ArticleBMC plant biology2013
Global RNA sequencing reveals that genotype-dependent allele-specific expression contributes to differential expression in rice F1 hybrids.
Article in BMC plant biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed, 65 citations in OpenAlex.
- Quantitative Insights into the Genetic Mechanisms of Crop Heterosis.Advanced genetics (Hoboken, N.J.) · 2025Review
- Transcriptome analysis of substrate temperature effects on adventitious root formation in peach rootstocks.PeerJ · 2025Article
- Molecular Mechanisms of Heterosis and Its Applications in Tree Breeding: Progress and Perspectives.International journal of molecular sciences · 2024Review
- Insights into heterosis from histone modifications in the flag leaf of inter-subspecific hybrid rice.BMC plant biology · 2024Article
- Natural variations of heterosis-related allele-specific expression genes in promoter regions lead to allele-specific expression in maize.BMC genomics · 2024Article
- Comparative transcriptomic analysis reveals the molecular mechanism underlying seedling heterosis and its relationship with hybrid contemporary seeds DNA methylation in soybean.Frontiers in plant science · 2024Article
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- Characterization of Genes That Exhibit Genotype-Dependent Allele-Specific Expression and Its Implications for the Development of Maize Kernel.International journal of molecular sciences · 2023Article
- Overdominant expression of genes plays a key role in root growth of tobacco hybrids.Frontiers in plant science · 2023Article
- Comparative transcriptomic analysis of maize ear heterosis during the inflorescence meristem differentiation stage.BMC plant biology · 2022Article
- Nonadditive gene expression is correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow (Salix spp.).G3 (Bethesda, Md.) · 2022Article
- Genetic Basis of Dorper Sheep (Frontiers in genetics · 2022Article
- Large structural variations in the haplotype-resolved African cassava genome.The Plant journal : for cell and molecular biology · 2021Article
- Biased allelic expression in tissues of F1 hybrids between tropical and temperate lotus (Nelumbo nuicfera).Plant molecular biology · 2021Article
- Comparative transcriptome analysis between inbred and hybrids reveals molecular insights into yield heterosis of upland cotton.BMC plant biology · 2020Article
- Changes in DNA Methylation in Response to 6-Benzylaminopurine Affect Allele-Specific Gene Expression inInternational journal of molecular sciences · 2020Article
- The Role of Transcriptional Regulation in Hybrid Vigor.Frontiers in plant science · 2020Review
- Implications of Gene Inheritance Patterns on the Heterosis of Abdominal Fat Deposition in Chickens.Genes · 2019Article
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- Phylogenetic Origin of Primary and Secondary Metabolic Pathway Genes Revealed byFrontiers in plant science · 2019Article
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13 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundExtensive studies on heterosis in plants using transcriptome analysis have identified differentially expressed genes (DEGs) in F1 hybrids. However, it is not clear why yield in heterozygotes is superior to that of the homozygous parents or how DEGs are produced. Global allele-specific expression analysis in hybrid rice has the potential to answer these questions.
resultsWe report a genome-wide allele-specific expression analysis using RNA-sequencing technology of 3,637-3,824 genes from three rice F1 hybrids. Of the expressed genes, 3.7% exhibited an unexpected type of monoallelic expression and 23.8% showed preferential allelic expression that was genotype-dependent in reciprocal crosses. Those genes exhibiting allele-specific expression comprised 42.4% of the genes differentially expressed between F1 hybrids and their parents. Allele-specific expression accounted for 79.8% of the genes displaying more than a 10-fold expression level difference between an F1 and its parents, and almost all (97.3%) of the genes expressed in F1, but non-expressed in one parent. Significant allelic complementary effects were detected in the F1 hybrids of rice.
conclusionsAnalysis of the allelic expression profiles of genes at the critical stage for highest biomass production from the leaves of three different rice F1 hybrids identified genotype-dependent allele-specific expression genes. A cis-regulatory mechanism was identified that contributes to allele-specific expression, leading to differential gene expression and allelic complementary effects in F1 hybrids.
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