ArticlePloS one2015
Genetic analysis of cold tolerance at the germination and booting stages in rice by association mapping.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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46 citing papers in PubMed, 108 citations in OpenAlex.
- Haplotype-based multi-locus genome-wide association study reveals genomic regions associated with reproductive stage high temperature stress tolerance in rice.Plant molecular biology · 2026Article
- The Pentatricopeptide Repeat Protein OsPPR7 Confers Cold Tolerance at the Booting Stage in Rice by Regulating ABA and ROS Homeostasis.Rice (New York, N.Y.) · 2026Article
- Genetic architecture of seedling stage chilling tolerance in United States rice germplasm.Frontiers in plant science · 2026Article
- Natural variation in OsTPS8 confers differential regulation of chalkiness and seed vigor in indica and japonica rice.Nature genetics · 2026Article
- Identification of Candidate Genes for Cold Tolerance at Seedling Stage by GWAS in Rice (Biology · 2024Article
- Impact of Abiotic Stress on Rice and the Role of DNA Methylation in Stress Response Mechanisms.Plants (Basel, Switzerland) · 2024Review
- Impact of rice GENERAL REGULATORY FACTOR14h (GF14h) on low-temperature seed germination and its application to breeding.PLoS genetics · 2024Article
- Advances and opportunities in unraveling cold-tolerance mechanisms in the world's primary staple food crops.The plant genome · 2024Review
- Uncovering Novel QTLs and Candidate Genes for Salt Tolerance at the Bud Burst Stage in Rice through Genome-Wide Association Study.Plants (Basel, Switzerland) · 2024Article
- 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
- Identification of a key locus, qNL3.1, associated with seed germination under salt stress via a genome-wide association study in rice.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 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 Mapping Identifies New Candidate Genes for Cold Stress and Chilling Acclimation at Seedling Stage in Rice (International journal of molecular sciences · 2022Article
- Article
- Identification of cold tolerance QTLs at the bud burst stage in 211 rice landraces by GWAS.BMC plant biology · 2021Article
- Genome-wide analysis of Dof transcription factors and their response to cold stress in rice (Oryza sativa L.).BMC genomics · 2021Article
- NILs of Cold TolerantFrontiers in genetics · 2021Article
- Advances in the Identification of Quantitative Trait Loci and Genes Involved in Seed Vigor in Rice.Frontiers in plant science · 2021Review
- Population genetic structure and association mapping for iron toxicity tolerance in rice.PloS one · 2021Article
- The Candidate Genes Underlying a Stably Expressed QTL for Low Temperature Germinability in Rice (Oryza sativa L.).Rice (New York, N.Y.) · 2020Article
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Authors and funding
13 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Low temperature affects the rice plants at all stages of growth. It can cause severe seedling injury and male sterility resulting in severe yield losses. Using a mini core collection of 174 Chinese rice accessions and 273 SSR markers we investigated cold tolerance at the germination and booting stages, as well as the underlying genetic bases, by association mapping. Two distinct populations, corresponding to subspecies indica and japonica showed evident differences in cold tolerance and its genetic basis. Both subspecies were sensitive to cold stress at both growth stages. However, japonica was more tolerant than indica at all stages as measured by seedling survival and seed setting. There was a low correlation in cold tolerance between the germination and booting stages. Fifty one quantitative trait loci (QTLs) for cold tolerance were dispersed across all 12 chromosomes; 22 detected at the germination stage and 33 at the booting stage. Eight QTLs were identified by at least two of four measures. About 46% of the QTLs represented new loci. The only QTL shared between indica and japonica for the same measure was qLTSSvR6-2 for SSvR. This implied a complicated mechanism of old tolerance between the two subspecies. According to the relative genotypic effect (RGE) of each genotype for each QTL, we detected 18 positive genotypes and 21 negative genotypes in indica, and 19 positive genotypes and 24 negative genotypes in japonica. In general, the negative effects were much stronger than the positive effects in both subspecies. Markers for QTL with positive effects in one subspecies were shown to be effective for selection of cold tolerance in that subspecies, but not in the other subspecies. QTL with strong negative effects on cold tolerance should be avoided during MAS breeding so as to not cancel the effect of favorable QTL at other loci.
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