Genome-Wide Association Study on Seedling Phenotypic Traits of Wheat under Different Nitrogen Conditions
Abstract
:1. Introduction
2. Results
2.1. Trait Phenotyping
2.2. SNP Distribution, Linkage Disequilibrium, and Population Structure
2.3. GWAS of Root-Related Traits
2.4. GWAS of Shoot-Related Traits
2.5. GWAS of Biomass and Root–Shoot Ratio
2.6. Haplotype Analysis
2.7. Candidate Genes for Pleiotropic SNPs
3. Discussion
3.1. Phenotypic Analysis of Wheat under Different Conditions
3.2. Analysis Related Loci of Wheat Seedling Traits
3.3. Prediction of Relevant Candidate Genes
4. Materials and Methods
4.1. Plant Material
4.2. Experimental Design
4.3. Phenotype Measurement and Data Analysis
4.4. Population Structure and Linkage Disequilibrium Analysis
4.5. Genome-Wide Association Analysis and Candidate Gene Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Conditions | Index | RL | RSR | RDW | RFW | SL | SDW | SFW | TDW | TFW |
---|---|---|---|---|---|---|---|---|---|---|
HN | Min | 13.14 | 0.17 | 0.004 | 0.077 | 16.82 | 0.020 | 0.144 | 0.022 | 0.227 |
Max | 15.30 | 0.39 | 0.007 | 0.109 | 24.97 | 0.027 | 0.170 | 0.038 | 0.264 | |
Ave | 14.17 | 0.22 | 0.005 | 0.089 | 19.83 | 0.024 | 0.157 | 0.029 | 0.246 | |
SD | 0.36 | 0.03 | 0.001 | 0.005 | 1.51 | 0.001 | 0.005 | 0.003 | 0.008 | |
Coef. of var (%) | 2.56 | 12.15 | 7.130 | 5.272 | 7.62 | 5.850 | 2.987 | 9.666 | 3.122 | |
h2 | 0.92 | 0.47 | 0.470 | 0.774 | 0.57 | 0.381 | 0.860 | 0.398 | 0.618 | |
NN | Min | 12.76 | 0.21 | 0.005 | 0.077 | 18.02 | 0.021 | 0.161 | 0.015 | 0.233 |
Max | 19.17 | 0.32 | 0.009 | 0.159 | 36.03 | 0.050 | 0.305 | 0.064 | 0.455 | |
Ave | 16.02 | 0.26 | 0.007 | 0.117 | 25.74 | 0.035 | 0.237 | 0.035 | 0.354 | |
SD | 1.09 | 0.02 | 0.001 | 0.014 | 3.43 | 0.005 | 0.027 | 0.009 | 0.041 | |
Coef. of var (%) | 6.76 | 7.93 | 11.299 | 12.161 | 13.34 | 14.268 | 11.519 | 24.837 | 11.44 | |
h2 | 0.79 | 0.72 | 0.684 | 0.597 | 0.40 | 0.777 | 0.673 | 0.327 | 0.620 | |
LN | Min | 14.33 | 0.34 | 0.007 | 0.113 | 17.69 | 0.016 | 0.135 | 0.023 | 0.251 |
Max | 20.59 | 0.66 | 0.013 | 0.206 | 30.78 | 0.037 | 0.229 | 0.048 | 0.434 | |
Ave | 17.58 | 0.44 | 0.010 | 0.154 | 22.27 | 0.024 | 0.185 | 0.035 | 0.339 | |
SD | 1.12 | 0.04 | 0.001 | 0.016 | 2.16 | 0.004 | 0.017 | 0.004 | 0.031 | |
Coef. of var (%) | 6.39 | 9.49 | 9.097 | 10.065 | 9.70 | 14.362 | 9.341 | 11.671 | 9.044 | |
h2 | 0.92 | 0.62 | 0.698 | 0.473 | 0.59 | 0.135 | 0.450 | 0.288 | 0.467 |
Marker | Chromosome | Position | Pleiotropic Effect | SNP | p-Value |
---|---|---|---|---|---|
AX-108847203 | 1A | 567714120 | RDWL, RDWN, SLL, SLN, SDWL, SDWN, TDWL, TDWN | G | <0.001 |
AX-111170306 | 1A | 567967912 | RDWN, SLL, SLN, SDWL, SDWN, SFWN, TDWL, TDWN, TFWN | T | <0.001 |
AX-108737478 | 1B | 375098459 | TDWL, TFWN | C | <0.001 |
AX-111695833 | 1B | 374522868 | RDWL, TDWH | A | <0.001 |
AX-108962141 | 1B | 403813869 | RDWN, RFWN, SLL, SDWL, SDWN, TDWH, TDWL, TDWN | T | <0.001 |
AX-110392069 | 1B | 639638582 | SDWN, SFWN, TDWH, TDWN, TFWN | G | <0.001 |
AX-109326114 | 1D | 21743856 | RDWN, SLL, SDWL, SDWN, SFWN, TDWN | A | <0.001 |
