ArticlePlant molecular biology1998
Use of alternate splice sites in granule-bound starch synthase mRNA from low-amylose rice varieties.
Article in Plant molecular biology, 1998. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 101 citations in OpenAlex.
- Transcriptional Divergence of Conserved Starch Metabolism Genes During Grain Filling inCurrent issues in molecular biology · 2026Article
- Q allele overexpression and alternative splicing can improve wheat yield by increasing thousand-kernel weight and grain number per spike.BMC plant biology · 2026Article
- Effects of a novel loss-of-function waxy endosperm allele on sorghum seed development and grain quality.G3 (Bethesda, Md.) · 2025Article
- Research Progress on the Regulatory Mechanism of theCurrent issues in molecular biology · 2025Review
- Du13 encodes a CPlant biotechnology journal · 2022Article
- Effects ofFrontiers in plant science · 2022Article
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- Improved 93-11 Genome and Time-Course Transcriptome Expand Resources for Rice Genomics.Frontiers in plant science · 2021Article
- Genetic diversity analysis of specialty glutinous and low-amylose rice (Journal of biosciences · 2020Article
- A Coordinated Suite of Wild-Introgression Lines inFrontiers in plant science · 2020Article
- IR64: a high-quality and high-yielding mega variety.Rice (New York, N.Y.) · 2018Review
- Differential Regulation of Starch-synthetic Gene Expression in Endosperm Between Indica and Japonica Rice Cultivars.Rice (New York, N.Y.) · 2017Article
- Association Analysis of Markers Derived from Starch Biosynthesis Related Genes with Starch Physicochemical Properties in the USDA Rice Mini-Core Collection.Frontiers in plant science · 2017Article
- Systems Genetics Identifies a Novel Regulatory Domain of Amylose Synthesis.Plant physiology · 2017Article
- Evolutionary Insights Based on SNP Haplotypes of Red Pericarp, Grain Size and Starch Synthase Genes in Wild and Cultivated Rice.Frontiers in plant science · 2017Article
- Deep sequencing transcriptional fingerprinting of rice kernels for dissecting grain quality traits.BMC genomics · 2015Article
- Designing climate-resilient rice with ideal grain quality suited for high-temperature stress.Journal of experimental botany · 2015Review
- Genetic controls on starch amylose content in wheat and rice grains.Journal of genetics · 2014Review
- Improvement of marker-based predictability of Apparent Amylose Content in japonica rice through GBSSI allele mining.Rice (New York, N.Y.) · 2014Article
- Splicing and alternative splicing in rice and humans.BMB reports · 2013Review
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The rice Waxy gene encodes a granule-bound starch synthase (GBSS) necessary for the synthesis of amylose in endosperm tissue. We have previously shown that a CT microsatellite near the transcriptional start site of the GBSS gene can distinguish 7 alleles that accounted for more than 80% of the variation in apparent amylose content in an extended pedigree of 89 US rice cultivars (Oryza sativa L.). Furthermore, all the cultivars with 18% or less amylose were shown to have the sequence AGTTATA at the putative leader intron 5' splice site, while all cultivars with a higher proportion of amylose had AGGTATA. Here we demonstrate that this single-base mutation reduces the efficiency of GBSS pre-mRNA processing and results in alternate splicing at three cryptic sites. The predominant 5' splice site in CT18 low-amylose varieties is 93 bp upstream of the splice site used in intermediate and high amylose varieties and is immediately 5' to the CT microsatellite that we previously demonstrated to be tightly correlated with amylose content. Use of the leader intron 5' splice site at either -93 or -1 in conjunction with the predominant 3' splice site results in formation of a small open reading frame 38 bp upstream of the normal ATG and out of frame with it. This open reading frame is not produced when any of the 5' leader intron splice sites are used in conjunction with an alternate 3' splice site five bases further downstream which was observed in all rice varieties tested.
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