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<p>Seed oil and protein content are crucial agronomic traits in soybean breeding; however, the regulatory mechanisms underlying their accumulation and trade-off are not yet fully understood. In this study, transcriptomic and co-expression network analyses were conducted on seeds from two high-oil and two high-protein soybean cultivars across five developmental stages (S1–S5). The results revealed that transcriptional divergence related to oil and protein accumulation primarily occurred during the later stages (S4 and S5). In high-oil cultivars, the S4-specific module was associated with calcium–lipid signaling, while the S5-specific module was linked to carbohydrate degradation, triacylglycerol (TAG) biosynthesis, and phospholipid signaling. In contrast, in high-protein cultivars, the S5-specific module exhibited strong activation of nitrogen assimilation, amino acid metabolism, organic acid metabolism, abscisic acid (ABA) signaling, and protein processing pathways. This antagonistic activation of lipid- and nitrogen-centric pathways underlies the oil–protein trade-off in soybean seeds. Further analysis identified 89 oil-related and 112 protein-related candidate genes, including 23 and 17 previously reported genes, respectively. Among the novel candidates, 39 (59.09%) oil-related and 57 (60.00%) protein-related genes were located within known quantitative trait loci (QTLs) for these traits. Notably, core network analysis revealed 22 oil-specific core regulators (e.g., <i>CLO1</i>, <i>PEBP</i>) that direct lipid metabolism and 15 protein-specific core regulators (e.g., <i>GS</i>, <i>PTR1</i>) that govern nitrogen allocation. Together, these regulators constitute a hierarchical framework that spatiotemporally orchestrates the trade-off between oil and protein biosynthesis. These findings provide valuable genetic targets for precision breeding programs aimed at optimizing resource allocation.</p>

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Construction of regulatory networks related to oil and protein accumulation in developing soybean seeds

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年7月7日

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  • Yuan Niu,
  • Jiang Wu,
  • Henan Li,
  • Huicong Wang,
  • Hongliang Zhao,
  • Zhiwei Huang,
  • Feiyu Yan,
  • Guoliang Zhang

摘要

Seed oil and protein content are crucial agronomic traits in soybean breeding; however, the regulatory mechanisms underlying their accumulation and trade-off are not yet fully understood. In this study, transcriptomic and co-expression network analyses were conducted on seeds from two high-oil and two high-protein soybean cultivars across five developmental stages (S1–S5). The results revealed that transcriptional divergence related to oil and protein accumulation primarily occurred during the later stages (S4 and S5). In high-oil cultivars, the S4-specific module was associated with calcium–lipid signaling, while the S5-specific module was linked to carbohydrate degradation, triacylglycerol (TAG) biosynthesis, and phospholipid signaling. In contrast, in high-protein cultivars, the S5-specific module exhibited strong activation of nitrogen assimilation, amino acid metabolism, organic acid metabolism, abscisic acid (ABA) signaling, and protein processing pathways. This antagonistic activation of lipid- and nitrogen-centric pathways underlies the oil–protein trade-off in soybean seeds. Further analysis identified 89 oil-related and 112 protein-related candidate genes, including 23 and 17 previously reported genes, respectively. Among the novel candidates, 39 (59.09%) oil-related and 57 (60.00%) protein-related genes were located within known quantitative trait loci (QTLs) for these traits. Notably, core network analysis revealed 22 oil-specific core regulators (e.g., CLO1, PEBP) that direct lipid metabolism and 15 protein-specific core regulators (e.g., GS, PTR1) that govern nitrogen allocation. Together, these regulators constitute a hierarchical framework that spatiotemporally orchestrates the trade-off between oil and protein biosynthesis. These findings provide valuable genetic targets for precision breeding programs aimed at optimizing resource allocation.