Distribution of recombination sites in the 195-kb regionsurrounding the wx gene in rice

21. Distribution of recombination sites in the 195-kb region surrounding the wx gene in rice KHIN-THIDAR, Y. TANAKA, T. INUKAI and Y. SAN0 Plant Breeding Laboratory, Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan Meiotic recombination does not occur uniformly in the chromosomes in plants or other eukaryotic organisms (Puchta and Hohn 1996; Schnable et al. 1998). Inukai et al.(1998) previously reported that the average frequency of recombination in the wx locus in rice was 27.1 kb/cM, about 10 times higher than the whole rice genome (250 kb/cM). This result suggests two different possibilities, the wx intragenic region is specifically active for meiotic recombination or the wx intragenic region resides in a recombinationally active interval which is larger than the wx gene. We investigated recombination sites in the 195-kb region surrounding the wx gene in the present study. The physical map of 300-kb including the wx locus in rice had been constructed by Nagano et al. (1997). By using seven RFLP probes (four cDNA clones C01, C02, C03 and C04, and two genomic clones G01 and G02) on this map, recombination frequency and distribution of recombination sites in the 195-kb region surrounding the wx locus was investigated. To estimate the recombination frequency in this region, 381 F₂ plants of a cross between the Japonica cultivar T65wx and the Indica cultivar IR36 were analyzed with the DNA clones G0l and C04. The genomic DNA clone G01 was located at 72-kb in the direction of 5' side of the wx gene while cDNA clone C04 was located at 123-kb in the direction of 3' side of the wx gene (Fig. 1). In all ten recombinants were detected in the F₂ population and the recombination frequency within the 195-kb region was estimated as 148 kb/cM. This frequency was two times higher than the genome average, but five times lower than the recombination frequency within the wx locus. The distribution of recombination sites in this region was shown in Fig. 1, suggesting that recombination sites were randomly distributed in the 195-kb region rather than concentrated in the regions near the wx locus. These results indicated that the wx intragenic region is specifically active for meiotic recombination in the 195-kb region. References Inukai,T., A. Sako, Khin-Thidar and Y. Sano, 1998. Frequency and distribution of intragenic recombination at the wx locus in rice. RGN 15: 169-170. Nagano, H., L. Wu, S. Kawasaki, Y. Kishima and Y. Sano, 1997. Construction of a 300-Kb BAC contig containing waxy locus in Japonica rice. RGN 14: 121-123. Puchta, H. and B. Hohn, 1996. From centiMorgans to base pairs: homologous recombination in plants. Trends Plant Sci. 1: 340-348. Schnable, P.S.,A.-P. Hsia and B.L. Nikolau, 1998. Genetic recombination in plants. Curr. Opin. Plant Biol. 1:123-129.

21. Distribution of recombination sites in the 195-kb region surrounding the wx gene in rice

KHIN-THIDAR, Y. TANAKA, T. INUKAI and Y. SAN0
Plant Breeding Laboratory, Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan

Meiotic recombination does not occur uniformly in the chromosomes in plants or other eukaryotic organisms (Puchta and Hohn 1996; Schnable et al. 1998). Inukai et al.(1998) previously reported that the average frequency of recombination in the wx locus in rice was 27.1 kb/cM, about 10 times higher than the whole rice genome (250 kb/cM). This result suggests two different possibilities, the wx intragenic region is specifically active for meiotic recombination or the wx intragenic region resides in a recombinationally active interval which is larger than the wx gene. We investigated recombination sites in the 195-kb region surrounding the wx gene in the present study.

The physical map of 300-kb including the wx locus in rice had been constructed by Nagano et al. (1997). By using seven RFLP probes (four cDNA clones C01, C02, C03 and C04, and two genomic clones G01 and G02) on this map, recombination frequency and distribution of recombination sites in the 195-kb region surrounding the wx locus was investigated. To estimate the recombination frequency in this region, 381 F₂ plants of a cross between the Japonica cultivar T65wx and the Indica cultivar IR36 were analyzed with the DNA clones G0l and C04. The genomic DNA clone G01 was located at 72-kb in the direction of 5' side of the wx gene while cDNA clone C04 was located at 123-kb in the direction of 3' side of the wx gene (Fig. 1). In all ten recombinants were detected in the F₂ population and the recombination frequency within the 195-kb region was estimated as 148 kb/cM. This frequency was two times higher than the genome average, but five times lower than the recombination frequency within the wx locus. The distribution of recombination sites in this region was shown in Fig. 1, suggesting that recombination sites were randomly distributed in the 195-kb region rather than concentrated in the regions near the wx locus. These results indicated that the wx intragenic region is specifically active for meiotic recombination in the 195-kb region.

References

Inukai,T., A. Sako, Khin-Thidar and Y. Sano, 1998. Frequency and distribution of intragenic recombination at the wx locus in rice. RGN 15: 169-170.

Nagano, H., L. Wu, S. Kawasaki, Y. Kishima and Y. Sano, 1997. Construction of a 300-Kb BAC contig containing waxy locus in Japonica rice. RGN 14: 121-123.

Puchta, H. and B. Hohn, 1996. From centiMorgans to base pairs: homologous recombination in plants. Trends Plant Sci. 1: 340-348.

Schnable, P.S.,A.-P. Hsia and B.L. Nikolau, 1998. Genetic recombination in plants. Curr. Opin. Plant Biol. 1:123-129.