Genome-Wide Dissection of Shade Tolerance in Soybean at Seedling Stage
Abstract
:1. Introduction
2. Materials and Methods
2.1. Experimental Materials, Design, and Phenotypic Measurements
2.2. Statistical Analysis of Phenotype Data
2.3. SNP Linkage Disequilibrium (LD), PCA, and Kinship
2.4. Genome-Wide Association Analysis and Candidate Genes Identification
3. Results
3.1. Descriptive Statistics of Shade-Tolerance-Related Traits
3.2. LD, PCA, and Kinship
3.3. Light Intensity Effects on Soybean Plant Height in Control Group
3.4. Finding Superior Shade-Tolerant Soybean Germplasm
3.5. GWAS and Proposed QTLs and Candidate Genes
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Trait | Min | Max | Mean | 1 SD | 2 PCV (%) | 3 H2 (%) |
---|---|---|---|---|---|---|
PH_0 | 3.32 | 12.32 | 7.66 | 1.76 | 22.97 | 83.81 |
PH_75 | 8.8 | 27.32 | 18.08 | 4.94 | 27.33 | 77.13 |
PH_r | 1.3 | 5.41 | 2.43 | 0.75 | 30.71 | 57.49 |
MSL_0 | 1.3 | 8.86 | 4.56 | 1.23 | 26.99 | 80.06 |
MSL_75 | 5.5 | 24.05 | 13.18 | 4.19 | 31.82 | 73.29 |
MSL_r | 1.01 | 8.37 | 3.01 | 1.08 | 35.79 | 50 |
HL_0 | 0.68 | 5.36 | 3.10 | 0.88 | 28.48 | 73.88 |
HL_75 | 2.22 | 8.25 | 4.92 | 1.56 | 31.77 | 67.75 |
HL_r | 0.66 | 4.73 | 1.66 | 0.61 | 36.85 | 31.66 |
Source of Variation | DF | MSE | F | p | η2 |
---|---|---|---|---|---|
Intercept | 1 | 464.79 | 73.94 | 0 | 0.21 |
Light | 1 | 1.91 | 0.31 | 0.58 | 0.001 |
Accession | 306 | 18.22 | 2.90 | 0 | 0.76 |
Error | 284 | 6.29 | |||
Total | 592 |
Trait | QTLs | SNPLDBs | Chr. | Model p Value | Allele No. | SNP No. | QTL Main Effect | Candidate Genes | |||
---|---|---|---|---|---|---|---|---|---|---|---|
−log10(p) | R2 (%) | ZH13 Gene Number | W82.a2 Gene Number | Description | |||||||
PH_r | |||||||||||
PH_r_shade.1.1 | Block_1_11646785_11746784 | 1 | 8.23 × 10−5 | 11 | 320 | 3.66 | 3.78 | SoyZH13_01G064100 | Glyma.01G068600 | Transcription factor bHLH49 | |
PH_r_shade.3.1 | Block_3_3114852_3115149 | 3 | 1.38 × 10−11 | 4 | 7 | 7.25 | 5.76 | ||||
PH_r_shade.10.1 | Block_10_4801122_4860661 | 10 | 0.001718 | 8 | 219 | 2.68 | 2.39 | SoyZH13_10G051100 | Glyma.10G053500 | Auxin response factor 16 | |
PH_r_shade.12.1 | Block_12_37743951_37744542 | 12 | 0.000161 | 2 | 4 | 3.63 | 1.47 | ||||
PH_r_shade.15.1 | Block_15_23412759_23416902 | 15 | 3.06 × 10−6 | 5 | 56 | 4.52 | 3.25 | ||||
PH_r_shade.16.1 | Block_16_33893242_33893951 | 16 | 3.29 × 10−18 | 6 | 24 | 10.89 | 10.18 | ||||
PH_r_shade.16.2 | Block_16_35747737_35749257 | 16 | 4.49 × 10−9 | 8 | 12 | 6.04 | 5.62 | ||||
PH_r_shade.16.3 | Chr16_36081826 | 16 | 0.000499 | 2 | 2 | 3.3 | 1.25 | ||||
PH_r_shade.17.1 | Block_17_7316304_7397881 | 17 | 2.52 × 10−5 | 5 | 333 | 3.91 | 2.77 | ||||
PH_r_shade.17.2 | Block_17_11907536_11926235 | 17 | 2.2 × 10−7 | 7 | 134 | 5.12 | 4.4 | SoyZH13_17G140200 | Glyma.17G145300 | Ethylene-responsive transcription factor 5 | |
SoyZH13_17G140300 | Glyma.17G145400 | Ethylene-responsive transcription factor 1A | |||||||||
PH_r_shade.17.3 | Block_17_11933118_12033106 | 17 | 1.04 × 10−10 | 11 | 507 | 6.56 | 7.37 | ||||
