ArticlePloS one2017
Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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61 citing papers in PubMed, 169 citations in OpenAlex.
- Stage-specific screening reveals differential resilience response to cold stress in rice.PloS one · 2026Article
- Genetic architecture of seedling stage chilling tolerance in United States rice germplasm.Frontiers in plant science · 2026Article
- Selection on genome-wide gene expression plasticity of rice in wet and dry field environments.Molecular ecology · 2025Article
- Divergent genetic architecture of cold stress tolerance inFrontiers in plant science · 2025Article
- CRISPR/Cas9 mediated genome editing for crop improvement against Abiotic stresses: current trends and prospects.Functional & integrative genomics · 2024Review
- Impact of rice GENERAL REGULATORY FACTOR14h (GF14h) on low-temperature seed germination and its application to breeding.PLoS genetics · 2024Article
- Genome-Wide Association Study of Rice Diversity Panel Reveals New QTLs for Tolerance to Water Deficit Under the Egyptian Conditions.Rice (New York, N.Y.) · 2024Article
- A transposon insertion in the promoter of OsUBC12 enhances cold tolerance during japonica rice germination.Nature communications · 2024Article
- Advances and opportunities in unraveling cold-tolerance mechanisms in the world's primary staple food crops.The plant genome · 2024Review
- Meta-QTL and ortho analysis unravels the genetic architecture and key candidate genes for cold tolerance at seedling stage in rice.Physiology and molecular biology of plants : an international journal of functional plant biology · 2024Article
- Analysis of genome-wide association studies of low-temperature germination in Xian and Geng rice.Frontiers in plant science · 2024Article
- Genome-wide association mapping combined with gene-based haplotype analysis identify a novel gene for shoot length in rice (Oryza sativa L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Genome Editing and Improvement of Abiotic Stress Tolerance in Crop Plants.Life (Basel, Switzerland) · 2023Review
- Comparative transcriptomic analysis of germinating rice seedlings to individual and combined anaerobic and cold stress.BMC genomics · 2023Article
- Identification of Rice Accessions Having Cold Tolerance at the Seedling Stage and Development of Novel Genotypic Assays for Predicting Cold Tolerance.Plants (Basel, Switzerland) · 2023Article
- Genome-wide association analysis for emergence of deeply sown rice (Frontiers in plant science · 2023Article
- Navigating rice seedling cold resilience: QTL mapping in two inbred line populations and the search for genes.Frontiers in plant science · 2023Article
- Drought stress in rice: morpho-physiological and molecular responses and marker-assisted breeding.Frontiers in plant science · 2023Review
- Article
- Fine mapping of a QTL and identification of candidate genes associated with cold tolerance during germination in peanut (Frontiers in plant science · 2023Article
1 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 3 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Cold temperature is an important abiotic stress which negatively affects morphological development and seed production in rice (Oryza sativa L.). At the seedling stage, cold stress causes poor germination, seedling injury and poor stand establishment; and at the reproductive stage cold decreases seed yield. The Rice Diversity Panel 1 (RDP1) is a global collection of over 400 O. sativa accessions representing the five major subpopulations from the INDICA and JAPONICA varietal groups, with a genotypic dataset consisting of 700,000 SNP markers. The objectives of this study were to evaluate the RDP1 accessions for the complex, quantitatively inherited cold tolerance traits at the germination and reproductive stages, and to conduct genome-wide association (GWA) mapping to identify SNPs and candidate genes associated with cold stress at these stages. GWA mapping of the germination index (calculated as percent germination in cold divided by warm treatment) revealed 42 quantitative trait loci (QTLs) associated with cold tolerance at the seedling stage, including 18 in the panel as a whole, seven in temperate japonica, six in tropical japonica, 14 in JAPONICA, and nine in INDICA, with five shared across all subpopulations. Twenty-two of these QTLs co-localized with 32 previously reported cold tolerance QTLs. GWA mapping of cold tolerance at the reproductive stage detected 29 QTLs, including seven associated with percent sterility, ten with seed weight per panicle, 14 with seed weight per plant and one region overlapping for two traits. Fifteen co-localized with previously reported QTLs for cold tolerance or yield components. Candidate gene ontology searches revealed these QTLs were associated with significant enrichment for genes related to with lipid metabolism, response to stimuli, response to biotic stimuli (suggesting cross-talk between biotic and abiotic stresses), and oxygen binding. Overall the JAPONICA accessions were more tolerant to cold stress than INDICA accessions.
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