Abstract

Cotton roots adopt a stage-specific "growth-defense trade-off" adaptation strategy. • Phenylpropanoid pathway acts as the core hub in cotton root drought resistance. • Multi-omics reveals dynamic phenylpropanoid flux across cotton root genotypes. • Mantel test and GSVA quantified inter-pathway synergistic patterns among genotypes. Cotton ( Gossypium hirsutum L.) is a vital global fiber and oilseed crop, yet its productivity is increasingly threatened by water scarcity. As the primary organ for water uptake and stress perception, the root system is the fundamental determinant of cotton survival and yield under drought; however, the mechanisms of the drought response in cotton roots remain under investigation. We monitored morphological and physiological root changes in three cotton varieties with contrasting drought resistance. Utilizing an integrated multi-omics (transcriptome and metabolome) dataset across multiple stress treatments and developmental stages, we systematically explored their responsive mechanisms and quantified the synergistic metabolic regulatory network using Mantel test and GSVA method. Under mild drought, the highly drought-resistant variety (ZY168) exhibited significant growth, with total root length, volume, and surface area increasing by 63.3%, 38.7%, and 50.3%, respectively. Multi-omics analyses identified the phenylpropanoid biosynthesis pathway as the core drought resistance mechanism, yet its internal dynamic metabolic flux exhibited genotype-specific patterns. Under severe stress, resistant varieties achieved tight coordination between the efficient activation of upstream precursors and the robust catalysis of downstream key enzymes (e.g., CAD, F5H, and POD), driving lignin synthesis and antioxidant defense. Conversely, the sensitive variety suffered a severe metabolic flux bottleneck. Further investigation revealed that the specificity of the drought responses among different genotypes were primarily due to differences in the synergi