Study on the Transcriptome Response of Melon to Aaline—Alkaline Stress

To decipher the molecular response mechanism of melon to saline–alkaline stress, seedlings of the melon cultivar “Xikaixin” were treated with 50 mmol·L−1 mixed solutions of NaCl and NaHCO3 at ratios of 1:1, 1:2, and 2:1 to simulate saline–alkaline stress. Transcriptome sequencing of roots (four biological replicates per group, with each replicate consisting of one pot containing four robust seedlings as the experimental unit) yielded 78.98 Gb of clean data (≥6.02 Gb per sample) with Q30 ≥ 96.61% and genome alignment rates of 97.00–98.02%, identifying 588, 686, and 1107 differentially expressed genes (DEGs) in the 1:1, 1:2, and 2:1 groups, respectively. Notably, the 1:1 treatment—mimicking the natural NaCl:NaHCO3 ratio of saline–alkaline soil in southern Xinjiang—had 588 DEGs with the plant hormone signal transduction pathway as its most significantly enriched pathway, representing the core molecular response of “Xikaixin” to near-natural saline–alkaline stress. DEGs were significantly enriched in 50 pathways categorized into five major classes, with the plant hormone signal transduction pathway showing the highest enrichment across all treatments. A key observation from gene expression patterns is a potential auxin–ABA balance modulation, inferred from the differential expression of annotation-based auxin-related and ABA-related genes/pathways (no direct measurement of hormone levels or signaling was performed): two auxin-related genes (auxin-induced protein gene MELO3C013403 and auxin response factor gene MELO3C004381) were specifically upregulated (≥two fold vs. control) in the high-salt 2:1 group, while ABA-related genes were upregulated and auxin/jasmonic acid/gibberellin-related genes were downregulated in the 1:2 group, indicating a putative cultivar-specific hormone-related gene expression pattern associated with auxin–ABA crosstalk in “Xikaixin” under saline–alkaline stress. In contrast, photosynthesis-antenna protein genes (e.g., MELO3C021567) were significantly downregulated (to 32% of the control) under the 2:1 treatment. RT-qPCR validation confirmed the consistency of these candidate genes’ expression with transcriptomic data. Therefore, melon may respond to saline–alkaline stress by regulating the plant hormone signal transduction (especially auxin–ABA balance), photosynthesis, and carbon metabolism pathways. This study provides novel candidate genes and a theoretical basis for the genetic improvement of saline–alkaline-tolerant melon cultivars, with the unique auxin–ABA balance modulation as a key original contribution.