Integrating transcriptome and target metabolome variability in doubled haploids of Allium cepa for abiotic stress protection

Environmental stress conditions such as drought, heat, salinity, or pathogen infection can have a devastating impact on plant growth and yield, resulting in a need for stress-tolerant crop varieties. Crossbreeding tropical and cultivated onion species produced a hybrid F₁ generation possessing genetic and metabolic parental properties that aided abiotic stress tolerance. Targeted metabolite profiling using liquid chromatography–tandem mass spectrometry integrated with transcriptional analysis of their relevant genes provided insights into the metabolic and genomic architecture of the onion doubled haploid (Allium cepa L., DHC), shallot doubled haploid (A. cepa L. Aggregatum group, DHA), and F₁ hybrid. Out of a complete set of 113 targeted metabolites, 49 metabolites were found to be statistically significantly different between genotypes: 11 metabolites were characteristic for DHC, 10 for DHA, 14 for F₁, and 14 metabolites were shared among the three genotypes. Several key genes and metabolites introgressed in abiotic stress response were up-regulated in DHA and F₁ genotypes as compared to DHC. Principal component analysis and Volcano plot analysis revealed that metabolic traits and their relevant genes (namely, amino acid, carbohydrate, flavonoid, and phospholipid biosynthesis) were strongly linked with DHA and F₁, reflecting the adaptability of DHA and F₁ toward abiotic stress as compared to DHC.