ArticleNature genetics2018
Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice.
Article in Nature genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 303 papers, 3 of them syntheses that pooled it.
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Who cites it
303 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Advancing crop improvement through GWAS and beyond in mung bean.Frontiers in plant science · 2024Pooled it
- The Effect of Methodological Considerations on the Construction of Gene-Based Plant Pan-genomes.Genome biology and evolution · 2023Pooled it
- Exploring and exploiting genetics and genomics for sweetpotato improvement: Status and perspectives.Plant communications · 2022Pooled it
- Unlocking the future of crop improvement with crop wild relatives.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Uncovering structural variation in conifer gigagenomes: evolutionary insights and technical challenges.Molecular biology and evolution · 2026Article
- Subspecies-specific metabolic gene clusters shape polyphenol dynamics for modular metabolic breeding in sugarcane.Plant communications · 2026Article
- Article
- Advances in genomics-driven genetic decoding and genomic design breeding in tomato.Horticulture research · 2026Article
- Empowering Plant Biotechnology Research: Super-Pangenomes as a Novel Arsenal for Crop Breeding and Improvement.Molecular biotechnology · 2026Review
- Genome assemblies and annotations are not static and need support for tracking their evolution.Briefings in bioinformatics · 2026Review
- Graph-based pan-genome reveals structural variations associated with agronomic traits in mung bean.Nature genetics · 2026Article
- Graph-based pan-genome reveals structural and functional diversity across oil palm domestication gradients.BMC plant biology · 2026Article
- Network analysis reveals that bHLH transcription factors positively regulate rice resistance to Magnaporthe oryzae.BMC plant biology · 2026Article
- Challenges in Bringing Pangenome Research Into Breeding: A Case Study in Rice.Plant biotechnology journal · 2026Review
- Pangenomics for Agricultural Breeding: Construction Strategies, Evidence Integration, and Translational Constraints.Biology · 2026Review
- Cis-regulatory editing of SD1 promoter enhances TCP19-mediated repression to optimize plant height in Kam sweet rice.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Pan-Genome-Wide Analysis and Expression Profiling of the Potato GST Gene Family.Plants (Basel, Switzerland) · 2026Article
- Chromosome-Level Genome Assembly Identifies RIRE2 and CACTA Transposable Elements at the Sub1 Locus in Submergence-Tolerant Rice Varieties.Rice (New York, N.Y.) · 2026Article
- Integrative multi-omics analysis reveals the domestication mechanism of black rice.National science review · 2026Article
- Pangenome Analysis Reveals Structural Variations Associated With Citric Acid Accumulation in Prunus mume.Plant biotechnology journal · 2026Article
243 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
24 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The rich genetic diversity in Oryza sativa and Oryza rufipogon serves as the main sources in rice breeding. Large-scale resequencing has been undertaken to discover allelic variants in rice, but much of the information for genetic variation is often lost by direct mapping of short sequence reads onto the O. sativa japonica Nipponbare reference genome. Here we constructed a pan-genome dataset of the O. sativa-O. rufipogon species complex through deep sequencing and de novo assembly of 66 divergent accessions. Intergenomic comparisons identified 23 million sequence variants in the rice genome. This catalog of sequence variations includes many known quantitative trait nucleotides and will be helpful in pinpointing new causal variants that underlie complex traits. In particular, we systemically investigated the whole set of coding genes using this pan-genome data, which revealed extensive presence and absence of variation among rice accessions. This pan-genome resource will further promote evolutionary and functional studies in rice.
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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.