The miR172a-ERF416/413 module regulates soybean seed traits

doi:10.1111/jipb.70015

. 2025 Aug 14.

doi: 10.1111/jipb.70015. Online ahead of print.

The miR172a-ERF416/413 module regulates soybean seed traits

Meng Jin^{1

2}, Jia-Qi Han^{1

2}, Lu-Yao Zhang^{1

2}, Zhi-Hao Jiang^{1

2}, Yue Liu^{1

2}, Jun-Jie Wei^{1

2}, Ling-Yi Zheng^{1

2}, Shang-Shang Xiong^{1

2}, Yang Hu¹, Tong Cheng¹, Xiao-Hua Bian¹, Chun-Mei Wu¹, Wei Wei¹, Yi-Hua Huang¹, Cui-Cui Yin¹, Feng Gao³, Wei Li⁴, Ying-Dong Bi⁴, Yong-Cai Lai⁴, Bin Zhou⁵, De-Yue Yu⁶, Shou-Yi Chen¹, Jian-Jun Tao¹, Wan-Ke Zhang¹, Jin-Song Zhang^{1

2}

Affiliations

¹ State Key Lab of Seed Innovation, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing, 100101, China.
² College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
³ Qilu Zhongke Academy of Modern Microbiology Technology, Jinan, 250018, China.
⁴ Crop Tillage and Cultivation Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China.
⁵ Crop Research Institute of Anhui Academy of Agricultural Sciences, Hefei, 230031, China.
⁶ National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.

PMID: 40808470
DOI: 10.1111/jipb.70015

The miR172a-ERF416/413 module regulates soybean seed traits

Meng Jin et al. J Integr Plant Biol. 2025.

. 2025 Aug 14.

doi: 10.1111/jipb.70015. Online ahead of print.

Authors

Affiliations

¹ State Key Lab of Seed Innovation, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing, 100101, China.
² College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
³ Qilu Zhongke Academy of Modern Microbiology Technology, Jinan, 250018, China.
⁴ Crop Tillage and Cultivation Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China.
⁵ Crop Research Institute of Anhui Academy of Agricultural Sciences, Hefei, 230031, China.
⁶ National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.

PMID: 40808470
DOI: 10.1111/jipb.70015

Abstract

Soybean (Glycine max) provides vegetable oils and proteins for human consumption. Its production depends on seeds and other production-related agronomic traits. How the seed traits are regulated in soybean remains largely unclear. In this study, we identified a miR172a-ERF416/413 module for the regulation of seed traits. The miR172a can cleave the targets ERF416 and ERF413 to affect the downstream gene expression for the reduction of soybean seed size and weight. Both the MIR172a-overexpressing transgenic soybean plants and the erf416/413 mutants produced smaller seeds than the control. Consistently, the ERF416-overexpressing transgenic soybean plants generated larger seeds. ERF416 and ERF413 were directly targeted to the promoter of GmKIX8-1 and GmSWEET10a to regulate their gene expression for seed size/weight control. Interestingly, the erf416/413 mutants showed higher seed yield per plant and higher total seed fatty acid (FA) content, whereas the MIR172a-transgenic soybean had lower total seed FA content compared with the control cultivar, suggesting that miR172a and ERF416/413 may function in FA accumulation through different pathways. Haplotypes of the ERF416 promoter region were further analyzed and Hap1 was correlated with higher gene expression and higher seed weight, while Hap3 was correlated with higher total seed lipid content. Our study revealed a new module for seed trait control. Manipulation of such alleles should facilitate breeding for high-oil and high-yield soybean cultivars.

Keywords: ERF416/ERF413 transcription factors; fatty acids; miR172a; seed size/weight; soybean.

