In
the current era of global climate change, environmental stresses,
especially drought and salt, have impaired the growth and productivity
of crops, e.g., cotton. Understanding the mechanisms of plants’
adaptation to these abiotic stresses is crucial to breed stress-tolerant
crop species. In the present study, integrated metabolomics, lipidomics,
and mass spectrometry imaging (MSI) were used to discover the spatial
distribution of differential metabolites and lipids in two cottonseed
cultivars with contrasting drought and salt tolerance properties.
Seventeen differential metabolites and 125 differential lipids were
identified. Their possible roles in augmenting stress tolerance were
illustrated, which were involved in reactive oxygen species scavenging,
osmotic adjustment, and cell membrane structure reconstruction. MSI
analysis provided a visualization of nine differential lipids and
four differential metabolites in cottonseeds with varied abundances
and distributions. The results may help understand cottonseeds’
convictive metabolic and lipidomic regulatory networks in coping with
salinity and drought stresses and give new insights into the stress-tolerance
traits relevant to other crops.