Elucidating the genetic architecture of key quality traits and understanding population differentiation in walnut (Juglans regia) are critical for advancing molecular breeding and enhancing environmental adaptability. In this study, we performed whole-genome resequencing of 282 representative walnut accessions encompassing wild populations, ancient landraces, and modern cultivars. Walnuts in Xinjiang exhibit clear genetic differentiation and can be categorized into two main groups: wild walnuts from Yili and ancient landraces from Aksu, Kashi, and Hotan. The Yili region in northern Xinjiang, China, represents an independent center of walnut genetic diversity. In contrast, the ancient landraces and cultivated walnuts from other regions of Xinjiang are closely related to wild walnuts from the Middle East, suggesting a shared origin. Analysis of deleterious mutations uncovered contrasting accumulation patterns between Wild-Yili_China and Ancient Landrace-Xinjiang_China groups, likely shaped by demographic history and local environmental adaptation. Genome-wide association studies (GWAS) identified key loci and candidate genes, including JruL2x, JrCRK26, and JrRHF2A, that are associated with important quality traits. Furthermore, we functionally validated JrCYP98A2, which encodes a ferulate 5-hydroxylase, as a regulator of shell thickness. Together, these findings provide insights into walnut domestication and the genetic basis of quality trait variation, offering valuable genomic resources for future molecular breeding and genetic improvement of walnut.

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