Genome-Wide Association Study for Ultraviolet-B Resistance in Soybean (Glycine max L.)
Abstract
:1. Introduction
2. Results
2.1. Phenotypic Evaluation of Soybean Germplasm Collection under Enhanced UV-B Conditions
2.2. Genome-Wide Association Study (GWAS)
2.3. Linkage Disequilibrium (LD) Analysis
2.4. Gene Expression Analysis by qRT-PCR
3. Discussion
4. Materials and Methods
4.1. Plant Materials and Growth Conditions
4.2. Evaluation of UV-B Resistance
4.3. Genome-Wide Association Study (GWAS)
4.4. Linkage Disequilibrium (LD) Analysis and Candidate Gene Identification
4.5. Real-Time Quantitative Reverse Transcription PCR
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Trait | Chr. | SNP | Position | FDR Unadjusted p-Values | −log(p) | maf | R2 without SNP | R2 with SNP | FDR Adjusted p-Values | Effect | Linkage Disequilibrium Block | Distance | No. of Genes |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
DLC | 10 | AX-90454793 | 38322497 | 8.65 × 10−5 | 4.06 | 0.16 | 0.02 | 0.04 | 0.57 | −0.46 | 382,934~383,225 | 292 bp | 1 |
11 | AX-90522955 | 1168027 | 4.22 × 10−5 | 4.38 | 0.40 | 0.02 | 0.05 | 0.46 | 0.37 | 9,939,957~1,013,188 | 19,194 bp | 18 | |
AX-90521132 | 9939957 | 6.50 × 10−6 | 5.19 | 0.08 | 0.02 | 0.05 | 0.28 | −0.69 | 1,144,379-1,168,553 | 24,174 bp | 8 | ||
AX-90466824 | 9955814 | 7.83 × 10−5 | 4.11 | 0.16 | 0.02 | 0.05 | 0.57 | −0.45 | - | - | - | ||
AX-90325683 | 10099676 | 1.27 × 10−5 | 4.90 | 0.08 | 0.02 | 0.05 | 0.28 | −0.65 | - | - | - | ||
AX-90318887 | 10104602 | 1.27 × 10−5 | 4.90 | 0.08 | 0.02 | 0.05 | 0.28 | −0.65 | - | - | - | ||
AX-90379400 | 10109488 | 3.77 × 10−5 | 4.42 | 0.10 | 0.02 | 0.05 | 0.46 | −0.57 | - | - | - | ||
AX-90353742 | 10119213 | 3.73 × 10−5 | 4.43 | 0.10 | 0.02 | 0.05 | 0.46 | −0.58 | - | - | - | ||
AX-90477047 | 10121857 | 6.84 × 10−5 | 4.16 | 0.10 | 0.02 | 0.05 | 0.56 | −0.56 | - | - | - | ||
AX-90427669 | 10126101 | 5.30 × 10−5 | 4.28 | 0.10 | 0.02 | 0.05 | 0.50 | −0.58 | - | - | - | ||
DLS | 2 | AX-90319706 | 15429030 | 6.67 × 10−5 | 4.18 | 0.18 | 0.05 | 0.07 | 0.63 | −0.45 | - | - | - |
AX-90457128 | 15430402 | 6.26 × 10−5 | 4.20 | 0.18 | 0.05 | 0.08 | 0.63 | −0.46 | - | - | - | ||
AX-90334094 | 15460775 | 4.56 × 10−5 | 4.34 | 0.18 | 0.05 | 0.08 | 0.63 | −0.47 | 1,516,984~1,550,224 | 29,095 bp | 9 | ||
AX-90344232 | 15464333 | 0.0000847 | 4.07 | 0.19 | 0.05 | 0.07 | 0.64 | −0.45 | - | - | - | ||
AX-90436068 | 15467717 | 6.09 × 10−5 | 4.22 | 0.18 | 0.05 | 0.08 | 0.63 | −0.46 | - | - | - | ||
AX-90474824 | 15473795 | 6.60 × 10−5 | 4.18 | 0.18 | 0.05 | 0.07 | 0.63 | −0.45 | - | - | - | ||
AX-90329251 | 15474547 | 6.60 × 10−5 | 4.18 | 0.18 | 0.05 | 0.07 | 0.63 | −0.45 | - | - | - | ||
6 | AX-90333167 | 8071856 | 5.13 × 10−5 | 4.29 | 0.23 | 0.05 | 0.08 | 0.63 | −0.43 | 7,516,555~8,315,464 | 798,909 bp | 94 |
Trait | Chr. | Linkage Disequilibrium Block | Candidate Gene | Gene Position | Description |
---|---|---|---|---|---|
DLC 1 | 11 | 9,939,957–10,131,882 | Glyma.11g130800 | 9,983,698–9,993,001 | Transducin/WD40 repeat-like superfamily protein, WD40 repeat family |
DLS 2 | 2 | 1,516,984–1,550,224 | Glyma.02g017500 | 1,550,874–1,554,518 | CRYPTOCHROME, photolyase/blue-light receptor 2, DNA repair, DNA photolyase activity |
6 | 7,516,555–8,315,464 | Glyma.06g095400 | 7,530,783–7,533,737 | Auxin F-box protein 5, protein binding | |
Glyma.06g097800 | 7,725,465–7,766,431 | Protein binding, related BEACH and WD40 repeat proteins, WD domain | |||
Glyma.06g103200 | 8,205,073–8,210,842 | CRYPTOCHROME 1, DNA repair, blue/ultraviolet sensing protein C terminal, DNA photolyase activity |
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Lee, T.; Kim, K.D.; Kim, J.-M.; Shin, I.; Heo, J.; Jung, J.; Lee, J.; Moon, J.-K.; Kang, S. Genome-Wide Association Study for Ultraviolet-B Resistance in Soybean (Glycine max L.). Plants 2021, 10, 1335. https://doi.org/10.3390/plants10071335
Lee T, Kim KD, Kim J-M, Shin I, Heo J, Jung J, Lee J, Moon J-K, Kang S. Genome-Wide Association Study for Ultraviolet-B Resistance in Soybean (Glycine max L.). Plants. 2021; 10(7):1335. https://doi.org/10.3390/plants10071335
Chicago/Turabian StyleLee, Taeklim, Kyung Do Kim, Ji-Min Kim, Ilseob Shin, Jinho Heo, Jiyeong Jung, Juseok Lee, Jung-Kyung Moon, and Sungteag Kang. 2021. "Genome-Wide Association Study for Ultraviolet-B Resistance in Soybean (Glycine max L.)" Plants 10, no. 7: 1335. https://doi.org/10.3390/plants10071335