鹽害逆境（salt stress）是限制全球水稻（Oryza sativa L.）生產力最嚴重的非生物逆境之一。過量鹽分累積會破壞植物體內離子平衡、引發滲透壓逆境、促進活性氧（reactive oxygen species, ROS）產生，進而抑制植物生長並降低產量。因此，瞭解水稻耐鹽性的分子調控機制，對於培育具耐逆境能力之水稻品種具有重要意義。本研究利用比較轉錄體分析（comparative transcriptomic analysis），探討耐鹽品種 Pokkali 與鹽敏感品種 IR29 在鹽害處理下之分子反應機制。
本研究分析不同鹽害處理時間點之差異表現基因（Differentially Expressed Genes, DEGs）。Pokkali 在鹽害處理後 0.5、1、3、6、24、48 與 72 小時所鑑定之 DEGs 數量分別為 636、1784、3192、4502、4416、5190 與 5885 個；而 IR29 在相同時間點之 DEGs 數量則分別為 1382、2337、4286、5283、5262、5922 與 6916 個。Gene Ontology以及Kyoto Encyclopedia of Genes and Genomes富集分析結果顯示，與抗氧化反應及滲透壓調節相關之植物荷爾蒙訊號傳遞與代謝途徑在耐鹽反應中扮演重要角色。
早期鹽害反應主要表現為植物荷爾蒙訊號傳遞途徑之顯著富集，包括離層酸（abscisic acid, ABA）、乙烯（ethylene）、生長素（auxin）、茉莉酸（jasmonic acid, JA）、細胞分裂素（cytokinin）、吉貝素（gibberellin, GA）、油菜素內酯（brassinosteroid, BR）及水楊酸（salicylic acid, SA）等途徑，顯示植物能迅速感知鹽害逆境並啟動訊號傳遞機制。隨著鹽害處理時間延長，丙酮酸代謝（pyruvate metabolism）、β-丙胺酸代謝（β-alanine metabolism）以及精胺酸與脯胺酸代謝（arginine and proline metabolism）等代謝途徑呈現顯著富集，顯示其與能量供應、滲透調節及氧化還原穩定性（redox homeostasis）密切相關。
在丙酮酸代謝途徑中，ADH（Os02g0815500、Os03g0189400）、MDH（Os07g0630800、Os03g0773800）、NADP-MDH（Os08g0562100）、LPD（Os01g0337900）、PDHE1A（Os03g0645100）、D-LDH（Os11g0591600、Os04g0671700）、PK（Os07g0181000、Os10g0571200）及 PEPC（Os01g0208700、Os08g0366000）等基因可能參與能量生成與代謝調節。在 β-丙胺酸代謝途徑中，PS（Os03g0851800）可能透過促進泛酸（pantothenate）及輔酶 A（coenzyme A）生合成，進而維持呼吸作用及脂肪酸代謝相關功能。在精胺酸與脯胺酸代謝途徑中，SPMS（Os07g0408700）、CPA（Os02g0533900）、NOA（Os02g0104700）以及 AAT（Os02g0236000、Os02g0797500）等基因可能參與氧化還原平衡維持及碳氮代謝調控。
研究結果表明，在鹽逆境下，Pokkali 品種的滲透調節和抗氧化活性顯著優於 IR29 品種。由此，研究結果揭示了可能參與水稻耐鹽性調控和功能的潛在基因。

Salt stress is one of the most severe abiotic stresses limiting rice (Oryza sativa L.) productivity worldwide. Excessive salt accumulation disrupts ionic balance, induces osmotic stress, promotes ROS production, and ultimately reduces plant growth and yield. Understanding the molecular mechanisms underlying salinity tolerance is therefore essential for the development of stress-resilient rice cultivars. In this study, a comparative transcriptomic analysis was conducted to investigate the molecular responses of the salt-tolerant rice cultivar Pokkali and the salt-sensitive cultivar IR29 under salt stress. Differentially expressed genes (DEGs) were identified across multiple time points following salt treatment. Pokkali DEGs exposed to salt for 0.5h, 1h, 3h, 6h, 24h, 48h and 72h were 636, 1784, 3192, 4502, 4416, 5190 and 5885 respectively identified. For IR29, the respective time points of total DEGs were 1382, 2337, 4286, 5283, 5262, 5922 and 6916. GO and KEGG enrichment analyses showed that hormone signaling and metabolic pathways related to antioxidative responses and osmotic balance played a vital role in salt tolerance. Early responses were primarily characterized by the enrichment of hormone signaling pathways including abscisic acid (ABA), ethylene, auxin, jasmonic acid (JA), cytokinin, gibberellin (GA), brassinosteroid (BR), and salicylic acid (SA) indicating rapid stress perception and signal transduction as result, significant enrichment of metabolic pathways such as pyruvate metabolism, β-alanine metabolism and, arginine and proline metabolism showed a positive response to salt stress which as associated with energy production, osmotic adjustment, and redox homeostasis. Several genes in pyruvate metabolism including ADH (Os02g0815500 and Os03g0189400), MDH (Os07g0630800 and Os03g0773800), NADP-MDH (Os08g0562100), LPD (Os01g0337900), PDHE1A (Os03g0645100), D-LDH (Os11g0591600 and Os04g0671700), PK (Os07g0181000 and Os10g0571200) and PEPC (Os01g0208700 and Os08g0366000) might play a crucial role for energy production. Genes included in β-alanine metabolism such as PS (Os03g0851800) might play a crucial role in respiration and fatty acid metabolism which may support coenzyme A biosynthesis and thereby contribute to energy metabolism under salt stress. Genes which are involved in arginine and proline metabolism including SPMS (Os07g0408700), CPA (Os02g0533900), NOA (Os02g0104700) and AAT (Os02g0236000 and Os02g0797500) might play a crucial role in redox homeostasis and carbon–nitrogen balance. According to the findings, Pokkali regulated its osmotic and antioxidant activity significantly better than IR29 under salt stress. As a result, highlighted potential genes that may be involved in the regulation and function of rice’s salt tolerance.

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