Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material and Genotyping
2.2. Cold Treatment and Cold Tolerance Evaluation
2.3. Population Structure and Linkage Disequilibrium (LD) Decay Analysis
2.4. GWAS
2.5. Candidate Gene Prediction and Haplotype Analysis
3. Results
3.1. Cold Tolerance in Rice at the Seedling Stage
3.2. Population Structure and LD Decay
3.3. GWAS of Cold Stress Tolerance in Rice Seedlings
3.4. Haplotype Analysis to Identify Candidate Genes Underlying Cold Tolerance
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Conflicts of Interest
References
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QTL | Lead SNP | Chr | −log10(P) | Reported QTL | Reference of Previously Reported QTLs | |
---|---|---|---|---|---|---|
QTL Accession ID | Related Trait | |||||
qCTS1 | 14,648,882 | 1 | 6.64 | AQAL060 | Root thickness | [44] |
qCTS4 | 3,829,001 | 4 | 6.34 | CQAA8 | Cold tolerance | [42,46] |
qCTS5-1 | 4,437,944 | 5 | 6.40 | CQE39 | Rubisco content | [45] |
qCTS5-2 | 19,300,152 | 5 | 6.97 | AQFR028 | Seedling vigor | [47] |
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Ham, T.-H.; Kwon, Y.; Lee, Y.; Choi, J.; Lee, J. Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage. Agriculture 2021, 11, 318. https://doi.org/10.3390/agriculture11040318
Ham T-H, Kwon Y, Lee Y, Choi J, Lee J. Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage. Agriculture. 2021; 11(4):318. https://doi.org/10.3390/agriculture11040318
Chicago/Turabian StyleHam, Tae-Ho, Yebin Kwon, Yoonjung Lee, Jisu Choi, and Joohyun Lee. 2021. "Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage" Agriculture 11, no. 4: 318. https://doi.org/10.3390/agriculture11040318