Metabolomic and Transcriptomic Analyses of Flavonoid Biosynthesis in Different Colors of Soybean Seed Coats
Abstract
1. Introduction
2. Results
2.1. Metabolic Differences Among the Seed Coat of Soybean Germplasms
2.2. Analysis of the DAMs in the Flavonoid Biosynthetic Pathway
2.3. Transcriptomic Profiling of Soybean Seed Coat
2.4. KEGG Pathway Enrichment Analysis of the Expected Changes in DAMs and DEGs
2.5. Candidate Genes Related to the Flavonoid Biosynthetic Pathway
3. Discussion
3.1. Identification of Flavonoid Compounds in Soybean Seed Coat
3.2. DEGs Related to the Biosynthesis of Flavonoids in the Seed Coat of Soybean
4. Materials and Methods
4.1. Plant Materials and Experimental Site
4.2. Metabolome Measurement
4.3. Transcriptome Analysis
4.4. Quantitative Real-Time Polymerase Chain Reaction Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Code | Name | Seed Coat Color | 100-Seed Weight (g) |
---|---|---|---|
S141 | Huangdou | Yellow | 16.4 |
S26 | Hongpixiangdou | Red | 36.8 |
S62 | Bendihuangdou | Brown | 19.7 |
S100 | Bendilvhuangdou | Green | 20.5 |
S124 | Heipidadou | Black | 20.7 |
S26_vs._S141 | S62_vs._S141 | S100_vs._S141 | S124_vs._S141 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Fold Change | p-Value | Regu-lation | Fold Change | p-Value | Regu-lation | Fold Change | p-Value | Regu-lation | Fold Change | p-Value | Regu lation | |
SoyZH13_02G120600(CHS6) | 8.65 | 0.010 | up | 1.54 | 0.660 | up | 17.30 | 0.000 | up | 11.24 | 0.000 | up |
SoyZH13_11G010700(CHS) | 2.83 | 0.000 | up | 1.36 | 0.580 | up | 0.95 | 0.860 | down | 0.54 | 0.010 | down |
SoyZH13_08G103500(CHS1) | 10.75 | 0.000 | up | 0.23 | 0.060 | down | 18.76 | 0.000 | up | 10.30 | 0.000 | up |
SoyZH13_06G290900(UGT88F4) | 1.51 | 0.014 | up | 0.41 | 0.000 | down | 1.75 | 0.000 | up | 0.50 | 0.001 | down |
SoyZH13_02G046100(FHT) | 5.35 | 0.000 | up | 0.12 | 0.000 | down | 7.71 | 0.000 | up | 1.51 | 0.260 | up |
SoyZH13_14G066200(DFR) | 10.47 | 0.000 | up | 0.21 | 0.200 | down | 33.06 | 0.000 | up | 0.72 | 0.730 | down |
SoyZH13_02G147700(DFR) | 7.51 | 0.000 | up | 0.57 | 0.220 | down | 5.87 | 0.000 | up | 1.71 | 0.100 | up |
SoyZH13_01G196800(ANT17) | 3.17 | 0.000 | up | 0.08 | 0.010 | down | 16.61 | 0.000 | up | 12.17 | 0.000 | up |
SoyZH13_08G058800(ANR) | 0.04 | 0.010 | down | 0.05 | 0.030 | down | 0.63 | 0.550 | down | 0.08 | 0.030 | down |
SoyZH13_20G171400(LAR) | 18.82 | 0.000 | up | 0.68 | 0.580 | down | 9.39 | 0.000 | up | 0.19 | 0.030 | down |
SoyZH13_05G078700(FLS) | 7.76 | 0.000 | up | 0.26 | 0.020 | down | 4.39 | 0.000 | up | 0.05 | 0.000 | down |
SoyZH13_12G118300(FG3) | 78.61 | 0.000 | up | 26.24 | 0.000 | up | 6.81 | 0.000 | up | |||
SoyZH13_20G225300(CHI2-A) | 7.42 | 0.000 | up | 7.42 | 0.000 | up | ||||||
SoyZH13_05G020900(CYP75B2) | 9.275 | 0.002 | up | |||||||||
SoyZH13_12G061300(CYP93B1) | 21.265 | 0.001 | up |
Time (min) | A% | B% |
---|---|---|
0.01 | 95 | 5 |
2 | 95 | 5 |
4 | 70 | 30 |
8 | 50 | 50 |
10 | 20 | 80 |
14 | 0 | 100 |
15 | 0 | 100 |
15.1 | 95 | 5 |
16 | 95 | 5 |
Parameters | Positive Ion Mode | Negative Ion Mode |
---|---|---|
Mass scan range (m/z) | 100–1200 | 100–1200 |
Resolution (full scan) | 70,000 | 70,000 |
Resolution (HCD MS/MS scans) | 17,500 | 17,500 |
Spray voltage (V) | 3800 | −3000 |
Sheath gas flow rate (Arb) | 40 | 35 |
Aux gas flow rate (Arb) | 10 | 8 |
Capillary temperature (°C) | 320 | 320 |
Auxiliary gas heater temperature (°C) | 350 | 350 |
S-lens radio frequency (RF) level | 50 | 50 |
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Fan, Y.; Hussain, S.; Wang, X.; Yang, M.; Zhong, X.; Tao, L.; Li, J.; Zhou, Y.; Xiang, C. Metabolomic and Transcriptomic Analyses of Flavonoid Biosynthesis in Different Colors of Soybean Seed Coats. Int. J. Mol. Sci. 2025, 26, 294. https://doi.org/10.3390/ijms26010294
Fan Y, Hussain S, Wang X, Yang M, Zhong X, Tao L, Li J, Zhou Y, Xiang C. Metabolomic and Transcriptomic Analyses of Flavonoid Biosynthesis in Different Colors of Soybean Seed Coats. International Journal of Molecular Sciences. 2025; 26(1):294. https://doi.org/10.3390/ijms26010294
Chicago/Turabian StyleFan, Yuanfang, Sajad Hussain, Xianshu Wang, Mei Yang, Xiaojuan Zhong, Lei Tao, Jing Li, Yonghang Zhou, and Chao Xiang. 2025. "Metabolomic and Transcriptomic Analyses of Flavonoid Biosynthesis in Different Colors of Soybean Seed Coats" International Journal of Molecular Sciences 26, no. 1: 294. https://doi.org/10.3390/ijms26010294
APA StyleFan, Y., Hussain, S., Wang, X., Yang, M., Zhong, X., Tao, L., Li, J., Zhou, Y., & Xiang, C. (2025). Metabolomic and Transcriptomic Analyses of Flavonoid Biosynthesis in Different Colors of Soybean Seed Coats. International Journal of Molecular Sciences, 26(1), 294. https://doi.org/10.3390/ijms26010294