Frontiers in plant science · 2026
Aconserved salt-stress co-expression network in japonica rice reveals partially dissociated hub gene connectivity and transcriptional induction.
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Xie Kun, Hou Song, Li Na-Na, Liu Min, Xin Fu-Gang, Tian Ru-Mei, Bai Jing, Cong Yun-Zhe, Li Guan, Li Run-Fang, Ding Han-Feng, Yang Yong-Yi
Аннотация
INTRODUCTION: Soil salinity severely compromises rice (Oryza sativa L.) growth and grain yield by disrupting ionic and osmotic homeostasis. Although transcriptome profiling has advanced understanding of salt-stress responses in rice, the conservation of co-expression networks across genetic backgrounds and the relationship between network connectivity and transcriptional induction remain poorly characterized.
METHODS: We performed integrated RNA sequencing and weighted gene co-expression network analysis (WGCNA) on three japonica rice varieties under control (0 mM), moderate (85.6 mM), and severe (136.9 mM) NaCl stress.
RESULTS: All three varieties exhibited basal salt tolerance. Differential expression analysis identified 2,067 and 4,900 non-redundant differentially expressed genes (DEGs) under moderate and severe stress, with 205 and 1,093 DEGs shared across the three varieties, respectively. WGCNA identified 32 co-expression modules. The brown module showed the strongest dose-dependent response to salt stress and was enriched in phenylpropanoid biosynthesis, plant hormone signal transduction, and MAPK signaling; its eigengene was highly concordant across varieties (mean r = 0.987), consistent with a shared leaf-level transcriptional program. Across brown-module genes, intramodular connectivity and salt-induced fold change were positively but only moderately correlated (Pearson r = 0.377): OsDREB1A was the most connected gene but not the most strongly induced, whereas LOC_Os10g35080 was the most strongly induced yet ranked 14th in connectivity. In the 15-node hyperosmotic salinity response subnetwork, no single hub dominated, and OsDREB1A occupied a peripheral position.
DISCUSSION: Connectivity and induction thus reflect complementary aspects of the salt-stress response, and candidate hub genes for molecular breeding should be prioritized by both criteria jointly, followed by validation across diverse genetic backgrounds.
METHODS: We performed integrated RNA sequencing and weighted gene co-expression network analysis (WGCNA) on three japonica rice varieties under control (0 mM), moderate (85.6 mM), and severe (136.9 mM) NaCl stress.
RESULTS: All three varieties exhibited basal salt tolerance. Differential expression analysis identified 2,067 and 4,900 non-redundant differentially expressed genes (DEGs) under moderate and severe stress, with 205 and 1,093 DEGs shared across the three varieties, respectively. WGCNA identified 32 co-expression modules. The brown module showed the strongest dose-dependent response to salt stress and was enriched in phenylpropanoid biosynthesis, plant hormone signal transduction, and MAPK signaling; its eigengene was highly concordant across varieties (mean r = 0.987), consistent with a shared leaf-level transcriptional program. Across brown-module genes, intramodular connectivity and salt-induced fold change were positively but only moderately correlated (Pearson r = 0.377): OsDREB1A was the most connected gene but not the most strongly induced, whereas LOC_Os10g35080 was the most strongly induced yet ranked 14th in connectivity. In the 15-node hyperosmotic salinity response subnetwork, no single hub dominated, and OsDREB1A occupied a peripheral position.
DISCUSSION: Connectivity and induction thus reflect complementary aspects of the salt-stress response, and candidate hub genes for molecular breeding should be prioritized by both criteria jointly, followed by validation across diverse genetic backgrounds.