Genome-Wide Association Study Identifies Quantitative Trait Loci and Candidate Genes Involved in Deep-Sowing Tolerance in Maize (Zea mays L.)
Abstract
:1. Introduction
2. Results
2.1. Evaluation of Deep-Sowing Tolerance-Related Traits
2.2. Linkage Disequilibrium and Structure Analysis
2.3. GWAS of Deep-Sowing Tolerance-Related Traits in Maize
2.4. Candidate Genes Co-Localized by ML, PL, and SL
2.5. Functional Verification of Candidate Gene ZmGCP2
2.6. Natural Variation in ZmGCP2
3. Discussion
3.1. GWAS Is Effective for Dissecting the Genetic Basis of Maize Deep-Sowing Tolerance
3.2. Comparison of Co-Localized QTLs with Previously Reported QTLs
3.3. Functional Analysis of Candidate Gene ZmGCP2
4. Materials and Methods
4.1. Plant Materials and Growth Conditions
4.2. Phenotyping and Statistical Analysis
4.3. SNP Genotyping
4.4. LD and Structure Analysis
4.5. GWAS
4.6. Gene Expression Patterns Analysis
4.7. Candidate Gene Association Study
4.8. Cell Observation
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
Iodent | Iowa Experiment Station Reid Yellow Dent |
NSS | Non-Stiff Stalk |
PA | Group A germplasm derived from modern U.S. hybrids |
PB | Group B germplasm derived from modern U.S. hybrids |
SPT | Si Ping Tou |
SS | Stiff Stalk |
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Env. | Traits | Range (cm) | Mean (cm) | SD | CV% | Skewness | Kurtosis |
---|---|---|---|---|---|---|---|
20ZC | ML | 3.25–21.74 | 10.47 | 3.40 | 31.67% | 0.53 | 0.16 |
CL | 1.25–7.78 | 4.59 | 1.09 | 24.26% | −0.13 | 0.33 | |
PL | 1.10–16.35 | 9.16 | 3.49 | 38.14% | −0.07 | −0.63 | |
SL | 5.13–33.37 | 19.44 | 5.14 | 26.44% | −0.17 | 0.04 | |
PRL | 4.85–36.85 | 23.95 | 6.53 | 27.27% | −0.48 | −0.28 | |
20YN | ML | 3.00–24.25 | 10.74 | 3.59 | 33.43% | 0.66 | 0.74 |
CL | 1.40–8.02 | 4.51 | 1.08 | 23.88% | 0.15 | 0.67 | |
PL | 1.4–17.38 | 8.84 | 3.43 | 38.80% | −0.04 | −0.66 | |
SL | 6.03–33.83 | 19.48 | 5.45 | 27.96% | −0.10 | −0.31 | |
PRL | 3.20–40.10 | 24.48 | 7.38 | 30.14% | −0.48 | 0.10 | |
21CZ | ML | 2.70–22.03 | 10.79 | 3.72 | 34.47% | 0.40 | −0.08 |
CL | 1.52–7.57 | 4.44 | 1.03 | 23.19% | −0.17 | 0.24 | |
PL | 1.20–17.75 | 8.97 | 3.66 | 40.73% | −0.10 | −0.55 | |
SL | 4.70–31.68 | 19.30 | 5.35 | 27.74% | −0.30 | −0.22 | |
PRL | 2.00–40.00 | 25.38 | 7.38 | 29.07% | −0.71 | 0.05 |
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Yang, J.; Liu, Z.; Liu, Y.; Fan, X.; Gao, L.; Li, Y.; Hu, Y.; Hu, K.; Huang, Y. Genome-Wide Association Study Identifies Quantitative Trait Loci and Candidate Genes Involved in Deep-Sowing Tolerance in Maize (Zea mays L.). Plants 2024, 13, 1533. https://doi.org/10.3390/plants13111533
Yang J, Liu Z, Liu Y, Fan X, Gao L, Li Y, Hu Y, Hu K, Huang Y. Genome-Wide Association Study Identifies Quantitative Trait Loci and Candidate Genes Involved in Deep-Sowing Tolerance in Maize (Zea mays L.). Plants. 2024; 13(11):1533. https://doi.org/10.3390/plants13111533
Chicago/Turabian StyleYang, Jin, Zhou Liu, Yanbo Liu, Xiujun Fan, Lei Gao, Yangping Li, Yufeng Hu, Kun Hu, and Yubi Huang. 2024. "Genome-Wide Association Study Identifies Quantitative Trait Loci and Candidate Genes Involved in Deep-Sowing Tolerance in Maize (Zea mays L.)" Plants 13, no. 11: 1533. https://doi.org/10.3390/plants13111533