ArticleGenome biology2023
A pangenome analysis pipeline provides insights into functional gene identification in rice.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
65 citing papers in PubMed.
- A pangenome-based approach reveals genes associated with polyploidy and apomixis in Eragrostis curvula.The plant genome · 2026Article
- The Pan-Genome of 1107 Spotted Sea Bass Accessions Reveals Gene Evolution Patterns During Domestication Selection.Molecular ecology resources · 2026Article
- Genome-Wide Association Mapping and Integrated Transcriptomic-Genomic Analysis Reveal Candidate Genes for Grain Transparency in Rice.International journal of molecular sciences · 2026Article
- Challenges in Bringing Pangenome Research Into Breeding: A Case Study in Rice.Plant biotechnology journal · 2026Review
- The pan-genome provides insights into evolutionary dynamics and fatty acid metabolism in Aceraceae family.Genome biology · 2026Article
- Graph-based and molecular modeling approaches to identify TpiA as a noval therapeutic target in Neisseria meningitidis.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- The pangenome enhances the understanding of the genetic diversity of papaya.Horticulture research · 2026Article
- Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize.Genome research · 2026Article
- High-quality draft genome assembly and functional annotation ofFrontiers in plant science · 2026Article
- The pangenome: a statistical model, not a fixed biological property.Bioinformatics advances · 2026Review
- Multispecies pangenomes reveal a pervasive influence of population size on structural variation.Science (New York, N.Y.) · 2025Article
- The pan-NLRome and diversity of Watkins wheat provide genetic resources for improving disease resistance and adaptation.Plant communications · 2025Article
- GWAS and multi-omics study reveal OsJAR2 associated jasmonate biosynthesis contributes to Southern rice black-streaked dwarf virus resistance in rice.BMC genomics · 2025Article
- Identification of new genomic loci for seed protein and oil content in the soybean pangenome using genome-wide association and haplotype analyses.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Transposable elements drive evolution and perturb gene expression in Brassica rapa and B. oleracea.The Plant journal : for cell and molecular biology · 2025Article
- The Endosperm-Specific GenePlants (Basel, Switzerland) · 2025Article
- Pangenome analysis of Liriodendron reveals presence/absence variations associated with growth traits.BMC plant biology · 2025Article
- Haplotype-resolved, gap-free genome assemblies provide insights into the divergence between Asian and European pears.Nature genetics · 2025Article
- Article
- Accurate, Scalable Structural Variant Genotyping in Complex Genomes at Population Scales.Molecular biology and evolution · 2025Article
5 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
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundA pangenome aims to capture the complete genetic diversity within a species and reduce bias in genetic analysis inherent in using a single reference genome. However, the current linear format of most plant pangenomes limits the presentation of position information for novel sequences. Graph pangenomes have been developed to overcome this limitation. However, bioinformatics analysis tools for graph format genomes are lacking.
resultsTo overcome this problem, we develop a novel strategy for pangenome construction and a downstream pangenome analysis pipeline (PSVCP) that captures genetic variants' position information while maintaining a linearized layout. Using PSVCP, we construct a high-quality rice pangenome using 12 representative rice genomes and analyze an international rice panel with 413 diverse accessions using the pangenome as the reference. We show that PSVCP successfully identifies causal structural variations for rice grain weight and plant height. Our results provide insights into rice population structure and genomic diversity. We characterize a new locus (qPH8-1) associated with plant height on chromosome 8 undetected by the SNP-based genome-wide association study (GWAS).
conclusionsOur results demonstrate that the pangenome constructed by our pipeline combined with a presence and absence variation-based GWAS can provide additional power for genomic and genetic analysis. The pangenome constructed in this study and the associated genome sequence and genetic variants data provide valuable genomic resources for rice genomics research and improvement in future.
Indexed as
Identifiers
What Socratic holds
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 Socratic graph.