ArticleGenome research2019
Structural variants in 3000 rice genomes.
Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 93 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
93 citing papers in PubMed, 1 synthesis or guideline pooled it, 203 citations in OpenAlex.
- Meta-QTL and ortho-MQTL analyses identified genomic regions controlling rice yield, yield-related traits and root architecture under water deficit conditions.Scientific reports · 2021Pooled it
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- Mapping recombination cold spots in wheat via meiotic recombination in a large biparental population.G3 (Bethesda, Md.) · 2026Article
- Wild tomato genome assemblies reveal structural variants and repeat content act as recombination barriers.Nature communications · 2026Article
- Recent Dominant Transposition Events Affect Gene Regulatory Regions, but Not Coding Sequences, in Polar and Brown Bear Genomes.Current issues in molecular biology · 2026Article
- Dissecting Agronomically favorable genotypes in temperate japonica rice via haplotype analysis of a Japan-MAGIC population.The Plant journal : for cell and molecular biology · 2026Article
- Accessing crop genetic diversity via pangenomics.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- AlleleMiner: a long-read pipeline for gene-wise de novo allele phasing and variant detection in diploid citrus cultivars.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- Transposable elements hitchhike on Starships across fungal genomes.Nature communications · 2026Article
- Investigating Intraspecific Diversity of Metabolic Gene Clusters with MLPA and Synthetic Probes.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Individual Genomic Distinctness of Rice Germplasm as Measured with an Average Pairwise Dissimilarity of Genome-Wide SNPs and Structural Variants.Plants (Basel, Switzerland) · 2025Article
- The Evolutionary Dynamics of Genetic Mutational Load Throughout Tomato Domestication History.Molecular ecology · 2025Article
- A 280 bp SINE insertion within the pig PLA2G16 could potentially modify gene expression through integration with its transcript.Journal of applied genetics · 2025Article
- Climate change and plant genomic plasticity.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- Pan-Genome-Based Characterization of the PYL Transcription Factor Family inPlants (Basel, Switzerland) · 2025Article
- FHY3/FAR1 transposable elements generate adaptive genetic variation in the Bassia scoparia genome.Pest management science · 2025Article
- Copy Number Variation Shapes Structural Genomic Diversity Associated With Ecological Adaptation in the Wild Tomato Solanum chilense.Molecular biology and evolution · 2025Article
- Accurate, Scalable Structural Variant Genotyping in Complex Genomes at Population Scales.Molecular biology and evolution · 2025Article
- Genome-Wide Analyses of Copy Number Variants in 751 Populus trichocarpa Individuals From Natural Populations.Genome biology and evolution · 2025Article
- Multi-omics analyses unveil dual genetic loci governing four distinct watermelon flesh color phenotypes.Molecular horticulture · 2025Article
33 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 6 institutions in 6 countries.
Funding
Abstract
Investigation of large structural variants (SVs) is a challenging yet important task in understanding trait differences in highly repetitive genomes. Combining different bioinformatic approaches for SV detection, we analyzed whole-genome sequencing data from 3000 rice genomes and identified 63 million individual SV calls that grouped into 1.5 million allelic variants. We found enrichment of long SVs in promoters and an excess of shorter variants in 5' UTRs. Across the rice genomes, we identified regions of high SV frequency enriched in stress response genes. We demonstrated how SVs may help in finding causative variants in genome-wide association analysis. These new insights into rice genome biology are valuable for understanding the effects SVs have on gene function, with the prospect of identifying novel agronomically important alleles that can be utilized to improve cultivated rice.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.