The Functional and Applied Plant Genomics section in the journal Frontiers in Plant Science chiefly publishes research exploring the mechanism of plant trait improvements under destructive stresses. This Research Topic aims to shed comprehensive light on the mechanism underlying plant responses to stresses at both biological and transcriptional levels. Climate change is one of the most significant threats to current and future global food security, exacerbating destructive stresses and posing severe challenges to agriculture. This includes the reduction and degradation of arable land, loss of plant biodiversity, altesatron of plant traits, and consequent impacts on plant yields. Such consequences have far-reaching effects on global food production and security. In recent times, the rapid development of omics-based technologies, such as transcriptomics and metabolomics, along with functional characterization approaches, has illuminated our understanding of the biological and molecular mechanisms of the plant responses to abiotic stresses such as cold, heat, salinity, and drought. Generating extensive ‘omic data’ is essential to draw a clear vision for plant traits improvement to cope with destructive stresses.