On March 3, 2026, Professor Yuan Wang’s research team from the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences published a research article entitled “Small RNA-directed DNA methylation by Pol IV and Pol V maintains immune homeostasis in soybean” in The Plant Cell. The study provides an answer to a fundamental question in plant immunity: the immune threshold of soybean is jointly established by genomic “dark matter” — LTR retrotransposons — through the regulation of the RNA-directed DNA methylation (RdDM) pathway.
During molecular biology experiments, including high-throughput sequencing analyses, soybean plants were cultivated in a Jiupo Plant Growth Chamber under controlled environmental conditions: 70% relative humidity, 25°C temperature, and a 16-hour light / 8-hour dark photoperiod.
During the study, plants were cultivated in a Jiupo Artificial Climate Chamber under controlled environmental conditions, including a temperature of 22°C, relative humidity of approximately 55%, a 16 h light / 8 h dark photoperiod (long-day conditions), and a light intensity maintained at 100–120 μmol·m⁻²·s⁻¹.
The study generated an Arabidopsis BSK-family undecuple mutant, revealing that BSK family members exhibit a high degree of functional redundancy yet are indispensable for brassinosteroid (BR) signaling. Furthermore, the researchers uncovered a novel regulatory mechanism whereby BR signaling suppresses adventitious root (AR) formation through the BSK–BZR1 signaling module, which represses the expression of LBD16.
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The immune system has a critical but often overlooked characteristic: its basal expression level, also known as the immune threshold. If this threshold is set too high, plants may suffer from autoimmune disorders caused by excessive immune activation. If it is set too low, plants may fail to rapidly respond to invading pathogens. Therefore, for soybean — a crop species with a large family of disease-resistance genes and a genome containing more than 50% transposable elements — what determines this essential immune threshold?
For a long time, transposable elements have been considered “selfish DNA” or genomic remnants. This study reveals that LTR transposable elements in soybean are not merely non-functional sequences; instead, they have been domesticated by plants and serve as molecular switches regulating immune gene expression.
Whole-genome DNA methylation sequencing demonstrated that the RdDM pathway primarily targets LTR transposable elements. These transposable elements are frequently located near protein-coding genes in the soybean genome and are enriched around key immune components, including Toll/interleukin-1 receptor (TIR)-nucleotide-binding leucine-rich repeat (TNL) immune receptor genes and EDS1/SAG101 pathway components, forming soybean-specific transposable element–immune gene regulatory modules.
Through epigenetic regulation, RdDM-mediated methylation of LTR transposable elements precisely controls the basal expression levels of adjacent disease-resistance genes.
Figure: Multi-omics analyses demonstrate that loss of GmNRPD1 results in extensive depletion of genome-wide 24-nt siRNAs in soybean. This reduction mainly occurs at RNA-directed DNA methylation-associated loci, partially overlaps with regions affected by GmNRPE1 mutation, and reveals the chromosomal distribution and corresponding genomic element categories of these differential regions.
Using CRISPR-mediated knockout of key RdDM genes GmNRPD1 and GmNRPE1, the research team demonstrated that the abundance of 24-nt small interfering RNAs (24-nt siRNAs) was significantly reduced. Meanwhile, CHH methylation levels of LTR transposable elements were substantially decreased, directly leading to abnormal activation of immune-related genes, including TNL immune receptor genes and EDS1/SAG101 pathway components.
Even in the absence of pathogen infection, soybean plants exhibited persistent activation of immune pathways, resulting in autoimmune imbalance, severely impaired growth, dwarf phenotypes, and developmental defects.
Figure: The soybean RdDM pathway maintains the balance between growth and immunity
These findings demonstrate that the RdDM–transposable element module plays a central role in maintaining soybean immune homeostasis, keeping disease-resistance genes in a low-expression standby state under normal conditions.
When soybean plants encounter Phytophthora infection stress, they actively reduce the expression of core RdDM factors, including NRPD1, NRPE1, and AGO4, thereby releasing methylation-mediated repression of LTR transposable elements. This enables rapid activation of downstream immune genes and facilitates a swift transition of immune responses from a primed state to active defense.
Author information
Ziming Zhang and Hongda Sun, Ph.D. students from the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, are co-first authors of this paper. Professor Yuan Wang from the same institute is the corresponding author.
Professor Jinfeng Chen from the Institute of Zoology, Chinese Academy of Sciences also contributed to this research. The authors acknowledge Professor Lei Li from the Institute of Genetics and Developmental Biology for guidance and assistance in soybean Phytophthora inoculation experiments and phenotypic analyses.
This research was supported by the National Natural Science Foundation of China.