Both semi-dwarf and photoperiod-insensitive traits in rice were important for the Green Revolution.

backgroundThe semi-dwarf high-yielding rice (Oryza sativa) variety IR8 was the major modern line that gave rise to the “Green Revolution” in Asia approximately 60 years ago. Although the sd1 mutation in IR8 responsible for semi-dwarfism is well known, the sequence variation, evolutionary origins, and functional impacts of SD1 haplotypes remain incompletely characterized.

resultsBy analyzing whole-genome sequences from the 3K Rice Genomes Project, Taiwanese landraces, and Asian wild rice, we classified SD1 into 12 haplotypes, including two newly identified loss-of-function alleles: a 1,279-bp deletion and an E100/R340 variant. Phylogenetic and nucleotide analyses traced the origins of several haplotypes, including the widely used 383-bp deletion (DGWG type), to the wild accession W1718 in southern China, from which they were later introgressed into landraces and subsequently brought to Taiwan. Protein structural modeling further revealed that distinct amino acid substitutions affect GA20ox-2 activity by altering the catalytic pocket or local protein stability. Screening of SD1 and Hd1 genotypes showed that most modern indica varieties carry loss-of-function alleles of both sd1 and hd1, reflecting strong post–Green Revolution selection for semi-dwarfism and early maturity.

conclusionOur results clarify the evolutionary history and functional consequences of SD1 variation and highlight that the combined loss-of-function sd1–hd1 genotype was central to the development of high-yielding, lodging-resistant, and photoperiod-insensitive rice varieties. These findings provide a comprehensive framework for understanding key Green Revolution genes and offer guidance for future rice improvement and genome-editing strategies.