ArticleBMC plant biology2007
Differential gene expression in an elite hybrid rice cultivar (Oryza sativa, L) and its parental lines based on SAGE data.
Article in BMC plant biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 51 citations in OpenAlex.
- Proteotoxicity caused by perturbed protein complexes underlies hybrid incompatibility in yeast.Nature communications · 2022Article
- Comparative transcriptomic analysis of maize ear heterosis during the inflorescence meristem differentiation stage.BMC plant biology · 2022Article
- Advances in Research on the Mechanism of Heterosis in Plants.Frontiers in plant science · 2021Review
- Heterotic patterns of primary and secondary metabolites in the oilseed crop Brassica juncea.Heredity · 2019Article
- Rice Genomics: over the Past Two Decades and into the Future.Genomics, proteomics & bioinformatics · 2018Review
- Article
- Transcriptome profiling and comparison of maize ear heterosis during the spikelet and floret differentiation stages.BMC genomics · 2016Article
- Genome-wide mapping of 5-hydroxymethylcytosine in three rice cultivars reveals its preferential localization in transcriptionally silent transposable element genes.Journal of experimental botany · 2015Article
- Comparative transcriptional profiling of three super-hybrid rice combinations.International journal of molecular sciences · 2014Article
- Comparative proteomic analysis of embryos between a maize hybrid and its parental lines during early stages of seed germination.PloS one · 2013Article
- Comparative transcriptional profiling and preliminary study on heterosis mechanism of super-hybrid rice.Molecular plant · 2010Article
- SuperSAGE analysis of the Nicotiana attenuata transcriptome after fatty acid-amino acid elicitation (FAC): identification of early mediators of insect responses.BMC plant biology · 2010Article
- A transcriptomic analysis of superhybrid rice LYP9 and its parents.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- HRGD: a database for mining potential heterosis-related genes in plants.Plant molecular biology · 2009Article
- Transcriptomic profiling of mature embryo from an elite super-hybrid rice LYP9 and its parental lines.BMC plant biology · 2008Article
- Differential SAGE analysis in Arabidopsis uncovers increased transcriptome complexity in response to low temperature.BMC genomics · 2008Article
- Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis.BMC plant biology · 2008Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIt was proposed that differentially-expressed genes, aside from genetic variations affecting protein processing and functioning, between hybrid and its parents provide essential candidates for studying heterosis or hybrid vigor. Based our serial analysis of gene expression (SAGE) data from an elite Chinese super-hybrid rice (LYP9) and its parental cultivars (93-11 and PA64s) in three major tissue types (leaves, roots and panicles) at different developmental stages, we analyzed the transcriptome and looked for candidate genes related to rice heterosis.
resultsBy using an improved strategy of tag-to-gene mapping and two recently annotated genome assemblies (93-11 and PA64s), we identified 10,268 additional high-quality tags, reaching a grand total of 20,595 together with our previous result. We further detected 8.5% and 5.9% physically-mapped genes that are differentially-expressed among the triad (in at least one of the three stages) with P-values less than 0.05 and 0.01, respectively. These genes distributed in 12 major gene expression patterns; among them, 406 up-regulated and 469 down-regulated genes (P < 0.05) were observed. Functional annotations on the identified genes highlighted the conclusion that up-regulated genes (some of them are known enzymes) in hybrid are mostly related to enhancing carbon assimilation in leaves and roots. In addition, we detected a group of up-regulated genes related to male sterility and 442 down-regulated genes related to signal transduction and protein processing, which may be responsible for rice heterosis.
conclusionWe improved tag-to-gene mapping strategy by combining information from transcript sequences and rice genome annotation, and obtained a more comprehensive view on genes that related to rice heterosis. The candidates for heterosis-related genes among different genotypes provided new avenue for exploring the molecular mechanism underlying heterosis.
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