Genome-Wide Association Study Reveals the Genetic Basis of Seed Germination in Japonica Rice
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials
2.2. Evaluation of Seed Germination
2.3. GWAS
2.4. Identification of the Causal Gene for qGR7.1
2.5. Population Genetics Analysis
2.6. Data Analysis
3. Results
3.1. Phenotypic Variation of Seed Germination in Japonica Rice
3.2. Mining Loci for Seed Germination in Japonica Rice through GWAS
3.3. OsGA2ox5 Is the Causal Gene of qGR7.1 for Seed Germination
3.4. Functional Validation of OsGA2ox5 through CRISPR-Cas9 System
3.5. Population Genetic Analysis of OsGA2ox5 in Wild Rice and Cultivated Rice
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Years | Range (%) | Mean (%) | SD (%) | CV | Heritability (%) | G × E |
---|---|---|---|---|---|---|
2016 | 0.00~100.00 | 61.31 | 33.97 | 0.55 | 92.68 | *** |
2017 | 0.00~100.00 | 68.59 | 35.18 | 0.51 |
Loci | Chr. | Lead SNP Position (bp) | −log10 (p) | R2 (%) | Position Range (bp) |
---|---|---|---|---|---|
qGR1.1 | 1 | 11,013,637 | 4.46 | 12.33 | 10,846,291–11,180,637 |
qGR2.1 | 2 | 8,489,330 | 5.08 | 12.35 | 8,321,790–8,656,330 |
qGR3.1 | 3 | 4,884,341 | 4.61 | 10.17 | 4,716,789–5,052,052 |
qGR7.1 | 7 | 192,333 | 7.05 | 17.19 | 0–456,217 |
qGR8.1 | 8 | 16,886,885 | 5.35 | 13.42 | 16,061,954–17,340,457 |
qGR9 | 9 | 10,886,406 | 4.63 | 12.38 | 10,716,563–11,142,754 |
Loci | Years | Chr. | Lead SNP Position (bp) | −log10 (p) | R2 (%) | Position Range (bp) |
---|---|---|---|---|---|---|
qGR1.2 | 2017 | 1 | 25,590,336 | 5.48 | 13.24 | 25,305,001–25,757,336 |
qGR1.3 | 2016 | 1 | 28,027,169 | 5.40 | 16.78 | 27,860,169–28,283,990 |
qGR2.2 | 2016 | 2 | 9,433,114 | 4.65 | 11.68 | 9,118,975–9,618,639 |
qGR2.3 | 2017 | 2 | 19,956,713 | 4.76 | 13.05 | 19,755,355–20,123,713 |
qGR2.4 | 2017 | 2 | 33,274,949 | 5.09 | 13.96 | 33,107,949–33,609,208 |
qGR3.2 | 2017 | 3 | 27,826,611 | 6.08 | 11.94 | 27,601,438–28,531,760 |
qGR4.1 | 2017 | 4 | 14,375,252 | 5.61 | 15.86 | 14,208,252–15,053,661 |
qGR4.2 | 2017 | 4 | 16,083,610 | 4.53 | 11.49 | 15,911,996–16,268,570 |
qGR4.3 | 2016 | 4 | 30,514,368 | 4.34 | 11.28 | 30,347,368–30,685,270 |
qGR5.1 | 2016 | 5 | 805,425 | 5.26 | 14.82 | 410,513–1,130,112 |
qGR5.2 | 2017 | 5 | 6,361,115 | 5.02 | 12.45 | 6,193,499–6,533,474 |
qGR6.1 | 2016 | 6 | 12,599,304 | 5.58 | 15.05 | 12,196,447–13,223,484 |
qGR6.2 | 2016 | 6 | 15,021,521 | 5.79 | 8.67 | 13,715,687–17,846,500 |
qGR7.2 | 2017 | 7 | 20,954,108 | 4.24 | 8.21 | 20,787,108–21,513,892 |
qGR8.2 | 2017 | 8 | 28,059,886 | 4.27 | 9.05 | 27,851,488–28,228,750 |
qGR12 | 2016 | 12 | 23,860,128 | 6.01 | 17.04 | 23,527,869–24,035,448 |
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Yang, B.; Zeng, J.; Chen, S.; Li, S.; Wu, L.; Wan, X. Genome-Wide Association Study Reveals the Genetic Basis of Seed Germination in Japonica Rice. Agriculture 2023, 13, 118. https://doi.org/10.3390/agriculture13010118
Yang B, Zeng J, Chen S, Li S, Wu L, Wan X. Genome-Wide Association Study Reveals the Genetic Basis of Seed Germination in Japonica Rice. Agriculture. 2023; 13(1):118. https://doi.org/10.3390/agriculture13010118
Chicago/Turabian StyleYang, Bin, Jiali Zeng, Shaona Chen, Shengyu Li, Longmei Wu, and Xiaorong Wan. 2023. "Genome-Wide Association Study Reveals the Genetic Basis of Seed Germination in Japonica Rice" Agriculture 13, no. 1: 118. https://doi.org/10.3390/agriculture13010118
APA StyleYang, B., Zeng, J., Chen, S., Li, S., Wu, L., & Wan, X. (2023). Genome-Wide Association Study Reveals the Genetic Basis of Seed Germination in Japonica Rice. Agriculture, 13(1), 118. https://doi.org/10.3390/agriculture13010118