ArticleProceedings of the National Academy of Sciences of the United States of America2019
Patterns of genome-wide allele-specific expression in hybrid rice and the implications on the genetic basis of heterosis.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 123 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
123 citing papers in PubMed.
- Haplotype-resolved 3D genome maps reveal RNAPII-mediated allelic regulation in hybrid rice.aBIOTECH · 2026Article
- The heterozygous pineapple genome demonstrates the importance of haplotype-resolved plant genomes.Horticulture research · 2026Article
- Haplotype-resolved genome assembly of femaleHorticulture research · 2026Article
- The hidden sources of spurious fusion transcripts in plants.Genome biology · 2026Article
- Dynamics of Gene and Allelic Expression During Modern Hybrid Maize Breeding.Plant biotechnology journal · 2026Article
- DNA methylation remodeling reveals epigenetic regulation of early embryogenesis in Arabidopsis hybrid.Communications biology · 2026Article
- Allele-specific methylation, and InDels ofHorticulture research · 2026Article
- Chromatin accessibility landscape and its association with heterosis in maize hybrids.Nature communications · 2026Article
- Restoration of ancestral transcriptional plasticity contributes to plastic heterosis in fatty liver of hybrid ducks.Communications biology · 2026Article
- Haplotype-resolved genome assembly provides insights into the unique floral scent of Rosa rugosa originated in China.Molecular horticulture · 2026Article
- The Camellia sinensis var. sinensis cv. Fuding Dabaicha genome unveils structural variation-driven metabolic innovation.Nature communications · 2026Article
- Host adaptation and genome evolution of the broad host range fungal rust pathogen, Austropuccinia psidii.G3 (Bethesda, Md.) · 2026Article
- 24-nt-phasiRNA associated CHG/CHH DNA methylation contributes to growth heterosis ofForestry research · 2026Article
- Inheritance of DNA Methylation Patterns and Its Role in Modulating Allelic Expression inPlants (Basel, Switzerland) · 2025Article
- Multi-omics interrogation of herbivorous phenotype acquisition in hybrid culter under a 30% crude protein diet.BMC genomics · 2025Article
- Overexpression of NtGSTU10 gene enhances nicotine content in hybrids by promoting the synthesis and transport metabolism of nicotine.BMC biotechnology · 2025Article
- Quantitative Insights into the Genetic Mechanisms of Crop Heterosis.Advanced genetics (Hoboken, N.J.) · 2025Review
- Using transcriptome analysis and QTL mapping to decipher the genetic basis of heterosis in potato root system.BMC plant biology · 2025Article
- Hybridization Drives Trait Integration in Telomere-To-Telomere Apocynum Genomes.Plant biotechnology journal · 2025Article
- From genome to gene expression: the genomic landscape of a hybrid species of Eucalyptus urophylla × Eucalyptus grandis and its divergence from parental species hybrid.BMC plant biology · 2025Article
63 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.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Utilization of heterosis has greatly increased the productivity of many crops worldwide. Although tremendous progress has been made in characterizing the genetic basis of heterosis using genomic technologies, molecular mechanisms underlying the genetic components are much less understood. Allele-specific expression (ASE), or imbalance between the expression levels of two parental alleles in the hybrid, has been suggested as a mechanism of heterosis. Here, we performed a genome-wide analysis of ASE by comparing the read ratios of the parental alleles in RNA-sequencing data of an elite rice hybrid and its parents using three tissues from plants grown under four conditions. The analysis identified a total of 3,270 genes showing ASE (ASEGs) in various ways, which can be classified into two patterns: consistent ASEGs such that the ASE was biased toward one parental allele in all tissues/conditions, and inconsistent ASEGs such that ASE was found in some but not all tissues/conditions, including direction-shifting ASEGs in which the ASE was biased toward one parental allele in some tissues/conditions while toward the other parental allele in other tissues/conditions. The results suggested that these patterns may have distinct implications in the genetic basis of heterosis: The consistent ASEGs may cause partial to full dominance effects on the traits that they regulate, and direction-shifting ASEGs may cause overdominance. We also showed that ASEGs were significantly enriched in genomic regions that were differentially selected during rice breeding. These ASEGs provide an index of the genes for future pursuit of the genetic and molecular mechanism of heterosis.
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.