Harnessing polyploidy for climate-resilient crops: Lessons from the evolutionary model, allotetraploid cotton

Escalating pressures of global climate change necessitate developing agricultural systems and crop varieties with enhanced resilience. Polyploidy, the state of possessing multiple complete sets of chromosomes arising from whole genome duplication (WGD), is a major evolutionary force in plants, often conferring novel genetic and regulatory capacities that facilitate adaptation. Allotetraploid cotton (Gossypium spp.), which formed through the merger of distinct A and D subgenomes approximately 1 to 1.6 Mya, is an exemplary model for elucidating polyploid genome evolution and molecular mechanisms underlying stress adaptation. Whereas combining divergent genomes introduces genetic novelty and hybrid vigor, long-term adaptive success and enhanced resilience rely on complex regulatory reprogramming subsequent to the merger event. In cotton, and by extension other polyploids, this reprogramming involves dynamic structural genomic rearrangements, functional diversification of duplicated genes, and pervasive alterations in epigenetic landscapes. These processes reshape transcriptional networks, leading to homoeologous expression bias and novel regulatory interactions. These polyploidy-specific phenomena underpin differential subgenome contributions to key developmental processes and adaptive responses to major abiotic stresses including drought, salinity, and extreme temperature. A comprehensive understanding of these interconnected genetic and epigenetic control mechanisms, the resulting landscape of subgenome coordination or independence, and associated physiological consequences, are essential for designing effective strategies to breed climate-resilient crops. Here, we synthesize current insights from cotton, emphasizing their broader significance for harnessing polyploidy as a tool for future crop improvement amid global environmental change.