| Summary: | The semi-dwarfing allele, <em>sd1-d,</em> has been widely utilized in developing high-yielding rice cultivars across the world. Originally identified from the rice cultivar Dee-Geo-Woo-Gen (DGWG), <em>sd1-d</em>, derived from a spontaneous mutation, has a 383-bp deletion in the <em>SD1 </em>gene. To date, as many as seven alleles of the <em>SD1</em> gene have been identified and used in rice improvement, either with a functional single-nucleotide polymorphism (SNP), with insertion–deletions (InDels), or both. Here, we report discovery of a novel SNP in the <em>SD1</em> gene from the rice genotype, Pusa 1652. Genetic analysis revealed that the inheritance of the semi-dwarfism in Pusa 1652 is monogenic and recessive, but it did not carry the <em>sd1-d</em> allele. However, response to exogenous gibberellic acid (GA<sub>3</sub>) application and the subsequent bulked segregant and linkage analyses confirmed that the <em>SD1</em> gene is involved in the plant height reduction in Pusa 1652. Sequencing of the <em>SD1</em> gene from Pusa 1652 revealed a novel transition in exon 3 (T/A) causing a nonsense mutation at the 300th codon. The stop codon leads to premature termination, resulting in a truncated protein of <em>OsGA20ox2</em> obstructing the GA<sub>3</sub> biosynthesis pathway. This novel recessive allele, named <em>sd1-bm</em>, is derived from Bindli Mutant 34 (BM34), a γ-ray induced mutant of a short-grain aromatic landrace, Bindli. BM34 is the parent of an aromatic semi-dwarf cultivar, Pusa 1176, from which Pusa 1652 is derived. The semi-dwarfing allele, <em>sd1-bm,</em> was further validated by developing a derived cleaved amplified polymorphic sequence (dCAPS) marker, AKS-sd1. This allele provides an alternative to the most widely used <em>sd1-d</em> in rice improvement programs and the functional dCAPS marker will facilitate marker-assisted introgression of the semi-dwarf trait into tall genotypes.
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