QTL Detection of Salt Tolerance at Soybean Seedling Stage Based on Genome-Wide Association Analysis and Linkage Analysis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material
2.2. Evaluation of Traits Related to Salt Tolerance
2.3. Genome-Wide Association Analysis
2.4. Linkage Analysis
2.5. Prediction of Candidate Gene
2.6. Development of Molecular Marker
3. Results
3.1. Statistics and Analysis of Phenotype
3.2. Linkage Disequilibrium Analysis
3.3. Kinship and Population Structure Analysis
3.4. Genome-Wide Association Analysis of Salt Tolerance-Related QTLs
3.5. Linkage Analysis of Salt Tolerance-Related QTLs
3.6. Comparison of Salt Tolerance QTL Consistency Regions in Soybean and Screening of Candidate Genes
3.7. Development and Validation of Salt-Tolerant Molecular Marker
4. Discussion
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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CC | PH | RL | AGFB | BGFB | AGDB | BGDB | Mean | |
---|---|---|---|---|---|---|---|---|
CC | 1 | |||||||
PH | −0.09 | 1 | ||||||
RL | −0.05 | 0.31 ** | 1 | |||||
AGFB | −0.07 | 0.26 ** | 0.0265 | 1 | ||||
BGFB | −0.03 | 0.31 ** | 0.32 ** | 0.38 ** | 1 | |||
AGDB | 0.013 | 0.23 ** | 0.19 * | 0.49 ** | 0.37 ** | 1 | ||
BGDB | −0.14 | 0.23 * | 0.28 ** | 0.30 ** | 0.68 ** | 0.2 * | 1 | |
Mean | 0.21 * | 0.32 ** | 0.23 * | 0.35 ** | 0.23 * | 0.21 * | 0.35 ** | 1 |
Trait Name | Chromosome | Genetic Position (cM) | Range (cM) A | Interval (bp) B | LOD | PVE (%) C | QTL Name |
---|---|---|---|---|---|---|---|
CC | 2 | 22 | 20.5–23.5 | 43637691–43932528 | 2.69 | 13.95 | qZJS-2-1 |
PH | 13 | 45 | 44.5–46.5 | 33207771–33517956 | 2.52 | 11.78 | qZJS-13-1 |
RL | 16 | 28 | 26.5–28.5 | 5342596–5565208 | 2.58 | 12.31 | qZJS-16-1 |
AGFB | 1 | 43 | 42.5–43.5 | 43519723–43535518 | 2.52 | 12.23 | qZJS-1-1 |
BGFB | 15 | 129 | 128.5–129.5 | 47731881–48413184 | 2.62 | 14 | qZJS-15-1 |
AGDB | 10 | 37 | 36.5–37.5 | 37207079–37242844 | 3.04 | 16.16 | qZJS-10-1 |
BGDB | 13 | 98 | 95.5–99.5 | 15309561–15581977 | 2.9 | 11.43 | qZJS-13-2 |
Mean | 2 | 22 | 20.5–23.5 | 43637691–43932528 | 6.69 | 13.95 | qZJS-2-1 |
2 | 74 | 73.5–74.5 | 10143604–10143635 | 3.68 | 6.9 | qZJS-2-2 | |
15 | 94 | 92.5–97.5 | 47731881–48413184 | 5.48 | 11.41 | qZJS-15-1 |
Stage | Name | Chromosome | Trait | Population | PVE (%) A |
---|---|---|---|---|---|
Seedling stage | rs43642631, qZJS-2-1 | 2 | CC | Natural population, RIL population | 5.98, 13.95 |
rs47665107, rs47934112, qZJS-15-1 | 15 | Mean | Natural population, RIL population | 17.16, 12.08, 11.41 |
Stage | Gene | Chromosome | Gene Function |
---|---|---|---|
Seedling stage | Glyma.02g249300 | 2 | Glycerol-3-phosphate acyltransferase 5 |
Glyma.02g249600 | 2 | Rubisco activase | |
Glyma.02g250200 | 2 | Protein phosphatase 2CA | |
Glyma.15G250100 | 15 | nine-cis-epoxycarotenoid dioxygenase 3 | |
Glyma.15G250200 | 15 | receptor-like protein kinase 1 | |
Glyma.15G251300 | 15 | Nicotianamine synthase 1 | |
Glyma.15G252600 | 15 | Leucine-rich receptor-like protein kinase family protein |
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Sun, M.; Zhao, T.; Liu, S.; Han, J.; Wang, Y.; Zhao, X.; Li, Y.; Teng, W.; Zhan, Y.; Han, Y. QTL Detection of Salt Tolerance at Soybean Seedling Stage Based on Genome-Wide Association Analysis and Linkage Analysis. Plants 2024, 13, 2283. https://doi.org/10.3390/plants13162283
Sun M, Zhao T, Liu S, Han J, Wang Y, Zhao X, Li Y, Teng W, Zhan Y, Han Y. QTL Detection of Salt Tolerance at Soybean Seedling Stage Based on Genome-Wide Association Analysis and Linkage Analysis. Plants. 2024; 13(16):2283. https://doi.org/10.3390/plants13162283
Chicago/Turabian StyleSun, Maolin, Tianxin Zhao, Shuang Liu, Jinfeng Han, Yuhe Wang, Xue Zhao, Yongguang Li, Weili Teng, Yuhang Zhan, and Yingpeng Han. 2024. "QTL Detection of Salt Tolerance at Soybean Seedling Stage Based on Genome-Wide Association Analysis and Linkage Analysis" Plants 13, no. 16: 2283. https://doi.org/10.3390/plants13162283