Abstract
The semi-dwarfing allele, sd1-d, has been widely utilized in developing high-yielding rice cultivars across the world. Originally identified from the rice cultivar Dee-Geo-Woo-Gen (DGWG), sd1-d, derived from a spontaneous mutation, has a 383-bp deletion in the SD1 gene. To date, as many as seven alleles of the SD1 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 SD1 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 sd1-d allele. However, response to exogenous gibberellic acid (GA3) application and the subsequent bulked segregant and linkage analyses confirmed that the SD1 gene is involved in the plant height reduction in Pusa 1652. Sequencing of the SD1 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 OsGA20ox2 obstructing the GA3 biosynthesis pathway. This novel recessive allele, named sd1-bm, 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, sd1-bm, 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 sd1-d in rice improvement programs and the functional dCAPS marker will facilitate marker-assisted introgression of the semi-dwarf trait into tall genotypes.
Highlights
The semi-dwarf genes in rice and wheat that spurred a ‘green revolution’ during the 1960s are the most utilized genes in modern plant breeding
We report the discovery of a novel SD1 allele in the short-grain aromatic rice genotype Pusa 1652, its causal mutation and the development of a functional marker
We found that the semi-dwarf genotype, Pusa 1652 did not carry the sd1-d allele when tested using the functional marker based on the characteristic 383bp deletion, but instead amplified a fragment of 731 bp, which was similar to tall genotypes
Summary
The semi-dwarf genes in rice and wheat that spurred a ‘green revolution’ during the 1960s are the most utilized genes in modern plant breeding. As per the recent reports, at least 76 plant height mutants and 85 genes have been identified in rice [1,2]. Barring the phenomenal success of a semi-dwarf allele, sd1-d from the Taiwanese cultivar Dee-Geo-Woo-Gen (DGWG), which led to the green revolution in rice, no other dwarfing gene has found to have such a wide utility in rice improvement programs. This is mainly due to these genes’ adverse phenotypic effects, including severe stunting, poor fertility, shorter grain size, etc. These plant height reduction genes are mostly found to be associated with the regulation or biosynthesis of phytohormones such as gibberellic acid (GA3 ) [4,5], brassinosteroids [6]
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