwater rice. Presence or absence of photoperiod sensitivity in breeding lines can be determined using appropriate planting dates, but this is inconvenient for many breeding programs and takes up much time and field space. Markers for the photoperiod sensitivity gene would be useful for detecting the trait in segregating populations.

Fig. 1. Film showing hybridization of rice clone RG64 to F3 lines insensitive and sensitive to photoperiod from the cross Puang Rai 2 X IR26760-27-1-3-2-1. DNA from five insensitive lines (lanes 2, 7, 13, 19 and 21) was degraded or concentration was not high enough to detect bands. None of the insensitive lines had the high molecular weight fragment found in the sensitive parent Puang Rai 2, but all the sensitive lines had this fragment. As sensitivity is dominant, and classification was based on F2 plants, heterzygotes could not be distinguished from homozygotes for the sensitive class.

Fig. 2. Location of RG64 on RFLP linkage map of chromosome 6 relative to the wx locus. This linkage map is based on the map developed at Cornell University. Numbers to the right are clone numbers; those to the left are map distances.

(Se-1) is tightly linked to the isozyme locus Pgi-2 (Kinoshita 1986). Linkage was confirmed in crosses with rainfed lowland cultivars (Poonyarit et al. 1987), but it was not tight enough to be of much use for selection (Salam et al. 1990). For this reason we have attempted to locate a RFLP marker linked to the photoperiod sensitivity gene. F3 lines from the F2 populations studied by Poonyarit et al. (1989) were used for this purpose. As photoperiod sensitivity is partially dominant, only the insensitive genotypes could be determined accurately from F2 data. Twenty F3 lines from homozygous insensitive F2 plants and six F3 lines from sensitive F2 plants (either homozygous or heterozygous) of the cross between Puang Rai 2 (sensitive) and IR26760-27-1-3-2-1 (insensitive) were planted in the greenhouse at Cornell University. DNA was extracted from these plants, digested with restriction enzymes and run on overnight agarose gels. The DNA was then transferred to nylon filters by Southern blotting, and probed with genomic clones known to map to chromosome 6 (McCouch et al. 1988).

Clone RG64 showed tight linkage with photoperiod sensitivity. None of the insensitive F3 lines had the RFLP allele of the sensitive parent (Fig. 1). Three of the six sensitive F3 lines were heterozygous for the RG64 alleles. From this data distance of 0 cM. However, we cannot rule out the possibility of some recombinants. One other clone, RG213, was found to be linked with photoperiod sensitivity, but recombinants were detected.

The direction of Se-1 from RG64 cannot be determined from the present study, but recombination is likely to be low and was not detected with the population used here. RG64 therefore appears to be a reliable marker for the sensitivity gene (Fig. 2). This result differs from those of studies in Japan, which indicate that Se-1 is tightly linked with Pgi-2 and Pi-z (Oosumi et al. 1989). Brar et al. (1990) confirmed that the linkage between RG64 and Pgi-2 is loose (11.6 map units). Furthermore, Yu et al. (1990) found that RG64 is tightly linked with a blast resistance gene (possibly allelic to Pi-z) in a near isogenic line developed at IRRI. Pi-z is known to be tightly linked with Se-1 (Yokoo and Fujimaki 1971). It seems likely that the photoperiod sensitivity gene studied here is the major gene for sensitivity (Se-1), as it appears to be present in most tropical photoperiod sensitive cultivars examined. Further allelism tests need to be made with Japanese isogenic lines to determine if there is an additional photoperiod sensitivity gene not tightly linked with Pgi-2.

Brar D. S., B. G. de los Reyes, O. Panaud, A. Cruz and G. S. Khush 1990. Genetic mapping in rice using morphological, isozyme and RFLP markers. Paper presented at the Second International Symposium on Rice Genetics, May 1990, International Rice Research Institute, Los Banos, Philippines.

Kinoshita, T., 1986. Standardization of gene symbols and linkage maps in rice. In Rice Genetics, p. 215-228. IRRI, Manila.

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

Oosumi, T., A. Miyazaki, H. Uchimiya, F. Kikuchi and M. Yokoo, 1989. Analysis of glucose phosphate isomerase in near-isogenic lines, and cultivars of rice (Oryza sativa L.). Bot. Mag. Tokyo 102: 283-289.

Poonyarit, M., D. J. Mackill and B. S. Vergara, 1987. Two genes affecting photoperiod sensitivity in rice. RGN 4: 87-89.

____, ____ and ____, 1989. Genetics of photoperiod sensitivity and critical daylength in rice. Crop Sci. 29: 647-652.

Yokoo, M. and H. Fujimaki, 1971. Tight linkage of blast-resistance with late maturity observed in different Indica varieties of rice. Jpn. J. Breed. 21: 35-39.

Yu, Z., D. J. Mackill, J. M. Bonman and S. D. Tanksley, 1990. RFLP tagging of blast resistance genes in rice. Paper presented at the Second International Symposium on Rice Genetics, May 1990, IRRI, Los Banos, Philippines (in press).