Transcriptome and metabolome insights into closely related upland cotton (Gossypium hirsutum) genotypes during differing responses to progressive soil drying

Background: Cotton is an important crop worldwide for producing natural fibres for textile, among other uses. Water input for cotton production is tightly linked to yield and ongoing climate changes require purpose-bred cotton genotypes able to be grown productively in water-conservative environments, particularly as most fertile land must be prioritised for food production. Here we investigate metabolome and transcriptome changes in the leaves of two closely related upland cotton (Gossypium hirsutum) genotypes with a differing fraction of transpirable soil water (FTSW) threshold trait, undergoing a progressive soil drying treatment in a controlled environment. Results: We show that gene expression and metabolite changes are present earlier in the genotype with a higher FTSW threshold (early-saver; ES), matching physiology data collected at the same time. There were unique gene expression patterns present in the ES genotype involving upregulation of predicted MEX1 and pGlct-2 genes involved in starch breakdown, as well as lower transcript levels of a predicted cold and drought responsive CORA-like protein. Integration of metabolome and transcriptome showed associations between genes and metabolites in each genotype, notable in ES were multiple aquaporin genes with L-proline, suggesting these may be key players in the higher FTSW-threshold response of cotton to progressive soil-drying. Conclusions: This work contributes to the understanding of genes and metabolites involved in cotton’s response to progressive soil drying and highlights potential differences between high and low FTSW threshold phenotypes. This will provide a basis for further studies to pursue the breeding of cotton genotypes with improved productivity and adaptation to water limited and rainfed production systems.