Positional cloning of rice semidwarfing gene, sd-1: Rice green revolution gene encodes a mutant enzyme involved in gibberellin synthesis

• Published in: DNA research 2002, Vol.9 (1), p.11-17
• Main Authors: MONNA, Lisa, KITAZAWA, Noriyuki, YOSHINO, Rika, SUZUKI, Junko, MASUDA, Haruka, MAEHARA, Yumiko, TANJI, Masao, SATO, Mizuho, NASU, Shinobu, MINOBE, Yuzo
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Amino Acid Substitution; Base Sequence; Biological and medical sciences; Classical genetics, quantitative genetics, hybrids; Cloning, Molecular - methods; Exons; Fundamental and applied biological sciences. Psychology; Gene Expression Regulation, Plant; Genes. Genome; Genetics of eukaryotes. Biological and molecular evolution; gibberellin 20-oxidase; Gibberellins - biosynthesis; Mixed Function Oxygenases - genetics; Mixed Function Oxygenases - metabolism; Molecular and cellular biology; Molecular genetics; Molecular Sequence Data; Mutation; Open Reading Frames; Oryza - genetics; Oryza - metabolism; Oryza - radiation effects; Plant Proteins - genetics; Plant Proteins - metabolism; Plant Proteins - radiation effects; Polymerase Chain Reaction - methods; Polymorphism, Single Nucleotide; Pteridophyta, spermatophyta; sd-1 gene; Sequence Deletion; Vegetals
• ISSN: 1340-2838; 1756-1663
• DOI: 10.1093/dnares/9.1.11

A rice semidwarfing gene, sd-1, known as the "green revolution gene," was isolated by positional cloning and revealed to encode gibberellin 20-oxidase, the key enzyme in the gibberellin biosynthesis pathway. Analysis of 3477 segregants using several PCR-based marker technologies, including cleaved amplified polymorphic sequence, derived-CAPS, and single nucleotide polymorphisms revealed 1 ORF in a 6-kb candidate interval. Normal-type rice cultivars have an identical sequence in this region, consisting of 3 exons (558, 318, and 291 bp) and 2 introns (105 and 1471 bp). Dee-Geo-Woo-Gen-type sd-1 mutants have a 383-bp deletion from the genome (278-bp deletion from the expressed sequence), from the middle of exon 1 to upstream of exon 2, including a 105-bp intron, resulting in a frame-shift that produces a termination codon after the deletion site. The radiation-induced sd-1 mutant Calrose 76 has a 1-bp substitution in exon 2, causing an amino acid substitution (Leu [CTC] to Phe [TTC]). Expression analysis suggests the existence of at least one more locus of gibberellin 20-oxidase which may prevent severe dwarfism from developing in sd-1 mutants.