Discovery of a Novel Induced Polymorphism in 1 Gene Governing Semi-Dwarfism in Rice and Development of a Functional Marker for Marker-Assisted Selection.

The semi-dwarfing allele, has been widely utilized in developing high-yielding rice cultivars across the world. Originally identified from the rice cultivar Dee-Geo-Woo-Gen (DGWG), , derived from a spontaneous mutation, has a 383-bp deletion in the gene. To date, as many as seven alleles of the 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 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 allele. However, response to exogenous gibberellic acid (GA) application and the subsequent bulked segregant and linkage analyses confirmed that the gene is involved in the plant height reduction in Pusa 1652. Sequencing of the 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 obstructing the GA biosynthesis pathway. This novel recessive allele, named , 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, 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 in rice improvement programs and the functional dCAPS marker will facilitate marker-assisted introgression of the semi-dwarf trait into tall genotypes.