Comparative Transcriptomics Reveals Novel Spatial Gene Expression Profiles in Cotton (Gossypium hirsutum L.) Under Herbivory and Drought Stress

Cotton is the major natural fiber-producing crop, contributing significantly to the global textile economy. However, the cotton crop encounters several biotic and abiotic stress challenges globally, causing substantial annual yield loss. Plant responses to such diverse stress conditions involve intricate molecular and physiological modifications at the cellular level. Here, we employed a genomics approach to illustrate comprehensive spatial transcriptomic profiles in response to various insect infestations, including aphids (Aphis gossypii), cotton boll weevils (Anthonomus grandis), cotton bollworms (Helicoverpa armigera), whiteflies (Bemisia tabaci), and drought stress. Comparative temporal expression analysis with a strict log-fold change threshold (> 2.0) revealed distinct gene expression patterns in different tissues of cotton plants, with selected pivotal 'stress-general' and 'stress-specific' genes involved in plant defense mechanisms against various infestations and drought conditions. The expression of at least 5 insect-general transcription factor-encoding genes, WRKY28, WRKY40, WRKY53, ERF4, and ERF5, was highly upregulated across cotton leaf tissues infested by aphids, cotton bollworms, and whiteflies. Additionally, a set of highly upregulated 'stress-specific' genes, including GH3.1, ACS1, CYP74A, TIFY10A, BHLH25, ABR1, and ERF025, were identified especially after a 6-h period of cotton bollworm infestation. Similarly, various sets of such 'stress-specific' spatially upregulated genes were identified across diverse insect infestations. Functional annotation of differentially expressed genes revealed the upregulation of various defense-related functions such as stress hormone signal transduction, MAPK signaling pathway, and biosynthesis of secondary metabolites, orchestrating the plant's defense mechanisms. Further, spatiotemporal expression analysis of 'stress-general' genes in response to abiotic stresses revealed that GhWRKY28 was highly upregulated in response to both biotic and abiotic stress conditions. The findings suggested that the identified 'stress-general' genes could serve as suitable candidates for manipulating crops for multiple stress resistance/tolerance.