AX-111161220 | 1B | 414806318 | RDWN, TDWH | T | <0.001 |
AX-108903381 | 1B | 415260486 | RSRH, SFWN | A | <0.001 |
AX-108786044 | 2A | 698009743 | RDWL, SFWH, TDWH, TDWL, TFWH | A | <0.001 |
AX-110362294 | 1B | 317448975 | RSRH, SFWN, TFWN | T | <0.001 |
AX-111575379 | 2B | 461886409 | RDWN, TDWH, TDWL | A | <0.001 |
AX-111672733 | 2B | 572628142 | SDWL, TDWH, TDWL | C | <0.001 |
AX-110010230 | 1B | 325283703 | RSRH, SFWN, TFWN | C | <0.001 |
AX-111405488 | 2D | 59943039 | SDWL, SFWL, TDWH, TDWL | C | <0.001 |
AX-110926323 | 1B | 325256496 | RSRH, SFWN | T | <0.001 |
AX-110438187 | 2A | 95830292 | RSRH, SLN | A | <0.001 |
AX-109815802 | 4B | 10916305 | RFWN, SFWH, SFWN, TFWH, TFWN | A | <0.001 |
AX-109327593 | 4B | 10944746 | RFWN, SFWH, SFWN, TDWH, TFWN | A | <0.001 |
AX-109365636 | 2B | 758808487 | SDWN, SFWN, TDWH, TFWN | T | <0.001 |
AX-110832233 | 4D | 507128999 | SLL, SLN, SDWL, SDWN, TDWH, TDWL, TDWN | A | <0.001 |
AX-111051748 | 5B | 44358312 | SDWL, TDWH, TDWL | A | <0.001 |
AX-89696347 | 2D | 647533340 | RLH, SDWL, TDWL | C | <0.001 |
AX-109325100 | 6A | 61431458 | SDWN, SFWN, TDWH, TDWN, TFWN | A | <0.001 |
AX-111342539 | 2D | 100544989 | TDWH, TFWN | A | <0.001 |
AX-109651481 | 6A | 310569613 | SDWL, SFWL, TDWH, TDWL, TFWL | C | <0.001 |
AX-108871687 | 6B | 553420734 | RDWL, RDWN, TDWH, TDWL | G | <0.001 |
AX-111605442 | 2D | 220630228 | TDWH, TFWN | C | <0.001 |
AX-110525380 | 3B | 25322853 | RFWH, TFWH | T | <0.001 |
AX-111123066 | 7A | 55431597 | SDWN, SFWN, TDWH, TDWN, TFWN | T | <0.001 |
AX-111526214 | 4D | 310458135 | SFWN, TDWH, TFWN | C | <0.001 |
AX-110483224 | 7B | 611776655 | SLL, SLN, SDWN | C | <0.001 |
AX-109327847 | 7B | 612256762 | SLL, SLN, SDWN, SFWN | A | <0.001 |
AX-111485326 | 7B | 627697145 | SDWN, TDWL, TDWN | A | <0.001 |
AX-109401644 | 5B | 50655258 | SDWN, TDWN | A | <0.001 |
AX-111721212 | 5D | 553775393 | RDWL, RFWN, TDWL | C | <0.001 |
AX-111762061 | 6B | 192866992 | RFWN, SDWN, SFWN, TDWH, TFWN | T | <0.001 |
AX-109624261 | 7A | 113627131 | SFWN, TDWH, TFWN | G | <0.001 |
AX-110595073 | 7B | 627636405 | SLL, SDWN, TDWN | A | <0.001 |
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Hu, C.; Li, J.; Liu, J.; Zhang, D.; Jin, L.; Yang, N.; Bai, B.; Wang, Z.; Feng, S.; Ru, Z.; et al. Genome-Wide Association Study on Seedling Phenotypic Traits of Wheat under Different Nitrogen Conditions. Plants 2023, 12, 4050. https://doi.org/10.3390/plants12234050
Hu C, Li J, Liu J, Zhang D, Jin L, Yang N, Bai B, Wang Z, Feng S, Ru Z, et al. Genome-Wide Association Study on Seedling Phenotypic Traits of Wheat under Different Nitrogen Conditions. Plants. 2023; 12(23):4050. https://doi.org/10.3390/plants12234050
Chicago/Turabian StyleHu, Chenchen, Jinghui Li, Jiajia Liu, Dazhong Zhang, Liqiao Jin, Nian Yang, Bipo Bai, Zenghao Wang, Suwei Feng, Zhengang Ru, and et al. 2023. "Genome-Wide Association Study on Seedling Phenotypic Traits of Wheat under Different Nitrogen Conditions" Plants 12, no. 23: 4050. https://doi.org/10.3390/plants12234050