Single-cell multi-omic characterization of the soybean root response to cyst nematode infection

Soybean cyst nematodes parasitize soybean roots by inducing the formation of multinucleate syncytia to feed and complete their life cycle. However, the molecular basis of syncytia initiation and development remains limited. Here, we generated an integrated single-nucleus RNA and chromatin accessibility profile of soybean roots from infected and uninfected plants. We profiled 56,448 high-quality nuclei and identified all major root cell types, including distinct subpopulations enriched with syncytial nuclei. Transcriptomic and chromatin accessibility analyses support their procambium cell signature that progresses through distinct stages associated with immune suppression, cell fusion, and endoreduplication. Integrative gene expression and transcription factor motif chromatin accessibility analyses identified CAMTA1, as a key transcriptional repressor of defense-related genes including receptor-like kinases (RLKs), whereas MYB, MYB-related, and E2F as transcriptional activators that coordinate cell wall remodeling, chromatin modification and DNA replication, respectively, across developmental trajectories. These findings provide mechanistic insights into host reprogramming during nematode parasitism and a foundational resource for engineering nematode-resistant soybean. Overall design: To dissect the molecular responses of soybean roots to SCN infection and track syncytium development, we performed snRNA-seq and scATAC-seq on mock-inoculated and SCN-infected soybean roots from the susceptible genotype Williams 82 at 5 days post-inoculation (DPI) with two biological replicates. The soybean roots were inoculated with infective J2 and allowed to infect the roots for 24 hours after which the roots were washed to remove any J2 that had not yet penetrated the roots. This step allowed for the collection of root tissue with a higher percentage of sedentary life stages of SCN enabling the capture of a mix of initial syncytial cells through developing syncytia up to a maximum of ~4 days old.

大豆孢囊线虫（Soybean cyst nematodes, SCN）通过诱导多核合胞体（syncytia）的形成以侵染大豆根系，获取营养并完成自身生命周期。然而，目前学界对合胞体起始与发育的分子基础认知仍较为有限。本研究针对受侵染与未受侵染的大豆根系，构建了整合的单细胞核转录组与染色质开放性图谱，共获得56448个高质量细胞核的测序数据，并鉴定出大豆根系所有主要细胞类群，其中包含一类富集合胞体细胞核的独特亚群。转录组与染色质开放性分析显示，该亚群具备原形成层细胞的特征，并经历了与免疫抑制、细胞融合及核内复制相关的不同发育阶段。通过整合基因表达与转录因子基序染色质开放性分析，本研究鉴定出CAMTA1是包括类受体激酶（receptor-like kinases, RLKs）在内的防御相关基因的关键转录抑制因子；而MYB、MYB相关及E2F则分别作为转录激活因子，在发育轨迹中协调细胞壁重塑、染色质修饰与DNA复制过程。本研究结果为解析线虫侵染过程中的宿主重编程机制提供了新的认知，同时也为抗线虫大豆品种的遗传改良提供了重要的基础资源。
实验设计：为解析大豆根系对SCN侵染的分子响应并追踪合胞体发育过程，本研究对感病品种威廉姆斯82（Williams 82）在接种后5天（days post-inoculation, DPI）的Mock接种与SCN侵染根系开展了单细胞核转录组测序（single-nucleus RNA sequencing, snRNA-seq）与单细胞核染色质转座酶可及性测序（single-cell assay for transposase-accessible chromatin using sequencing, scATAC-seq），设置2次生物学重复。本研究将大豆根系接种侵染性二龄幼虫（J2），使其侵染24小时后清洗根系以去除未侵入的J2。该操作可提升根系组织中SCN定居型发育阶段的占比，从而能够捕获从初始合胞体细胞到发育时长最多约4天的合胞体的混合样本。