State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
J Integr Plant Biol. 2023 Jun;65(6):1536-1552. doi: 10.1111/jipb.13495. Epub 2023 May 22.
Although root nodules are essential for biological nitrogen fixation in legumes, the cell types and molecular regulatory mechanisms contributing to nodule development and nitrogen fixation in determinate nodule legumes, such as soybean (Glycine max), remain incompletely understood. Here, we generated a single-nucleus resolution transcriptomic atlas of soybean roots and nodules at 14 days post inoculation (dpi) and annotated 17 major cell types, including six that are specific to nodules. We identified the specific cell types responsible for each step in the ureides synthesis pathway, which enables spatial compartmentalization of biochemical reactions during soybean nitrogen fixation. By utilizing RNA velocity analysis, we reconstructed the differentiation dynamics of soybean nodules, which differs from those of indeterminate nodules in Medicago truncatula. Moreover, we identified several putative regulators of soybean nodulation and two of these genes, GmbHLH93 and GmSCL1, were as-yet uncharacterized in soybean. Overexpression of each gene in soybean hairy root systems validated their respective roles in nodulation. Notably, enrichment for cytokinin-related genes in soybean nodules led to identification of the cytokinin receptor, GmCRE1, as a prominent component of the nodulation pathway. GmCRE1 knockout in soybean resulted in a striking nodule phenotype with decreased nitrogen fixation zone and depletion of leghemoglobins, accompanied by downregulation of nodule-specific gene expression, as well as almost complete abrogation of biological nitrogen fixation. In summary, this study provides a comprehensive perspective of the cellular landscape during soybean nodulation, shedding light on the underlying metabolic and developmental mechanisms of soybean nodule formation.
尽管根瘤对于豆科植物的生物固氮至关重要，但对于像大豆（Glycine max）这样的有限结瘤豆科植物中，参与结瘤和固氮的细胞类型和分子调控机制仍不完全清楚。在这里，我们生成了大豆根和接种后 14 天（dpi）的根瘤的单细胞分辨率转录组图谱，并注释了 17 种主要的细胞类型，包括 6 种特定于根瘤的细胞类型。我们确定了负责尿囊素合成途径中每个步骤的特定细胞类型，该途径使大豆固氮过程中的生化反应在空间上分隔开。通过利用 RNA 速度分析，我们重建了大豆根瘤的分化动态，这与 Medicago truncatula 中的不定根瘤不同。此外，我们鉴定了几个大豆结瘤的假定调节因子，其中两个基因，GmbHLH93 和 GmSCL1，在大豆中尚未被描述。这两个基因在大豆毛状根系中的过表达验证了它们各自在结瘤中的作用。值得注意的是，大豆根瘤中细胞分裂素相关基因的富集导致鉴定出细胞分裂素受体 GmCRE1 是结瘤途径中的一个重要组成部分。大豆中 GmCRE1 的敲除导致结瘤表型显著，固氮区减少，类菌体血红蛋白耗竭，同时伴随着结瘤特异性基因表达的下调，以及生物固氮几乎完全被阻断。总之，本研究提供了大豆结瘤过程中细胞景观的全面视角，揭示了大豆结瘤形成的潜在代谢和发育机制。
