Discovery of a Novel Induced Polymorphism in SD1 Gene Governing Semi-Dwarfism in Rice and Development of a Functional Marker for Marker-Assisted Selection

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.

Untargeted Metabolite Profiling of Specialty Rice Grains Using Gas Chromatography Mass Spectrometry

“…Few studies have attempted to analyze the metabolite diversity of different Chakhao rice types in North East India [29,30] but no studies have attempted to profile their aroma.…”

Detection of QTLs for Plant Height Architecture Traits in Rice (Oryza sativa L.) by Association Mapping and the RSTEP-LRT Method

“…After pyramiding the favorable alleles located on these five loci into a single genotype, the PH could be reduced by −30.57 cm. A moderate plant height is an important basis for rice breeding, and this is supported by Andrew-Peter-Leon, et al [ 40 ] and Bhuvaneswari, et al [ 41 ], who have reported that OsGA20ox2 and OsFBX26 , have important roles in regulating semi-dwarfism and early flowering in rice. Likewise, this finding is supported by Liu, et al [ 29 ], who reported that several semi-dwarf rice varieties have been bred by genetic introduction of the mutant alleles of SD1, which encodes OsGA20ox2 for catalyzing GA biosynthesis.…”

“…Previous studies in rice plants indicate that the reduced height of the sd-1 is due to the defect in the GA biosynthetic pathway [ 6 , 47 , 48 ], as opposed to the wheat Rht-B1/Rht-D1mutant plants in which the GA signal transduction pathway is weakened [ 49 , 50 ]. Importantly, the OsGA20ox gene corresponds to the Sd-1 locus in the rice genome [ 41 , 51 ]. Similar results were found by Liu, et al [ 29 ], who reported that the culm content of bioactive gibberellin, especially in the basal internodes, is reduced by a semi-dominant lodging resistance gene, SBI , which encodes a culm-specific expressed OsGA2ox , and, thereafter, the higher activity of the SBI considerably reduced the rice PH and contributed to breed enhanced lodging resistant rice varieties and, therefore, increased the yield.…”

Genetic Mapping and Identification of the Gibberellin 3-Oxidase Gene GA3ox Leading to a GA-Deficient Dwarf Phenotype in Pumpkin (Cucurbita moschata D.)

“…Many dwarfing mutants have been found in important food crops such as maize, wheat, and rice [6,7]. Among them, more than 90 dwarfing genes in rice, 26 in wheat, and 20 in maize were identified by using dwarfing materials, such as predominant semidwarf1 (sd1) [8], shortened basal internodes (SBI) [9], reduced height genes Rht-B1b, Rht-D1b and Rht18 [10,11], and brassinolide biosynthesis inhibitor BRI1 [12].…”