Root Transcriptome Analysis Identifies Salt-Tolerance Genes in Sweet Corn Chromosome Segment Substitution Lines (CSSLs)

Salt stress severely constrains global crop productivity. However, most sweet corn cultivars exhibit weak tolerance to salt stress. In this study, two sweet corn CSSLs, salt-tolerant line D55 and salt-sensitive line D96, were selected as materials. We conducted comparative phenotyping and physiological profiling of seedlings under salinity treatment, and transcriptome analysis was carried out by sampling root tissues at 0 h, 4 h, 12 h, and 72 h post-treatment. The results indicated that D55 exhibited enhanced seedling height, root length, fresh weight, relative chlorophyll content, and antioxidant enzyme activities, while showing reduced malondialdehyde accumulation in comparison to D96. Pairwise comparisons across time points (0 h, 4 h, 12 h, 72 h) identified 6317 and 6828 differentially expressed genes (DEGs) in D55 and D96. A total of 49 shared DEGs across four time points were identified in D55 and D96, which were enriched in 12 significant Gene Ontology (GO) terms. Only eight DEGs were shared between genotypes across all comparisons. Transcriptomic analysis revealed 1281, 1946, and 1717 DEGs in genotypes D55 and D96 at 4 h, 12 h, and 72 h post-salt treatment, respectively. Genes associated with reactive oxygen species (ROS) homeostasis, phenylpropanoid metabolism, cutin, suberin and wax biosynthesis, and benzoxazinoid synthesis exhibit enhanced sensitivity in the salt-tolerant genotype D55. This leads to an enhanced ROS scavenging capacity and the establishment of a multi-layered defense mechanism. Additionally, brassinosteroid (BR), gibberellin (GA), and abscisic acid (ABA) and auxin-related genes exhibited different responses to salt stress in sweet corn. A hypothetical model, which established a multi-layered salt adaptation strategy, by integrating ROS detoxification, osmotic balance, and phytohormone signaling, was put forward. By integrating transcriptome and differential chromosomal fragment data, our findings identify 14 candidate genes for salt tolerance, providing potential ideal target genes in breeding to improve salt tolerance in sweet corn.