Global Genomic Diversity of Persian Walnut Reveals A Selective Sweep Underlying Domestication

Persian walnut (Juglans regia L.) is cultivated globally for its large edible nuts, which have a dehiscent hull that simplifies nut harvest and a papery inner shell or septum that allows easy kernel extraction. Here, we use reduced-representation sequencing to genotype the largest panel of J. regia ever assembled (n = 2,850) and evaluate its evolutionary history and population structure. Haplotype length analysis and genome-wide trait association identify a selective sweep on chromosome 14 associated with the hard septum characteristic, providing new insight into the origin and domestication of J. regia . A YABBY transcription factor in the swept region shows exon skipping that causes frame-shift and deletion of the YABBY domain and is enriched in J. regia hull and shell tissues. These results suggest both a mechanism underlying walnut domestication and a blueprint for domesticating other tree nuts in the Juglandaceae .