Bioscience Evidence 2025, Vol.15, No.5, 237-248 http://bioscipublisher.com/index.php/be 240 4.2.2 Acyl carrier proteins and desaturases (FAD2, FAD3) Acyl carrier proteins (ACP) are responsible for transporting intermediates in fatty acid synthesis. FAD2 and FAD3 are key desaturases that respectively control the production of linoleic acid and alpha-linolenic acid, directly determine the ratio of oleic acid, linoleic acid, and alpha-linolenic acid, and are important targets for improving lipid quality (Yao et al., 2020; Ma et al., 2021; Silva et al., 2021; Cai et al., 2023). In addition, genes such as GmFATA1B and GmFATB1 also affect oil content and fatty acid composition (Ma et al., 2021; Cai et al., 2023). 4.3 Functional mechanisms: partitioning of carbon into lipid biosynthesis, transcriptional control The synthesis of soybean oil relies on the distribution of carbon flow, shifting from precursors such as sucrose and glucose to fatty acids and TAG. Sugar transporters (such as GmSWEET10a/b, GmSWEET39) regulate oil accumulation by regulating the transport of sugar between seed coat and endosperm and affecting the utilization of carbon sources (Miao et al., 2019; Wang et al., 2020; 2025). Some transcription factors (such as WRI1, LEC1, MYB, bZIP, etc.) coordinate lipid synthesis by regulating genes related to fatty acid synthesis and TAG assembly (Zhang et al., 2019; Liu et al., 2020; Zhao et al., 2024). 4.4 Breeding implications: efforts to improve oil quality (oleic vs linoleic vs linolenic acid) Increasing the oil content and optimizing the proportion of fatty acids (such as increasing oleic acid and reducing linoleic acid and alpha-linolenic acid) are important goals in soybean breeding. Through QTL mapping, molecular markers and gene editing, some excellent genotypes have been combined (Cao et al., 2017; Zhang et al., 2019; Ma et al., 2021; Silva et al., 2021; Cai et al., 2023; Jia et al., 2024). For example, the FAD2-1A/B mutant can stably increase the oleic acid content, and the knockout of GmFATB1 can reduce saturated fatty acids (Ma et al., 2021; Silva et al., 2021). However, there is a complex relationship between oil content, protein and yield. Multi-gene polymerization and precise regulation are required to achieve the breeding goals of high oil content and high quality (Zhang et al., 2019; Goettel et al., 2022; Jia et al., 2024; Yuan et al., 2024). 5 The Protein-Oil Trade-off 5.1 Physiological constraints: inverse relationship between protein and oil accumulation In soybean seeds, the content of protein and oil is usually negatively correlated. That is to say, when protein levels increase, oil content tends to decrease, and vice versa (Wang et al., 2020; Liu et al., 2023). This relationship not only occurs among different varieties and germplasms, but is also obvious under different environments and management conditions of the same variety (Assefa et al., 2018; 2019). Genetic studies have shown that some major QTLS (such as loci on chromosomes 15 and 20) regulate proteins and oils simultaneously, and often in opposite directions (Zhang et al., 2020; Zhu et al., 2020; Clevinger et al., 2023; Kim et al., 2023). Environmental conditions also have an impact. For example, water stress, nitrogen fertilizer and irrigation can all change the accumulation of protein and oil. But overall, it is difficult to improve both simultaneously (Assefa et al., 2019; Carciochi et al., 2023). 5.2 Regulatory networks: hormonal and metabolic crosstalk The relationship between protein and oil is not only determined by the genes themselves, but also related to the interaction of hormones and metabolic networks. Sugar transporters (such as GmSWEET10a/b, GmSWEET39) regulate the distribution of carbon sources such as sucrose between the seed coat and endosperm, thereby affecting whether carbon enters protein synthesis or lipid synthesis (Zhang et al., 2020; Wang et al., 2020; Mo et al., 2024). Some genes, such as GmMFT, can simultaneously affect seed development and material distribution, and have effects on both protein and oil (Cai et al., 2023). Furthermore, the interactive regulation of hormone signals (such as auxin and abscisic acid) and carbon-nitrogen metabolism is also regarded as an important mechanism of protein-oil balance (Duan et al., 2023; Mo et al., 2024) (Figure 1). 5.3 Systems biology perspectives: integrative omics evidence Multi-omics studies (genomics, transcriptomics, proteomics, metabolomics) have shown that the accumulation of proteins and oils involves many metabolic pathways and regulatory links. Transcriptomic and proteomic analyses revealed differential expression of genes related to fatty acid and amino acid synthesis in high-protein or high-oil varieties. The changes in the activities of carbon metabolism, glycolysis and TCA cycle will also directly affect
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