Deciphering crucial salt-responsive genes in Brassica napus via statistical modeling and network analysis on dynamic...

Soil salinization severely impacts crop yields, threatening global food security. Understanding the salt stress response of Brassica napus (B. napus), a vital oilseed crop, is crucial for developing salt-tolerant varieties. This study aims to comprehensively characterize the dynamic transcriptomic response of B. napus seedlings to salt stress, identifying key genes and pathways involved in this process. RNA-sequencing on 43 B. napus seedling samples are performed, including 24 controls and 19 salt-stressed plants, at time points of 0, 1, 3, 6, and 12 h. Differential expression analysis using 33 control experiments (CEs) identified 39,330 differentially expressed genes (DEGs). Principal component analysis (PCA) and a novel penalized logistic regression with k-Shape clustering (PLRKSC) method identify 346 crucial DEGs. GO enrichment, differential co-expression network analysis, and functional validation through B. napus transformation verify the functional roles of the identified DEGs. The analysis reveals highly dynamic and tissue-specific expression patterns of DEGs under salt stress. The identified 346 crucial DEGs include those involved in leaf and root development, stress-responsive transcription factors, and genes associated with the salt overly sensitive (SOS) pathway. Specifically, Overexpression of RD26 (BnaC07g40860D) in B. napus significantly enhances salt tolerance, confirming its role in salt stress response. This study provides a comprehensive understanding of the B. napus salt stress response at the transcriptomic level and identifies key candidate genes, such as RD26, for developing salt-tolerant varieties. The methodologies established can be applied to other omics studies of plant stress responses.