Persian walnut is one of the world’s most important nut crops, valued for kernels rich in oil and protein. Xinjiang has long been considered a key region for walnut cultivation and diversity, with many elite Chinese cultivars tracing their background to local germplasm. Yet the region’s walnut resources remain difficult to use efficiently because wild stands, ancient farmer-selected landraces, and modern cultivars preserve different signals of migration, domestication, and local adaptation. Key genes controlling flavor, kernel quality, shell traits, and stress resilience have also remained insufficiently characterized. Based on these challenges, there is a need to conduct in-depth research on the population history and quality-trait genetics of Xinjiang walnuts.
A research team from Tarim University, Henan Agricultural University, the Academy of Agricultural Sciences of Xinjiang Uyghur Autonomous Region, and collaborating institutions published (DOI: 10.1093/hr/uhag082) the study on March 31, 2026 in Horticulture Research. The article reports whole-genome resequencing of 282 walnut accessions, including wild walnuts, ancient Xinjiang landraces, modern cultivars, and outgroup species, to trace genetic divergence and identify loci linked to key quality traits.
The researchers generated sequencing data at an average depth of about 20.1× and identified 11.88 million single nucleotide polymorphisms (SNPs) and 2.88 million insertions and deletions (InDels). Phylogenetic analysis, principal component analysis (PCA), and population-structure analysis separated the accessions into distinct groups. Wild walnuts from Yili formed a unique genetic pool, supporting Yili as an independent center of walnut genetic diversity. In contrast, ancient landraces from Aksu, Kashi, and Hotan were closely related to wild walnuts from the Middle East, suggesting a shared origin and later movement through historical exchange routes. Genome scans using fixation index (FST), reduction of diversity (ROD), and Tajima’s D identified 68 highly differentiated regions spanning 13.95 megabases and containing 1,217 protein-coding genes. These regions were enriched in stress-related pathways, including mitogen-activated protein kinase (MAPK) signaling and cytochrome P450-related processes. Genome-wide association study (GWAS) further linked tannin content to 27 loci, including UDP-glycosyltransferase genes and JruL2x. Oleic acid content was associated with 14 loci, including JrCRK26 and JrRHF2A, with favorable genotypes more common in wild walnuts. For shell thickness, the team functionally validated JrCYP98A2, a gene encoding ferulate 5-hydroxylase, and showed that it affects lignin and cell-wall development in transgenic Arabidopsis thaliana.
The authors said the findings change how Xinjiang walnut germplasm should be understood and used. They said wild Yili walnuts are not simply background material for cultivated varieties, but a distinct reservoir of adaptation, lower genetic load, and useful alleles for improving kernel oil quality. Ancient landraces, meanwhile, preserve the genetic imprint of domestication, regional cultivation, and long-distance exchange. Together, these resources provide complementary value: one offers resilience and hidden diversity, while the other reflects traits shaped by generations of selection in traditional walnut-growing regions.
Application and implications: The study provides practical genomic resources for walnut conservation, molecular breeding, and germplasm management. Wild Yili walnuts may be prioritized as donor material for improving oleic acid content and stress resilience, while ancient landraces can support breeding for flavor and locally adapted horticultural traits. Candidate genes such as JruL2x, JrCRK26, JrRHF2A, and JrCYP98A2 could be developed into markers for marker-assisted selection (MAS) or early screening in breeding populations. More broadly, the work shows how combining evolutionary history with trait mapping can turn underused perennial-fruit resources into precise tools for developing walnut cultivars with better taste, nutrition, shell quality, and climate adaptability.
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References
DOI
10.1093/hr/uhag082
Original Source URL
https://doi.org/10.1093/hr/uhag082
Funding information
This work was supported by grants from the Innovative Development of Key Industries in Southern Xinjiang (2022DB022), the Tianshan Talent Cultivation Program—Young Top-notch Scientific and Technological Talents (2022TSYCCX0120), the Tianchi Talent Project of Xinjiang Uygur—Science and Technology Innovation Leading Talents (2025), the National Natural Science Foundation of China (32160689; U2571220), and the Key R&D Program Projects of Xinjiang Uygur Autonomous Region (2024B02017).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.