Silicon Transporter Gene Lsi1 Linked to Bacterial Salinity Relief in Rice

Soil salinity is a major constraint on rice production worldwide, and a new study points to a silicon transporter gene as a candidate link between salt stress and the beneficial bacteria that help plants endure it.

The work, published in BMC Plant Biology, set out to identify candidate genes associated with rice responses to Bacillus amyloliquefaciens, a plant growth-promoting bacterium, under saline conditions. Because the molecular basis of how rice responds to helpful bacteria in salty soils remains poorly understood, the team used transcriptome network analysis as an exploratory, hypothesis-generating tool rather than a definitive test of mechanism.

From the publicly available root RNA-seq datasets, the network analysis consistently prioritized Lsi1 among candidate genes tied to the combined treatment of salinity and bacterial inoculation. The analysis generated predictions that the researchers could then examine experimentally.

Guided by those predictions, the team evaluated two rice genotypes that differ in salinity tolerance, growing them under saline conditions with or without B. amyloliquefaciens inoculation. They measured plant growth, physiological and biochemical traits, gene expression, and silicon accumulation, then applied multivariate analyses to the results.

The experiments supported the network’s lead candidate. Compared with uninoculated plants, bacterial inoculation alleviated salinity-induced growth inhibition, improved antioxidant capacity and osmotic adjustment, and increased biomass production. Inoculation also altered Lsi1 expression, and those changes in gene expression were accompanied by corresponding changes in how much silicon the plants accumulated.

Hierarchical clustering and partial least squares discriminant analysis, a multivariate method, further supported the separation of treatments. These analyses identified Lsi1 expression, oxidative stress markers, and antioxidant enzymes as the major contributors to the observed physiological responses, tying the molecular signal to measurable plant performance under salt stress.

The authors emphasize convergence rather than proof. The alignment of transcriptomic, molecular, physiological, and multivariate evidence supports Lsi1 as a candidate gene associated with rice responses to the bacterium under salinity, and suggests that modulating silicon uptake is an important component of how the host responds to beneficial bacterial inoculation.

Because the transcriptome component relied on exploratory reanalysis of existing datasets, the findings are framed as a rational basis for future functional studies investigating the role of Lsi1 in PGPB-mediated salinity tolerance, rather than as a demonstrated mechanism ready for breeding applications.

Even so, the study offers a concrete lead for a pressing problem. As salinity constrains rice yields globally, identifying candidate genes that connect beneficial microbes, silicon transport, and antioxidant defenses could guide the next round of experiments aimed at helping rice withstand salty soils.

Subject of Research: Candidate gene identification for rice responses to beneficial bacteria under salinity stress

Article Title: Transcriptome network analysis prioritizes Lsi1 as a candidate gene associated with rice responses to Bacillus amyloliquefaciens under salinity

Article References: Sorkheh, Z., Zarei, M., Shamloo-Dashtpagerdi, R., Dadkhodaie, A., Ghasemi -Fasaei, R., & Taghvaei, M. (2026). Transcriptome network analysis prioritizes Lsi1 as a candidate gene associated with rice responses to Bacillus amyloliquefaciens under salinity. BMC Plant Biology. https://doi.org/10.1186/s12870-026-10307-0

Image Credits: AI Generated

DOI: 10.1186/s12870-026-10307-0

Keywords: rice, salinity stress, Lsi1, silicon transporter, Bacillus amyloliquefaciens, plant growth-promoting bacteria, transcriptome network analysis, RNA-seq, antioxidant capacity, gene expression, silicon accumulation, BMC Plant Biology