ArticleRice (New York, N.Y.)2023
GWAS Combined with WGCNA of Transcriptome and Metabolome to Excavate Key Candidate Genes for Rice Anaerobic Germination.
Article in Rice (New York, N.Y.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 19 citations in OpenAlex.
- Differences in Nutritional Composition ofJournal of fungi (Basel, Switzerland) · 2026Article
- Germination as a Strategy to Enhance the Bioactivity of Whole Grains: Phytochemical Remodeling and Health Implications.Comprehensive reviews in food science and food safety · 2026Review
- Identification of candidate genes for heat tolerance in rice by genome-wide association study and transcriptome sequencing.BMC plant biology · 2026Article
- Aconserved salt-stress co-expression network in japonica rice reveals partially dissociated hub gene connectivity and transcriptional induction.Frontiers in plant science · 2026Article
- Genome-wide association analysis reveals novel genetic loci involved in rice brown spot resistance.BMC genomics · 2025Article
- Identification of submergence tolerance QTLs/genes during seed germination in 432 rice varieties by GWAS.BMC plant biology · 2025Article
- GWAS Combined with Meta-Analysis Identifies OsDREB6 as a Regulator of Coleoptile Elongation Under Anaerobic Conditions in Rice.Rice (New York, N.Y.) · 2025Article
- Identification of Candidate Genes for Hypoxia Tolerance in Rice by Genome-Wide Association Analysis and Transcriptome Sequencing.Rice (New York, N.Y.) · 2025Article
- Multi-Omics Analysis Decodes Biosynthesis of Specialized Metabolites Constituting the Therapeutic Terrains ofInternational journal of molecular sciences · 2025Article
- Mining Heat-Resistant Key Genes of Peony Based on Weighted Gene Co-Expression Network Analysis.Genes · 2024Article
- mRNA-miRNA analyses reveal the involvement of CsbHLH1 and miR1446a in the regulation of caffeine biosynthesis inHorticulture research · 2024Article
- Analysis of plant metabolomics data using identification-free approaches.Applications in plant sciencesReview
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Authors and funding
16 authors at 1 institution in 1 country.
Funding
Abstract
Direct seeding of rice is a lightweight and simple cultivation method, which can effectively promote rice production. Anaerobic germination tolerance is one of the main traits of rice adaptability to direct seeding. The mining of related genetic loci, analysis of anaerobic traits and screening of tolerance genes provided valuable genetic resources for improving the anaerobic germination ability of direct seeding rice. This study conducted a dynamic genome-wide association study (GWAS) based on coleoptile-related traits of 591 rice natural populations, and a total of 317 SNP sites were detected. Integrated dynamic widely targeted metabolomics analysis, we found that xanthine, L-alanine and GABA may be key biomarkers that are sensitive and respond strongly to hypoxic stress perception. By WGCNA analysis of targeted metabolomics and transcriptomics, a total of 3 modules were obtained that were significantly correlated with the above three marker metabolites, namely dark green, dark gray and light green modules, respectively, and several key structural genes of OsAlaAT1, OsGAD4, OsAAH and Os09g0424600 that may affect hypoxic germination were screened from the 3 modules. Among them, OsAlaAT1 (Os10g0390500), located in Chr10-12877840, which is within the GWAS location range of CVAN3d, is considered to be a more reliable candidate gene. Overall, in addition to providing new insight into the metabolic regulation of L-alanine, GABA and xanthine during hypoxic germination of rice. This study also provided a reference for the basic theoretical research and breeding application research on the related traits of anaerobic germination in direct-seeding rice.
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