ArticleNature plants2020
An inferred fitness consequence map of the rice genome.
Article in Nature plants, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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
21 citing papers in PubMed.
- Translating functional molecular knowledge into crop-breeding success.Nature reviews. Genetics · 2026Review
- System drift in the evolution of plant meristem development.PLoS genetics · 2026Article
- Uncovering the multi-layer cis-regulatory landscape of rice via integrative nascent RNA analysis.Genome biology · 2025Article
- Enhancers in Plant Development, Adaptation and Evolution.Plant & cell physiology · 2025Review
- Topologically associating domains and the evolution of three-dimensional genome architecture in rice.The Plant journal : for cell and molecular biology · 2025Article
- Article
- Systems genomics of salinity stress response in rice.bioRxiv : the preprint server for biology · 2024Article
- Recent advances in exploring transcriptional regulatory landscape of crops.Frontiers in plant science · 2024Review
- Review
- Deleterious Mutations and the Rare Allele Burden on Rice Gene Expression.Molecular biology and evolution · 2022Article
- The first long-read nuclear genome assembly of Oryza australiensis, a wild rice from northern Australia.Scientific reports · 2022Article
- A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants.The plant genome · 2022Article
- Evolutionary systems biology reveals patterns of rice adaptation to drought-prone agro-ecosystems.The Plant cell · 2022Article
- Cis-regulatory sequences in plants: Their importance, discovery, and future challenges.The Plant cell · 2022Review
- Rice functional genomics: decades' efforts and roads ahead.Science China. Life sciences · 2022Review
- Selection on Accessible Chromatin Regions in Capsella grandiflora.Molecular biology and evolution · 2021Article
- Single cell gene regulatory networks in plants: Opportunities for enhancing climate change stress resilience.Plant, cell & environment · 2021Review
- Genomic mosaicism due to homoeologous exchange generates extensive phenotypic diversity in nascent allopolyploids.National science review · 2021Article
- Advancing crop genomics from lab to field.Nature genetics · 2021Review
- A quantitative genomics map of rice provides genetic insights and guides breeding.Nature genetics · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
The extent to which sequence variation impacts plant fitness is poorly understood. High-resolution maps detailing the constraint acting on the genome, especially in regulatory sites, would be beneficial as functional annotation of noncoding sequences remains sparse. Here, we present a fitness consequence (fitCons) map for rice (Oryza sativa). We inferred fitCons scores (ρ) for 246 inferred genome classes derived from nine functional genomic and epigenomic datasets, including chromatin accessibility, messenger RNA/small RNA transcription, DNA methylation, histone modifications and engaged RNA polymerase activity. These were integrated with genome-wide polymorphism and divergence data from 1,477 rice accessions and 11 reference genome sequences in the Oryzeae. We found ρ to be multimodal, with ~9% of the rice genome falling into classes where more than half of the bases would probably have a fitness consequence if mutated. Around 2% of the rice genome showed evidence of weak negative selection, frequently at candidate regulatory sites, including a novel set of 1,000 potentially active enhancer elements. This fitCons map provides perspective on the evolutionary forces associated with genome diversity, aids in genome annotation and can guide crop breeding programs.
Indexed as
Identifiers
What OpenQuestion 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 OpenQuestion graph.