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Background  Common walnut ( Juglans regia  L.) is one of the top four most consumed nuts in the world due to its health benefits and pleasant taste. Despite its economic importance, the evolutionary history and genetic control of its adaptation and agronomic traits remain largely unexplored.    Results  We report a comprehensive walnut genomic variation map based on whole-genome resequencing of 815 walnut accessions. Evolutionary analyses suggest that Chinese  J. regia  diverged from  J. sigillata  with extensive hybridizations after the split of the two species. In contrast to annual crops, the genetic diversity and heterozygous deleterious mutations of Chinese common walnut trees have continued to increase during the improvement process. Selective sweep analyses identify 902 genes uniquely selected in the improved common walnut compared to its progenitor population. Five major-effect loci are identified to be involved in walnut adaptations to temperature, precipitation, and altitude. Genome-wide association studies reveal 27 genomic loci responsible for 18 important agronomic traits, among which  JrFAD2  and  JrANR  are the potentially major-effect causative genes controlling linoleic acid content and color of the endopleura of the nut, respectively.    Conclusions  The largest genomic resource for walnuts to date has been generated and explored in this study, unveiling their evolutionary history and cracking the genetic code for agronomic traits and environmental adaptation of this economically crucial crop tree.    Supplementary Information  The online version contains supplementary material available at 10.1186/s13059-021-02517-6.

A genome variation map provides insights into the genetics of walnut adaptation and agronomic traits