Integrating GWAS and Gene Expression Analysis Identifies Candidate Genes for Root Morphology Traits in Maize at the Seedling Stage
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials and Growth Conditions
2.2. Plant Phenotyping and Data Analysis
2.3. Genotypic Data and Genome-Wide Association Analysis
2.4. Candidate Gene Analysis and Transcriptome Sequencing
3. Results
3.1. Phenotypic Analysis of Root Traits at the Seedling Stage
3.2. Genome-Wide Association Studies
3.3. Determination of Candidate Genes
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Abbreviation | Full Name | Unit | Measuring Method |
---|---|---|---|
PH | Plant height | cm | measured from the coleoptilar to yhe tip of the longest leaf |
SPAD | Leaf chlorophyll concentrations | - | measured using a SPAD-502 PLUS chlorophyll (Minolta, Japan) |
SDW | Shoot dry weight | 10 mg | measured by electronic balance |
ARD | Average root diameter | mm | measured by image analysis software (WinRhizo Pro 2009) |
PRL | Primary root length | cm | measured by a ruler |
SRL | Seminal roots length | cm | measured by a ruler |
ASRL | Average seminal root length | cm | estimated by SRL and SRN |
SRN | Seminal roots numbers | number | Count of the seminal roots |
LRL | Lateral root length | cm | estimated by TRL, PRL and SRL |
TRL | Total root length | cm | measured by image analysis software |
RL005 | L ≤ 0.5 (Root length between 0 and 0.5 mm in diameter) | cm | measured by image analysis software |
RL0510 | 0.5 < L ≤ 1.0 (Root length between 0.5 mm and 1 mm in diameter) | cm | measured by image analysis software |
RL1015 | 1.0 < L ≤ 1.5 (Root length greater than 1 mm in diameter) | cm | measured by image analysis software |
RV | Root volume | cm3 | measured by image analysis software |
RA | Root surface area | cm2 | measured by image analysis software |
RDW | Root dry weight | 10 mg | measured by electronic balance |
Trait | Mean | SD | Min | Max | Fold Change | CV a | ANOVA | ||
---|---|---|---|---|---|---|---|---|---|
MS (Genotype) | MS (Error) | F (Genotype) | |||||||
PH | 32.47 | 5.74 | 18.80 | 48.69 | 2.59 | 17.67% | 63.36 | 7.70 | 8.23 ** b |
SPAD | 28.47 | 3.86 | 17.05 | 38.15 | 2.24 | 13.55% | 28.82 | 9.23 | 3.12 ** |
SDW | 8.86 | 2.60 | 3.85 | 17.12 | 4.45 | 29.34% | 12.34 | 2.38 | 5.18 ** |
ARD | 0.44 | 0.06 | 0.33 | 0.66 | 2.00 | 14.16% | 0.01 | 0.00 | 11.79 ** |
PRL | 30.12 | 3.62 | 21.27 | 42.98 | 2.02 | 12.01% | 25.68 | 4.11 | 6.24 ** |
SRL | 67.08 | 22.71 | 6.60 | 141.00 | 21.36 | 33.85% | 967.54 | 313.63 | 3.09 ** |
ASRL | 23.95 | 4.40 | 11.71 | 34.83 | 2.97 | 18.39% | 31.87 | 7.55 | 4.22 ** |
SRN | 2.81 | 0.76 | 1.00 | 5.33 | 5.33 | 27.19% | 1.09 | 0.60 | 1.83 ** |
LRL | 265.88 | 111.46 | 34.35 | 687.12 | 20.00 | 41.92% | 23267.84 | 1826.34 | 12.74 ** |
TRL | 319.86 | 114.79 | 78.31 | 756.81 | 9.66 | 35.89% | 24982.71 | 1914.59 | 13.05 ** |
RL005 | 236.78 | 96.32 | 42.79 | 599.84 | 14.02 | 40.68% | 17497.93 | 1603.34 | 10.91 ** |
RL0510 | 75.60 | 26.60 | 16.03 | 143.26 | 8.94 | 35.18% | 1372.08 | 173.74 | 7.90 ** |
RL1015 | 5.43 | 2.51 | 1.24 | 15.32 | 12.35 | 46.22% | 12.23 | 2.39 | 5.12 ** |
RV | 0.45 | 0.13 | 0.18 | 0.89 | 4.94 | 28.60% | 296.39 | 30.66 | 9.67 ** |
RA | 41.97 | 12.72 | 14.34 | 90.75 | 6.33 | 30.31% | 0.03 | 0.00 | 8.23 ** |
RDW | 9.15 | 2.43 | 2.40 | 15.75 | 6.56 | 26.52% | 11.74 | 1.66 | 7.09 ** |
Trait | QTL | Lead SNP | Chr. | Pos. a | Allele b | −log10(P) | R2 |
---|---|---|---|---|---|---|---|
ARD | qARD1 | SNP_1_213315833 | 1 | 213315833 | G/T | 4.67 | 8.50 |
qARD3 | SNP_3_147397047 | 3 | 147397047 | A/C | 4.63 | 7.96 | |
qARD4 | SNP_4_219099674 | 4 | 219099674 | C/T | 4.16 | 12.61 | |
