Sdt97: A Point Mutation in the 5′ Untranslated Region Confers Semidwarfism in Rice

Abstract

Semidwarfism is an important agronomic trait in rice breeding programs. The semidwarf mutant gene Sdt97 was previously described. However, the molecular mechanism underlying the mutant is yet to be elucidated. In this study, we identified the mutant gene by a map-based cloning method. Using a residual heterozygous line (RHL) population, Sdt97 was mapped to the long arm of chromosome 6 in the interval of nearly 60 kb between STS marker N6 and SNP marker N16 within the PAC clone P0453H04. Sequencing of the candidate genes in the target region revealed that a base transversion from G to C occurred in the 5′ untranslated region of Sdt97. qRT-PCR results confirmed that the transversion induced an obvious change in the expression pattern of Sdt97 at different growth and developmental stages. Plants transgenic for Sdt97 resulted in the restoration of semidwarfism of the mutant phenotype, or displayed a greater dwarf phenotype than the mutant. Our results indicate that a point mutation in the 5′ untranslated region of Sdt97 confers semidwarfism in rice. Functional analysis of Sdt97 will open a new field of study for rice semidwarfism, and also expand our knowledge of the molecular mechanism of semidwarfism in rice.

Assessment of efficacy of mutagenesis of gamma-irradiation in plant height and days to maturity through expression analysis in rice

“…However, use of this gene as the single source of semi-dwarfism in rice cultivars has resulted in loss of diversity. Hence, identification of a new allele as a source of semi-dwarfism has long been researched and reported [ 8 , 17 , 38 ].…”

“…Gamma-rays was utilized to develop semi-dwarf mutants of cultivars such as Basmati 370 [ 13 , 14 ]. Dominant type of semi dwarf cultivars were also developed through induced mutagenesis: Ssi1 allele through X-ray irradiation [ 15 ]; Sdt97 allele in a rice mutant [ 16 , 17 ]. Similarly, T-DNA insertion [ 18 ], RNA interference [ 19 ] and recently CRISPR/Cas9 [ 20 ] induced mutations were used to develop semi-dwarf cultivars in rice.…”

Development and validation of gene‐based markers for shrunken2‐Reference allele and their utilization in marker‐assisted sweet corn (Zea maysSachharata) breeding programme

“…So far, no report on universal gene‐based markers for sh2‐Ref gene is available in sweet corn. SNP markers are promptly replacing SSR (simple sequence repeats) because of their abundance, stability, high efficiency, cost‐effectiveness and amenability to automation (Tong et al, 2016).…”

The Brown Midrib Leaf (bml) Mutation in Rice (Oryza sativa L.) Causes Premature Leaf Senescence and the Induction of Defense Responses

“…BML was expressed in leaf, stem, root, and panicle tissues in both bml and WT plants [ 40 ]. A point mutation in the 5′UTRinduced alterations in the expression of BML in different tissues of rice [ 41 ]. In bml plants, a G to A substitution in the 5′UTR of BML might cause the significant reduction of transcript abundance compared to WT in the collected tissues.…”