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References

REFERENCES

1. Chen, X., Liu, C., Guo, P., Hao, X., Pan, Y., Zhang, K., Liu, W., Zhao, L., Luo, W., He, J., et al. (2023). Differential SW16.1 allelic effects and genetic backgrounds contributed to increased seed weight after soybean domestication. J. Integr. Plant Biol. 65: 1734–1752.
1. Du, J., Wang, S., He, C., Zhou, B., Ruan, Y.L., and Shou, H. (2017). Identification of regulatory networks and hub genes controlling soybean seed set and size using RNA sequencing analysis. J. Exp. Bot. 68: 1955–1972.
1. Duan, Z., Zhang, M., Zhang, Z., Liang, S., Fan, L., Yang, X., Yuan, Y., Pan, Y., Zhou, G., Liu, S., et al. (2022). Natural allelic variation of GmST05 controlling seed size and quality in soybean. Plant Biotechnol. J. 20: 1807–1818.
1. Ge, L., Yu, J., Wang, H., Luth, D., Bai, G., Wang, K., and Chen, R. (2016). Increasing seed size and quality by manipulating BIG SEEDS1 in legume species. Proc. Natl. Acad. Sci. U.S.A. 113: 12414–12419.
1. Gu, Y., Li, W., Jiang, H., Wang, Y., Gao, H., Liu, M., Chen, Q., Lai, Y., and He, C. (2017). Differential expression of a WRKY gene between wild and cultivated soybeans correlates to seed size. J. Exp. Bot. 68: 2717–2729.

Grants and funding

2023YFD1200602/National Key Research and Development Program of China

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[1] Chen, X., Liu, C., Guo, P., Hao, X., Pan, Y., Zhang, K., Liu, W., Zhao, L., Luo, W., He, J., et al. (2023). Differential SW16.1 allelic effects and genetic backgrounds contributed to increased seed weight after soybean domestication. J. Integr. Plant Biol. 65: 1734–1752.

[2] Chen, X., Liu, C., Guo, P., Hao, X., Pan, Y., Zhang, K., Liu, W., Zhao, L., Luo, W., He, J., et al. (2023). Differential SW16.1 allelic effects and genetic backgrounds contributed to increased seed weight after soybean domestication. J. Integr. Plant Biol. 65: 1734–1752.

[3] Du, J., Wang, S., He, C., Zhou, B., Ruan, Y.L., and Shou, H. (2017). Identification of regulatory networks and hub genes controlling soybean seed set and size using RNA sequencing analysis. J. Exp. Bot. 68: 1955–1972.

[4] Du, J., Wang, S., He, C., Zhou, B., Ruan, Y.L., and Shou, H. (2017). Identification of regulatory networks and hub genes controlling soybean seed set and size using RNA sequencing analysis. J. Exp. Bot. 68: 1955–1972.

[5] Duan, Z., Zhang, M., Zhang, Z., Liang, S., Fan, L., Yang, X., Yuan, Y., Pan, Y., Zhou, G., Liu, S., et al. (2022). Natural allelic variation of GmST05 controlling seed size and quality in soybean. Plant Biotechnol. J. 20: 1807–1818.

[6] Duan, Z., Zhang, M., Zhang, Z., Liang, S., Fan, L., Yang, X., Yuan, Y., Pan, Y., Zhou, G., Liu, S., et al. (2022). Natural allelic variation of GmST05 controlling seed size and quality in soybean. Plant Biotechnol. J. 20: 1807–1818.

[7] Ge, L., Yu, J., Wang, H., Luth, D., Bai, G., Wang, K., and Chen, R. (2016). Increasing seed size and quality by manipulating BIG SEEDS1 in legume species. Proc. Natl. Acad. Sci. U.S.A. 113: 12414–12419.

[8] Ge, L., Yu, J., Wang, H., Luth, D., Bai, G., Wang, K., and Chen, R. (2016). Increasing seed size and quality by manipulating BIG SEEDS1 in legume species. Proc. Natl. Acad. Sci. U.S.A. 113: 12414–12419.

[9] Gu, Y., Li, W., Jiang, H., Wang, Y., Gao, H., Liu, M., Chen, Q., Lai, Y., and He, C. (2017). Differential expression of a WRKY gene between wild and cultivated soybeans correlates to seed size. J. Exp. Bot. 68: 2717–2729.

[10] Gu, Y., Li, W., Jiang, H., Wang, Y., Gao, H., Liu, M., Chen, Q., Lai, Y., and He, C. (2017). Differential expression of a WRKY gene between wild and cultivated soybeans correlates to seed size. J. Exp. Bot. 68: 2717–2729.

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The miR172a-ERF416/413 module regulates soybean seed traits

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The miR172a-ERF416/413 module regulates soybean seed traits

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Abstract

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