ASRL | qASRL1 | SNP_1_121996211 | 1 | 121996211 | C/T | 4.35 | 9.49 |
qASRL3 | SNP_3_107899717 | 3 | 107899717 | C/T | 4.17 | 6.33 | |
qASRL4 | SNP_4_185942913 | 4 | 185942913 | A/T | 4.89 | 7.01 | |
qASRL10 | SNP_10_34244943 | 10 | 34244943 | A/G | 4.74 | 7.05 | |
LRL | qLRL2 | SNP_2_104416607 | 2 | 104416607 | C/T | 4.52 | 14.97 |
qLRL4 | SNP_4_168917747 | 4 | 168917747 | C/T | 5.39 | 9.27 | |
PRL | qPRL1 | SNP_1_120308712 | 1 | 120308712 | C/T | 4.30 | 6.34 |
qPRL10-1 | SNP_10_67350334 | 10 | 67350334 | G/T | 4.00 | 6.54 | |
qPRL10-2 | SNP_10_68587247 | 10 | 68587247 | A/G | 5.38 | 9.29 | |
RA | qRA2-1 | SNP_2_104416607 | 2 | 104416607 | C/T | 4.45 | 14.65 |
qRA2-2 | SNP_2_184016997 | 2 | 184016997 | C/T | 4.05 | 6.99 | |
qRA4 | SNP_4_168917747 | 4 | 168917747 | C/T | 4.57 | 7.58 | |
RDW | qRDW3 | SNP_3_156838240 | 3 | 156838240 | C/T | 4.70 | 8.29 |
qRDW4 | SNP_4_7135819 | 4 | 7135819 | A/C | 4.57 | 8.39 | |
RL005 | qRL005_2 | SNP_2_104416607 | 2 | 104416607 | C/T | 4.86 | 15.87 |
qRL005_4 | SNP_4_33081784 | 4 | 33081784 | C/T | 4.48 | 12.29 | |
qRL005_6 | SNP_6_63998692 | 6 | 63998692 | A/G | 4.97 | 10.66 | |
RL0510 | qRL0510_1-1 | SNP_1_22179639 | 1 | 22179639 | A/G | 4.62 | 9.52 |
qRL0510_1-2 | SNP_1_217582572 | 1 | 217582572 | G/T | 4.81 | 10.10 | |
qRL0510_2 | SNP_2_50742849 | 2 | 50742849 | A/G | 5.12 | 12.96 | |
RL1015 | qRL0510_4 | SNP_4_34568124 | 4 | 34568124 | G/T | 4.05 | 11.43 |
qRL0510_6 | SNP_6_153696612 | 6 | 153696612 | A/G | 5.01 | 13.90 | |
RV | qRV2 | SNP_2_184016997 | 2 | 184016997 | C/T | 4.39 | 7.65 |
qRV6 | SNP_6_54506432 | 6 | 54506432 | A/G | 4.65 | 9.37 | |
SPAD | qSPAD5 | SNP_5_25046214 | 5 | 25046214 | C/T | 5.12 | 8.17 |
qSPAD8 | SNP_8_160371425 | 8 | 160371425 | A/G | 4.38 | 6.36 | |
qSPAD9 | SNP_9_4832814 | 9 | 4832814 | A/T | 4.84 | 8.36 | |
SRN | qSRN2 | SNP_2_52559869 | 2 | 52559869 | C/T | 4.01 | 5.65 |
qSRN8 | SNP_8_19589120 | 8 | 19589120 | C/T | 5.42 | 9.39 | |
TRL | qTRL2 | SNP_2_104416607 | 2 | 104416607 | C/T | 4.64 | 15.22 |
qTRL4 | SNP_4_168917747 | 4 | 168917747 | C/T | 5.13 | 8.60 |
QTL | Candidate Genes | log2(FC) a | P | SNP | Amino Acid Polymorphism | Annotation |
---|---|---|---|---|---|---|
qARD3 | GRMZM2G138338 | −1.38 | 0.032 | 39 | 8 | Leucine-rich receptor-like protein kinase family protein |
qASRL4 | GRMZM2G174797 | −1.44 | 0.00017 | 21 | 6 | ELMO/CED-12 family protein |
GRMZM2G476902 | 3.74 | 0.00079 | 4 | 1 | Armadillo/beta-catenin repeat family protein | |
qLRL2/ qRA2-1/ qRL005_2/ qTRL2 | GRMZM2G397965 | −2.78 | 0.0082 | 8 | 3 | Vignain precursor/ (SAG12) senescence-associated gene 12 |
qRDW3 | GRMZM2G031528 | −2.48 | 0.00017 | 12 | 1 | Heavy metal transport/detoxification superfamily protein |
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Wang, H.; Wei, J.; Li, P.; Wang, Y.; Ge, Z.; Qian, J.; Fan, Y.; Ni, J.; Xu, Y.; Yang, Z.; et al. Integrating GWAS and Gene Expression Analysis Identifies Candidate Genes for Root Morphology Traits in Maize at the Seedling Stage. Genes 2019, 10, 773. https://doi.org/10.3390/genes10100773
Wang H, Wei J, Li P, Wang Y, Ge Z, Qian J, Fan Y, Ni J, Xu Y, Yang Z, et al. Integrating GWAS and Gene Expression Analysis Identifies Candidate Genes for Root Morphology Traits in Maize at the Seedling Stage. Genes. 2019; 10(10):773. https://doi.org/10.3390/genes10100773
Chicago/Turabian StyleWang, Houmiao, Jie Wei, Pengcheng Li, Yunyun Wang, Zhenzhen Ge, Jiayi Qian, Yingying Fan, Jinran Ni, Yang Xu, Zefeng Yang, and et al. 2019. "Integrating GWAS and Gene Expression Analysis Identifies Candidate Genes for Root Morphology Traits in Maize at the Seedling Stage" Genes 10, no. 10: 773. https://doi.org/10.3390/genes10100773