14. Mapping of a gene for notched kernel found in backcross progeny of Oryza sativa L. and Oryza glumaepatula Steud

Plant Breeding Laboratory, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, 812-8581 Japan

During the development of Oryza glumaepatula (IRGC 105668) introgression lines with O. sativa cv. Taichung 65 genetic background (Sobrizal et al. 1999), we found plants with notched kernels (Fig. 1) segregated in BC4F2 population. Notched kernels were wrinkled, brownish and white-cored, and notched at the belly. The BC4F2 population have retained O. glumaepatula chromosomal segment on chromosome 5, based on whole genome survey of candidate O. glumaepatula introgression lines (Sobrizal et al. 1999).

To determine the chromosomal location of the gene for notched kernel, RFLP analysis was conducted using the BC4F2 population. Phenotype of each BC4F2 plant was determined by observing BC4F3 seeds. Seeds were classified into the following three phenotypes: normal, notched and segregating. Linkage analysis between notched kernel and RFLP markers on chromosome 5 revealed that notched kernel co-segregated with RFLP marker R1607 on the long arm of chromosome 5 (Table 1). Six plants with notched kernel phenotype were homozygous for O. glumaepatula allele at R1607, 24 plants with normal phenotype were homozygous for Taichung 65 allele, and the other 29 plants with segregating phenotype were heterozygous. These results indicate that a single recessive gene controlling notched kernel was located on the long arm of chromosome 5 (Fig. 2).

So far, only one gene for notched kernel has been reported (Misro et al. 1966, Pavithran 1977). Nk was linked with gl1 (glabrous hull 1) on chromosome 5 with a recombination value of 23% (Misro et al. 1966, Pavithran 1977) and gl1 mapped on the short arm of chromosome 5 (Yoshimura et al. 2001) was far from the position of the notched kernel gene identified in this study. Because of the difference in dominance and map position on chromosome 5, Nk appeared to be different from the gene identified in this study. Therefore, the gene identified was designated as nk2. The gene nk2 was mapped between RFLP markers G1103 and R521 on the long arm of chromosome 5, with map distances of 3.5 cM and 3.6 cM, respectively (Fig. 2).

This study was supported by Bio-oriented Technology Research Advancement Institution (BRAIN), Japan.


Harushima, Y., M. Yano, A. Shomura, M. Sato, T. Shimano, Y. Kuboki, T. Yamamoto, S. Y. Lin, B. A. Antonio, A. Parco, H. Kajiya, N. Huang, K. Yamamoto, Y. Nagamura, N. Kurata, G. S. Khush and T. Sasaki, 1998. A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148: 479-494.

Misro, B., R.H. Richharia and R. Thakur, 1966. Linkage studies in rice (Oryza sativa L.) VII. Identification of linkage groups in indica rice. Oryza 3: 96-105.

Pavithran, K., 1977. Inheritance and linkage relationship of notched kernel in rice (Oryza sativa). Can. J. Genet. Cytol. 19: 483-486.

Sobrizal, K. Ikeda, P.L. Sanchez, K. Doi, E.R. Angeles, G.S Khush and A. Yoshimura, 1999. Development of Oryza glumaepatula introgression lines in rice, O. sativa L. RGN 16: 107-108.

Yoshimura, A., N. Takano-Kai, T. Eguchi, M. Ashikari, O, Ideta, K. Doi and H. Yasui, 2001. RFLP mapping of 95 morphological trait loci in rice. Breed. Res. 3 (Suppl.1): 94 ( in Japanese).