Genetic Basis of Tiller Dynamics of Rice Revealed by Genome-Wide Association Studies
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials and Phenotype Analysis
2.2. NGS Analysis and Genotyping
2.3. Population Structure and Genetic Relationships
2.4. Genome-Wide Association Mapping
2.5. Statistical Analysis
2.6. Estimation of Heritability
3. Results
3.1. Population Structure of Korean Rice Accessions
3.2. Variation and Changes in the Tiller Number among Growth Stages
3.3. Genome-Wide Association Studies with Factored Spectrally Transformed Linear Mixed Models (FaST-LMM)
3.4. Linear Regression Model for Three Tiller-Related Traits
4. Discussion
4.1. Phenotypic Relationships
4.2. Association Signals for Tillering and Heading
4.3. Genetic Determinants of TNM2, PTN, and PTR
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Trait | Chr | Lead SNP | p-Value | Candidate Gene | Gene ID a | Description | Reference |
---|---|---|---|---|---|---|---|
TNE | 1 | chr01:42957568 | 6.11 × 10−7 | OsRLCK57 | Os01g0973500 | Receptor-like cytoplasmic kinase | [10] |
TNE | 3 | chr03:9436356 | 1.47 × 10−7 | ||||
TNM1 | 2 | chr02:26906676 | 9.65 × 10−7 | OsHAM1; OsHAM2 | Os02g0662700; Os02g0663100 | Maintenance of shoot apical meristem indeterminacy; Regulation of vegetative to reproductive phase change | [20] |
TNM1 | 4 | chr04:31232808 | 1.36 × 10−7 | ||||
TNM2 | 2 | chr02:24685790 | 7.67 × 10−8 | OsTOC1/OsPRR1 | Os02g0618200 | Circadian-associated rice pseudo response regulator; Control of flowering time | [19] |
TNM2 | 4 | chr04:31093494 | 5.82 × 10−10 | ||||
TNM2 | 4 | chr04:31232808 | 2.88 × 10−11 | ||||
PTN | 4 | chr04:31093494 | 1.18 × 10−7 | ||||
PTR | 6 | chr06:8339606 | 3.52 × 10−16 | HD1 | Os06g0275000 | Zinc finger protein; Control of photoperiodic flowering time | [16,17] |
PTR | 11 | chr11:17720543 | 9.10 × 10−7 | ||||
HD | 1 | chr01:25634456 | 1.92 × 10−8 | ||||
HD | 1 | chr01:34991240 | 3.30 × 10−7 | ||||
HD | 6 | chr06:8365187 | 1.23 × 10−20 | HD1 | Os06g0275000 | Zinc finger protein; Control of photoperiodic flowering time | [16,17] |
HD | 6 | chr06:21572894 | 2.37 × 10−7 | ||||
HDI | 1 | chr01:29428424 | 4.54 × 10−7 | ||||
HDI | 2 | chr02:22024430 | 6.07 × 10−7 | ||||
HDI | 2 | chr02:33872721 | 7.49 × 10−7 | ||||
HDI | 6 | chr06:29529906 | 2.72 × 10−7 | ||||
HDI | 9 | chr09:18859830 | 7.24 × 10−7 | ||||
HDI | 10 | chr10:18000023 | 5.13 × 10−7 |
SNP | Coefficient | SD | ta | Allele b | |
---|---|---|---|---|---|
0 | 1 | ||||
TNM2 | |||||
chr03:9436356 | 4.51 | 1.49 | 3.034 ** | A | C |
chr01:42957568 | 1.04 | 0.48 | 2.167 * | A | G |
chr02:26906676 | 4.21 | 1.02 | 4.122 *** | A | C |
chr04:31232808 | 4.59 | 1.03 | 4.467 *** | T | A |
chr02:24685790 | 2.80 | 1.17 | 2.389 * | G | A |
HD1 | −2.37 | 0.67 | −3.521 *** | F | N |
chr06:21572894 | −1.73 | 0.55 | −3.132 ** | T | C |
Intercept | 16.53 | 0.34 | 47.949 *** | ||
p | 2.20 × 10−16 | ||||
R2 | 0.49 | ||||
PTN | |||||
chr03:9436356 | 1.83 | 1.02 | 1.798 | A | C |
chr01:42957568 | 0.64 | 0.30 | 2.131 * | A | G |
chr04:31232808 | 2.40 | 0.67 | 3.581 *** | T | A |
chr01:34991240 | 1.05 | 0.52 | 2.026 * | C | A |
chr02:22024430 | 4.13 | 1.00 | 4.149 *** | C | T |
chr10:18000023 | −1.36 | 0.64 | −2.129 * | C | T |
Intercept | 10.93 | 0.21 | 51.902 *** | ||
p | 8.68 × 10−6 | ||||
R2 | 0.22 | ||||
PTR | |||||
chr03:9436356 | −0.09437 | 0.05 | −1.975 | A | C |
chr02:26906676 | −0.0896 | 0.03 | −2.768 ** | A | C |
HD1 | 0.078779 | 0.02 | 3.446 *** | F | N |
chr01:25634456 | 0.053531 | 0.02 | 2.883 ** | C | T |
chr01:34991240 | 0.053239 | 0.03 | 1.872 | C | A |
chr06:21572894 | 0.087943 | 0.02 | 4.902 *** | T | C |
Intercept | 0.649476 | 0.01 | 66.599 *** | ||
p | 7.68 × 10−15 | ||||
R2 | 0.41 |
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Zhao, S.; Jang, S.; Lee, Y.K.; Kim, D.-G.; Jin, Z.; Koh, H.-J. Genetic Basis of Tiller Dynamics of Rice Revealed by Genome-Wide Association Studies. Plants 2020, 9, 1695. https://doi.org/10.3390/plants9121695
Zhao S, Jang S, Lee YK, Kim D-G, Jin Z, Koh H-J. Genetic Basis of Tiller Dynamics of Rice Revealed by Genome-Wide Association Studies. Plants. 2020; 9(12):1695. https://doi.org/10.3390/plants9121695
Chicago/Turabian StyleZhao, Shuyu, Su Jang, Yoon Kyung Lee, Dong-Gwan Kim, Zhengxun Jin, and Hee-Jong Koh. 2020. "Genetic Basis of Tiller Dynamics of Rice Revealed by Genome-Wide Association Studies" Plants 9, no. 12: 1695. https://doi.org/10.3390/plants9121695