More than 80% of the earth biosphere is permanently or seasonally subjected to temperatures below 5ºC, which determine the geographical locations suitable for growing crop and horticultural plants and periodically account for significant losses in plant productivity. It is therefore of great importance to understand how plants survive and grow under low-temperature stress. We recently discovered that the model plant Arabidopsis thaliana (Arabidopsis), conventionally classified as a chilling-resistant plant, has a chilling-sensitive root stem cell niche highly prone to DNA damage and DNA damage-induced cell death when exposed to low non-freezing temperatures. This finding provides us a unique opportunity to identify and to study, at spatial and temporal resolutions, developmental and physiological responses that help shape cold adaptation and survival strategies in plants. Most importantly, we have now an excellent cell-level model to investigate specialized responses of the stem cell niche to chilling injury. The wide distribution of Arabidopsis accessions in northern hemisphere makes our model particularly suited for genetic dissection of complex molecular variation that has underpinned the successful adaptation of plant stem cells to cold environments. The complexity of gene-trait associations can be further characterized in crop species and across kingdoms, from molecular to ecosystem level.