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<p>Soil alkalization, largely driven by sodium bicarbonate (NaHCO<sub>3</sub>) stress, severely impairs crop productivity. To elucidate the molecular mechanisms underlying alkali tolerance in rice, we conducted an integrated analysis of physiological traits, transcriptomics, and metabolomics using the alkali-tolerant cultivar ‘Qijing 10’ (QJ) and the sensitive cultivar ‘Longjing 31’ (LJ) under NaHCO<sub>3</sub> stress. The tolerant QJ line maintained higher photosynthetic efficiency (<i>F</i><sub><i>v</i></sub><i>/F</i><sub><i>m</i></sub>) and superior physiological performance. Multi-omics profiling identified starch and sucrose metabolism, phenylpropanoid biosynthesis, and flavonoid biosynthesis as major pathways associated with differential stress responses. NaHCO<sub>3</sub> stress induced substantial reprogramming of carbon metabolic flux. Under NaHCO<sub>3</sub> stress, QJ exhibited greater accumulations of osmoregulatory substances (sucrose, trehalose) and higher abundance of cellobiose, an important cell wall signaling molecule. Upregulation of phenylpropanoid metabolism was associated with increased accumulation of phenolic antioxidants (ferulic acid and sinapic acid) and lignin precursors in QJ under NaHCO<sub>3</sub> stress. Flavonoid metabolism in QJ was preferentially directed toward the accumulation of antioxidant flavonols, particularly rutin, rather than anthocyanins. Weighted gene and metabolite co-expression network analyses pinpointed core hub genes (<i>4CL</i>, <i>F5H</i>, <i>CHI</i>, <i>GBE</i>) and hub metabolites (sinapic acid, cellobiose, rutin), which were closely associated with rice adaptation to NaHCO<sub>3</sub> stress. This research suggests that the alkali-tolerant cultivar may enhance stress resilience through a multi-layered metabolic strategy integrating osmotic adjustment, antioxidant defense, and cell wall reinforcement. Our findings provide valuable candidate gene and metabolite targets for genetic improvement of alkali tolerance in rice.</p>

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Integrated Transcriptome and Metabolomics Analysis Identifies Metabolic Pathways Associated with Alkali Tolerance in Rice: Involvement of Starch Sucrose Metabolism and the Phenylpropanoid-Flavonoid Pathway

  • 期刊论文

  • 发表日期：

    2026年7月23日

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  • Bo Qin,
  • Tie Li,
  • Minglong Sun,
  • Yuanling Zhao,
  • Dongmei Li

摘要

Soil alkalization, largely driven by sodium bicarbonate (NaHCO3) stress, severely impairs crop productivity. To elucidate the molecular mechanisms underlying alkali tolerance in rice, we conducted an integrated analysis of physiological traits, transcriptomics, and metabolomics using the alkali-tolerant cultivar ‘Qijing 10’ (QJ) and the sensitive cultivar ‘Longjing 31’ (LJ) under NaHCO3 stress. The tolerant QJ line maintained higher photosynthetic efficiency (Fv/Fm) and superior physiological performance. Multi-omics profiling identified starch and sucrose metabolism, phenylpropanoid biosynthesis, and flavonoid biosynthesis as major pathways associated with differential stress responses. NaHCO3 stress induced substantial reprogramming of carbon metabolic flux. Under NaHCO3 stress, QJ exhibited greater accumulations of osmoregulatory substances (sucrose, trehalose) and higher abundance of cellobiose, an important cell wall signaling molecule. Upregulation of phenylpropanoid metabolism was associated with increased accumulation of phenolic antioxidants (ferulic acid and sinapic acid) and lignin precursors in QJ under NaHCO3 stress. Flavonoid metabolism in QJ was preferentially directed toward the accumulation of antioxidant flavonols, particularly rutin, rather than anthocyanins. Weighted gene and metabolite co-expression network analyses pinpointed core hub genes (4CL, F5H, CHI, GBE) and hub metabolites (sinapic acid, cellobiose, rutin), which were closely associated with rice adaptation to NaHCO3 stress. This research suggests that the alkali-tolerant cultivar may enhance stress resilience through a multi-layered metabolic strategy integrating osmotic adjustment, antioxidant defense, and cell wall reinforcement. Our findings provide valuable candidate gene and metabolite targets for genetic improvement of alkali tolerance in rice.