ArticleNature communications2023
Transcriptome-wide association analyses reveal the impact of regulatory variants on rice panicle architecture and causal gene regulatory networks.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 62 citations in OpenAlex.
- Translating functional molecular knowledge into crop-breeding success.Nature reviews. Genetics · 2026Review
- Review
- Rice LSD1-like Genes: Genome-Wide Characterization and Evidence Linking OsLSD3 to Plant Height.Plants (Basel, Switzerland) · 2026Article
- Conditionally Significant eQTL and TWAS Analyses Identify MsRD26 as a Major Candidate Positive Regulator of Salt Tolerance in Medicago sativa L.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Identification and Functional Characterization of the Mungbean Yellow Mosaic India Virus Resistant GeneJournal of agricultural and food chemistry · 2026Article
- Independent component analysis deciphers the genetic basis of cotton fiber elongation through eQTLs and sQTLs.Journal of advanced research · 2026Article
- Improved laser capture microdissection combined with transcriptome sequencing reveals gene expression reprogramming during rice panicle branch meristems differentiation.BMC plant biology · 2026Article
- Plant Genetic Engineering: Technological Pathways, Application Scenarios, and Future Directions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Multi-Tissue Omics Analysis Uncovers Translational Regulation Underlying Complex Traits in Pigs.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Identification of OsDB10.1 and OsGSTU17 mediate cadmium tolerance and accumulation in rice.Plant communications · 2026Article
- Identifying Causal Genes and Building Regulatory Networks in Crops Using the CisTrans-ECAS Method.Bio-protocol · 2026Article
- Nuclear factor OsNF-YC5 regulates grain size and quality in rice.Plant molecular biology · 2026Article
- Heat stress impact on rice reproductive processes: challenges and new approaches.Frontiers in genome editing · 2026Review
- Integrated multi-omics reveals terpenoid-driven metabolic and transcriptional regulation underlying sweetpotato resistance to black rot disease.BMC plant biology · 2025Article
- Uncovering the genetic architecture of pungency, carotenoids, and flavor inHorticulture research · 2025Article
- Grain shape in rice: a Genome-wide association study of the effector genes.BMC plant biology · 2025Article
- Integrative omics of the genetic basis for wheat WUE and drought resilience reveal the function of TaMYB7-A1.Nature communications · 2025Article
- Comprehensive analysis of 1,771 transcriptomes from 7 tissues enhance genetic and biological interpretations of maize complex traits.G3 (Bethesda, Md.) · 2025Article
- A panoramic view of cotton resistance toiMeta · 2025Article
- A system genetics analysis uncovers the regulatory variants controlling drought response in wheat.Plant biotechnology journal · 2025Article
Corrections and comments
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Authors and funding
25 authors at 2 institutions in 2 countries.
Funding
Abstract
Panicle architecture is a key determinant of rice grain yield and is mainly determined at the 1-2 mm young panicle stage. Here, we investigated the transcriptome of the 1-2 mm young panicles from 275 rice varieties and identified thousands of genes whose expression levels were associated with panicle traits. Multimodel association studies suggested that many small-effect genetic loci determine spikelet per panicle (SPP) by regulating the expression of genes associated with panicle traits. We found that alleles at cis-expression quantitative trait loci of SPP-associated genes underwent positive selection, with a strong preference for alleles increasing SPP. We further developed a method that integrates the associations of cis- and trans-expression components of genes with traits to identify causal genes at even small-effect loci and construct regulatory networks. We identified 36 putative causal genes of SPP, including SDT (MIR156j) and OsMADS17, and inferred that OsMADS17 regulates SDT expression, which was experimentally validated. Our study reveals the impact of regulatory variants on rice panicle architecture and provides new insights into the gene regulatory networks of panicle traits.
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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.