PH_r_shade.19.1 | Chr19_478140 | 19 | 9.47 × 10−5 | 2 | 2 | 3.63 | 1.58 | ||||
MSL_r | |||||||||||
MSL_r_shade.3.1 | Block_3_3253737_3254065 | 3 | 1.38 × 10−10 | 4 | 5 | 7.34 | 6.36 | ||||
MSL_r_shade.4.1 | Block_4_45771799_45788317 | 4 | 1.10 × 10−12 | 3 | 147 | 8.57 | 7.21 | ||||
MSL_r_shade.8.1 | Block_8_15201156_15201636 | 8 | 2.33 × 10−5 | 3 | 3 | 4.20 | 2.71 | ||||
MSL_r_shade.11.1 | Block_11_4331465_4356051 | 11 | 5.16 × 10−9 | 6 | 62 | 6.86 | 6.12 | ||||
MSL_r_shade.12.1 | Chr12_1168266 | 12 | 9.72 × 10−7 | 2 | 2 | 5.35 | 3.05 | ||||
MSL_r_shade.16.1 | Chr16_34243799 | 16 | 0.000268 | 2 | 2 | 3.42 | 1.68 | ||||
MSL_r_shade.17.1 | Block_17_11907536_11926235 | 17 | 5.3 × 10−9 | 7 | 134 | 5.12 | 4.4 | SoyZH13_17G140200 | Glyma.17G145300 | Ethylene-responsive transcription factor 5 | |
SoyZH13_17G140300 | Glyma.17G145400 | Ethylene-responsive transcription factor 1A | |||||||||
MSL_r_shade.18.1 | Chr18_55533676 | 18 | 0.000368 | 2 | 2 | 3.35 | 1.60 | SoyZH13_18G217700 | Glyma.18G246000 | Transcription factor bHLH25 | |
MSL_r_shade.19.1 | Block_19_476384_476514 | 19 | 5.79 × 10−5 | 3 | 4 | 3.95 | 2.47 | ||||
MSL_r_shade.20.1 | Block_20_1172558_1173696 | 20 | 0.00082 | 7 | 10 | 3.09 | 2.90 | SoyZH13_20G012300 | Glyma.20G013200 | U-box domain-containing protein 10 | |
HL_r | |||||||||||
HL_r_shade.1.1 | Block_1_55630414_55715065 | 1 | 4.04 × 10−11 | 11 | 224 | 8.09 | 10.38 | ||||
HL_r_shade.7.1 | Block_7_6887632_6888597 | 7 | 4.32 × 10−5 | 3 | 13 | 4.36 | 2.86 | ||||
HL_r_shade.7.2 | Block_7_27001385_27047263 | 7 | 6.66 × 10−6 | 7 | 44 | 4.97 | 4.88 | ||||
HL_r_shade.10.1 | Block_10_8406436_8478177 | 10 | 1.21 × 10−6 | 9 | 370 | 5.10 | 6.10 | ||||
HL_r_shade.13.1 | Block_13_35550086_35550267 | 13 | 5.67 × 10−6 | 2 | 2 | 4.89 | 2.93 | SoyZH13_13G214700 | Glyma.13G236500 | Ethylene-responsive transcription factor 9 | |
HL_r_shade.20.1 | Chr20_18734811 | 20 | 1.36 × 10−6 | 2 | 2 | 5.07 | 3.33 |
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Hu, L.; Arshad, K.; Zheng, M.; Ou, R.; Song, Y.; Xie, M.; Wei, Y.; Ling, L.; Zeng, W.; Zhang, J. Genome-Wide Dissection of Shade Tolerance in Soybean at Seedling Stage. Agronomy 2025, 15, 1382. https://doi.org/10.3390/agronomy15061382
Hu L, Arshad K, Zheng M, Ou R, Song Y, Xie M, Wei Y, Ling L, Zeng W, Zhang J. Genome-Wide Dissection of Shade Tolerance in Soybean at Seedling Stage. Agronomy. 2025; 15(6):1382. https://doi.org/10.3390/agronomy15061382
Chicago/Turabian StyleHu, Linfang, Kamran Arshad, Meiying Zheng, Ran Ou, Yinmeng Song, Mengyan Xie, Yazhi Wei, Luyi Ling, Weiying Zeng, and Jiaoping Zhang. 2025. "Genome-Wide Dissection of Shade Tolerance in Soybean at Seedling Stage" Agronomy 15, no. 6: 1382. https://doi.org/10.3390/agronomy15061382
APA StyleHu, L., Arshad, K., Zheng, M., Ou, R., Song, Y., Xie, M., Wei, Y., Ling, L., Zeng, W., & Zhang, J. (2025). Genome-Wide Dissection of Shade Tolerance in Soybean at Seedling Stage. Agronomy, 15(6), 1382. https://doi.org/10.3390/agronomy15061382