Genome-Wide Association Analysis of Plant Height Using the Maize F1 Population
Abstract
:1. Introduction
2. Materials and Methods
2.1. Materials and Field Trials
2.2. Analysis of Phenotypic Data
2.3. Analysis of Genotypic Data
2.4. Genome-Wide Association Study
3. Result
3.1. Phenotypic Analysis and Heritability
3.2. LD Analysis
3.3. Population Structure Analysis
3.4. Kinship Analysis
3.5. GWAS Analysis
4. Discussion
5. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
PH | Plant height |
GWAS | Genome-wide association analysis |
SNPs | single nucleotide polymorphisms |
QTLs | quantitative trait loci |
GBS | genotyping-by-sequencing |
BLUP | the best linear unbiased prediction |
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Trait | Mean | Minimum | Maximum | SD | Skewness | Kurtosis | CV (%) | H2 (%) |
---|---|---|---|---|---|---|---|---|
PH | 290.67 | 239.15 | 324.50 | 16.34 | −0.56 | 0.26 | 5.62 | 83.32 |
Trait | Source | SS | DF | MS | F Value | Sig |
---|---|---|---|---|---|---|
PH | G | 954,834.54 | 299 | 3193.43 | 32.98 | <0.01 ** |
E | 1,122,082.30 | 4 | 280,520.57 | 2897.20 | <0.01 ** | |
G×E | 363,150.96 | 1194 | 304.15 | 3.14 | <0.01 ** | |
Error | 142,235.55 | 1469 | 96.83 |
Trait | Chr | SNP ID | SNP Physical Position | p Value |
---|---|---|---|---|
PH | 1 | SNP−41465 | 157,566,180 | 5.19 × 10−10 |
1 | SNP−54654 | 208,218,658 | 3.05 × 10−8 | |
2 | SNP−137325 | 207,979,043 | 6.08 × 10−8 | |
4 | SNP−214914 | 7,407,530 | 1.14 × 10−8 | |
7 | SNP−382338 | 1,148,863 | 5.57 × 10−8 | |
7 | SNP−382339 | 1,148,876 | 1.20× 10−11 | |
9 | SNP−480424 | 3,878,215 | 1.31 × 10−10 | |
9 | SNP−516792 | 154,433,535 | 4.49 × 10−14 | |
10 | SNP−524015 | 13,705,944 | 8.83 × 10−10 |
Trait | Chr | SNP ID | Gen ID | Encoding |
---|---|---|---|---|
PH | 7 | SNP−382338 | Zm00001d018617 | gibberellin 2–oxidase 12 |
10 | SNP−524015 | Zm00001d023659 | auxin response factor 2 |
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Zhang, Y.; Wan, J.; He, L.; Lan, H.; Li, L. Genome-Wide Association Analysis of Plant Height Using the Maize F1 Population. Plants 2019, 8, 432. https://doi.org/10.3390/plants8100432
Zhang Y, Wan J, He L, Lan H, Li L. Genome-Wide Association Analysis of Plant Height Using the Maize F1 Population. Plants. 2019; 8(10):432. https://doi.org/10.3390/plants8100432
Chicago/Turabian StyleZhang, Yong, Jiyu Wan, Lian He, Hai Lan, and Lujiang Li. 2019. "Genome-Wide Association Analysis of Plant Height Using the Maize F1 Population" Plants 8, no. 10: 432. https://doi.org/10.3390/plants8100432