Identification of candidate genes in QTL regions for biochemical traits underlying salt response in bread wheat (Triticum aestivum L.) at the seedling stage

Salinity stress is a major environmental constraint limiting wheat (Triticum aestivum L.) production, highlighting the need for developing salt-tolerant varieties. This study aims to identify genes and molecular mechanisms underlying salinity tolerance, which play a crucial role in molecular breeding and genetic enhancement of wheat. A total of 186 F₁₂ recombinant inbred lines (RILs) were evaluated to identify quantitative trait loci (QTLs) associated with biochemical traits at the seedling stage under salt stress conditions. Composite interval mapping (CIM) analysis identified 21 QTLs linked to antioxidant activity, total protein content, and proline levels. These QTLs were distributed across chromosomes 1A1, 4A, 1B, 2B1, 2B2, 2B3, 3B, 5B1, 6B1, 6B2, 1D and 2D. Gene ontology (GO) enrichment analysis analyzed candidate genes within the identified QTLs. In total, 10,976 candidate genes (CGs) were classified into 99 GO terms, including 59 terms related to biological processes. By prioritizing candidate genes, we identified 236 genes associated with key biological processes, including defense response, glycolysis, oxidative stress response, peroxidase activity, wound response, L-phenylalanine catabolism, hydrogen peroxide catabolism, antioxidant activity, and metabolic pathways, among others. This comprehensive approach provides new insights into the genetic basis of salinity tolerance and facilitates the identification of candidate genes associated with QTLs for future breeding programs.