Plants are continuously exposed to environmental fluctuations and as such have the ability to sense changes in their environment and respond accordingly in terms of their growth, physiology and development. Although agronomic traits in crops often appear at later growth stages, it is becoming increasingly apparent that they are influenced by cumulative effects on crop-environment interactions endured throughout the life cycle of the plant. Therefore, an understanding of this relationship is important for gaining deeper insight into crop-environment interactions to help facilitate breeding of climate-resilient crop varieties. This Special Focus Issue organized by Takashi Hirayama, Alex Lipka and Keiichi Mochida highlights new strategies to help understand plant-environment interactions in various crop species (see editorial on pp. 1381–1383).