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By combining the amplified fragment length polymorphism (AFLP) technique with selective genotyping, we constructed a linkage map for rice and assigned each linkage group to a corresponding chromosome. The AFLP map, consisting of 202 AFLP markers, was generated from 74 recombinant inbred lines (RIL) which were selected from both extremes of the population (250 lines) with respect to the response to complete submergence. Map length was 1756 cM, with an average interval size of 8.5 cM. To assign linkage groups to chromosomes, we used 50 previously mapped AFLP markers as anchor markers distributed over the 12 chromosomes. Other AFLP markers were then assigned to specific chromosomes based on their linkage to anchor markers. This AFLP map is equivalent to the RFLP/AFLP map constructed previously as the anchors were in the same order in both maps. Furthermore, tests with two restriction fragment length polymorphism (RFLP) markers and two sequence-tagged site (STS) markers showed that they mapped in the expected positions. Using this AFLP map, a major gene for submergence tolerance was localized on chromosome 9. Quantitative trait loci (QTL) associated with submergence tolerance were detected on chromosomes 6, 7, 11, and 12. We conclude that the combination of AFLP mapping and selective genotyping provides a much faster and easier approach to QTL identification than the use of RFLP markers.

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The rice embryo is rich in lipid and protein bodies, bioactive chemicals such as dietary fiber, phytic acids, vitamin B and E, and gamma aminobutyric acid (GABA) than the endosperm. In this paper, we report a new giant embryo mutant, ge t , induced from somaclonal variation derived by anther culture in rice. Sequence analysis of Cytochrome P450 of the ge t mutant revealed that ge t is a new allele of the GE gene with a single point mutation with substitution of amino acid, W 395 to L 395 . The weight of the ge t mutant embryo was 3.7 times higher than normal embryo. Tocopherol and mineral content were also higher than the previously reported giant embryo rice variety, Keunnun. These results indicated that this new giant embryo rice (ge t ) offers a promising source of genetic material in improving nutritional quality of rice especially tocopherol, essential minerals, and GABA.

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