Chaiprom Usawadee, Miraeiz Esmaeil, Lee Tong Geon, Drnevich Jenny, Hudson Matthew
Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
G3 (Bethesda). 2024 Sep 19;14(12). doi: 10.1093/g3journal/jkae226.
Soybean yield loss due to soybean cyst nematode (SCN) infestation has a negative impact on the U.S. economy. Most SCN-resistant soybeans carry a common resistance locus (Rhg1), conferred by copy number variation of a 31.2-kb segment at the Rhg1 locus. To identify the effects of Rhg1 copy number on the plant prior to SCN infection, we investigated genome-wide expression profiles in isogenic Fayette plants carrying different copy numbers at the Rhg1 locus (9-11 copies), that confer different levels of resistance to SCN. We found that even small differences in copy number lead to large changes in expression of downstream defense genes. The co-expression network constructed from differentially expressed genes (DEGs) outside the Rhg1 locus revealed complex effects of Rhg1 copy number on transcriptional regulation involving signal transduction and ethylene-mediated signaling pathways. Moreover, we report a variation in expression levels of phytoalexin biosynthesis-related genes that is correlated with copy number, and the activation of different NBS-LRR gene sets, indicating a broad effect of copy number on defense responses. Using qRT-PCR time series during SCN infection, we validated the SCN responses of DEGs detected in the copy number comparison and showed a stable upregulation of genes related to phytoalexin biosynthesis in resistant Fayette lines during the early stages of the incompatible interaction between soybeans and SCN, before syncytium formation. These results suggest additional genes that could enhance Rhg1-mediated SCN resistance.
大豆胞囊线虫（SCN）侵染导致的大豆产量损失对美国经济产生负面影响。大多数抗SCN的大豆携带一个常见的抗性位点（Rhg1），该位点由Rhg1位点处一个31.2 kb片段的拷贝数变异赋予。为了确定Rhg1拷贝数在SCN感染之前对植株的影响，我们研究了在Rhg1位点携带不同拷贝数（9 - 11个拷贝）的同基因费耶特植株的全基因组表达谱，这些拷贝数赋予了对SCN不同水平的抗性。我们发现，即使拷贝数的微小差异也会导致下游防御基因表达的巨大变化。从Rhg1位点外差异表达基因（DEG）构建的共表达网络揭示了Rhg1拷贝数对涉及信号转导和乙烯介导信号通路的转录调控的复杂影响。此外，我们报道了植保素生物合成相关基因表达水平的变化与拷贝数相关，以及不同NBS - LRR基因集的激活，表明拷贝数对防御反应有广泛影响。在SCN感染期间使用qRT - PCR时间序列，我们验证了在拷贝数比较中检测到的DEG对SCN的反应，并表明在大豆与SCN不相容相互作用的早期阶段，即在合胞体形成之前，抗性费耶特品系中与植保素生物合成相关的基因稳定上调。这些结果表明了其他可能增强Rhg1介导的SCN抗性的基因。
