Fig. 1. Partial RFLP linkage map of rice showing linkage of alpha-amylase genes to DNA markers. Map distances are shown in centimorgans.
1) International Rice Research Institute, P. 0. Box 933, Manila, Philippines
2) Section of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
Rice alpha-amylases are encoded by a small gene family. A total of 10 alpha-amylase genes have been identified and 8 of them have been cloned and characterized (Huang et al. 1990a and b; Sutliff et al. 1991). These genes were localized on rice chromosomes through trisomic mapping (Ranjhan et al. 1991). Here, we report the mapping of the alpha-amylase genes on an RFLP linkage map.
Segregation of the rice alpha-amylase genes was examined against 135 RFLP markers on a doubled haploid mapping population. As shown in Fig. 1, the alpha-amylase genes were mapped on the same respective chromosomes as reported by Ranjhan et al. (1991). Through restriction mapping of alpha- amylase gene clones it was shown that Amy3A, B, and C as well as Amy3D and E were physically linked (Huang et al, 1990a; Sutliff et al. 1991). We had no idea regarding the crossover distance between Amy1A and 1C except that they are located on chromosome 2 (Ranjhan et al. 1991). Linkage analysis shows that these two genes are closely linked (Fig. 1).
To further examine the allelic polymorphism at alpha-amylase loci and their segregation relationships, we used Amy1A and 3E clones to survey a collection of rice germplasm consisting of 147 cultivated rices. An example of Southern blot is shown in Fig. 2. The blot was probed with pOS103, a cDNA of Amy1A gene (Fig. 2A). RFLP bands were interpreted schematically in Fig. 2B. Three major alleles were observed for each of the genes Amy1A, 1B and 1C.
There were very few recombinants among Amy1A and 1C alleles confirming strong linkage between these two genes. When the frequencies of their alleles were examined among isozyme varietal groups (Glaszmann 1987), we found that allele b is primarily associated with varietal group 1 while allele c is associated with groups 4 and 6. Allele a was predominant in groups 2, 3 and 5. AMY1B shows no association with Amy1A and 1C and all its alleles are present in varietal group 1 although alleles a and c were found only in groups 2 and 3 and in group 6 respectively. It appears that alpha-amylase genes diverged during the evolution
Fig. 1. Partial RFLP linkage map of rice showing linkage of alpha-amylase
genes to DNA markers. Map distances are shown in centimorgans.
of rice into distinct varietal group and very few exchanges of alleles
occurred since then. The alpha-amylase genes may therefore serve as suitable
DNA markers for phylogenetic investigations in rice.
References
Huang, N., T. D. Sutliff, J. C. Litts and R. L. Rodriguez, 1990. Classification and characterization of the rice alpha-amylase multigene family. Plant Molecular Biology 14: 655-668.
Huang, N., N. Koizumi, S. Reinl and R. L. Rodriguez, 1990. Structural organization and differential expression of rice alpha-amylase genes. Nucleic Acids Research 18: 7007-7014.
Glaszmann, J. C., 1987. Isozymes and Asian rice varieties. Theor. Appl. Genet. 74: 21-30. Ranjhan, S., J. C. Litts, M. R. Foolad and R. L. Rodriguez, 1991. Chromosomal localization and genomic organization of alpha-amylase genes in rice (Oryza sativa L.). Theor. Appl. Genet. 82: 481-488.
Sutliff, T. D., N. Huang, J. C. Litts and R. L. Rodriguez, 1991. Characterization of an alpha-amylase multigene cluster in rice. Plant Molecular Biology 16: 579-591.