Abstract
Commercial crop varieties (cultivars) have a narrow genetic diversity that makes them vulnerable to climate change. Yet most crops have related semi-domesticated varieties (landraces) and wild relatives that thrive under climates that would be considered extreme for cultivars. The genomes of such varieties are reservoirs of unknown adaptive traits, some of which could be used to extend the climatic tolerance of cultivars. To shed light on these traits, we built a genomic database of fourteen crop types, including landraces and wild relatives of staple crops. This database included individual-level genomic data for plants from over 3,000 locations worldwide. Leveraging remote sensing and climatic models, we reconstructed bioclimatic conditions, soil types, and human disturbance for each of these locations. Genes whose geographic variation correlates with an environmental gradient are potentially implicated in local adaptation; if the same gene repeatedly shows this association in different crops, its adaptive role is more likely. We found 16 groups of genes showing such repeated environmental associations, mainly linked to water availability and cold-season temperature. For some of these genes, the same climate association was observed in 6, 7, or even up to 13 crop types. Using A. thaliana as a reference, we found that many of these genes likely encode proteins already well known to regulate cellular responses to drought and cold stress. Our findings suggest that natural variation in these genes can enhance such responses, and that such variation exists in landraces and wild relatives of different crops. If validated, this finding could open new avenues to make cultivars more climate-tolerant via genomic-guided breeding.