ArticleRice (New York, N.Y.)2020
QTL Mapping and Candidate Gene Analysis for Alkali Tolerance in Japonica Rice at the bud Stage Based on Linkage Mapping and Genome-Wide Association Study.
Article in Rice (New York, N.Y.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed, 90 citations in OpenAlex.
- Research progress on genomic selection breeding technology for crops.Protoplasma · 2026Review
- Genome-Wide Association Study Identifies Candidate Genes for Salt Tolerance in Traditional Rice Landraces.Rice (New York, N.Y.) · 2026Article
- Article
- A multi-locus genome-wide association study uncovers candidate genes for alkali tolerance in maize (Zea Mays L.) seedlings.BMC genomics · 2025Article
- Integrated Transcriptomic and Metabolomic Analyses Reveal Key Responses of Cotton to Salt Stress Post-Germination.Current issues in molecular biology · 2025Article
- Mapping of low-nitrogen tolerance genes in Japonica rice at seedling stage by genome-wide association study.Scientific reports · 2025Article
- Response of different cotton genotypes to salt stress and re-watering.BMC plant biology · 2025Article
- Salt tolerance characterization and genome-wide association study ofFrontiers in plant science · 2025Article
- Evaluation and genome-wide association study of saline-alkali tolerance in high-latitude rice resource populations.Frontiers in genetics · 2025Article
- Genetic dissection of yield and yield-related traits in mungbean based on QTL meta-analysis.Frontiers in genetics · 2025Article
- OsWRKY49 on qAT5 positively regulates alkalinity tolerance at the germination stage in Oryza sativa L. ssp. japonica.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Candidate genes for alkali tolerance identified by genome-wide association study at the seedling stage in rice (Oryza sativa L.).Scientific reports · 2024Article
- Detection of Quantitative Trait Loci Associated with Alkaline Tolerance Using Recombinant Inbred Line Population Derived from Longdao5 × Zhongyouzao8 at Seedling Stage.Life (Basel, Switzerland) · 2024Article
- Mapping quantitative trait loci associated with self-(in)compatibility in goji berries (Lycium barbarum).BMC plant biology · 2024Article
- Article
- 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
- An intronic SNP affects skeletal muscle development by regulating the expression ofFrontiers in veterinary science · 2024Article
- GWAS combined with linkage analysis reveals major QTLs and candidate genes of salt tolerance inFrontiers in plant science · 2024Article
- Joint QTL Mapping and Transcriptome Sequencing Analysis Reveal Candidate Genes for Salinity Tolerance inInternational journal of molecular sciences · 2023Article
- Integrated Transcriptomic and Metabolomic Analyses Uncover the Differential Mechanism in Saline-Alkaline Tolerance betweenInternational journal of molecular sciences · 2023Article
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Authors and funding
11 authors at 1 institution in 2 countries.
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Abstract
backgroundSalinity-alkalinity stress is one of the major factors limiting rice production. Damage caused by alkaline salt stress is more severe than that caused by neutral salt stress. Alkali tolerance at the bud stage in rice directly affects seedling survival and final yield when using the direct seeding cultivation model. However, genetic resources (QTLs and genes) for rice breeders to improve alkali tolerance are limited. In this study, we combined linkage mapping and a genome-wide association study (GWAS) to analyze the genetic structure of this trait in japonica rice at the bud stage.
resultsA population of 184 recombinant inbred lines (RILs) was utilized to map quantitative trait loci (QTLs) for the root length under control condition (RL), alkaline stress (ARL) and relative root length (RRL) at the bud stage. A major QTL related to alkali tolerance at the rice bud stage, qAT11, was detected on chromosome 11. Interestingly, a GWAS identified a lead SNP (Chr_21,999,659) in qAT11 that was significantly associated with alkaline tolerance. After filtering by linkage disequilibrium (LD), haplotype analysis, quantitative real-time PCR, we obtained three candidate genes (LOC_Os11g37300, LOC_Os11g37320 and LOC_Os11g37390). In addition, we performed phenotype verification on the CRISPR/Cas9 mutant of LOC_Os11g37390.
conclusionBased on these results, LOC_Os11g37300, LOC_Os11g37320 and LOC_Os11g37390 were the candidate genes contributing to alkaline tolerance in japonica rice. This study provides resources for breeding aimed at improving rice responses to alkalinity stress.
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