Genomic insights into genome-wide heterozygosity and its impact on walnut adaptive evolution and improvement.

Walnut (Juglans regia L.), an important woody oil plant, is cultivated globally and has a prominent position in the world's major nuts. Heterozygosity enriches plant genetic diversity by providing a wider array of gene combinations, significantly enhancing their adaptability to the environment and consequently improving their survival ability. In this study, we found that the heterozygosity rate was significantly correlated with 21 traits. Heterogeneity rate showed the strongest positive correlation with yield and nutrition, while it showed the most significant negative correlation with tree height and precocity. Among these, 13 traits showed positive correlations, the remaining 8 traits exhibited negative correlations. We conducted an in-depth study on the characteristics of walnut whole-genome heterozygosity. By using the GWAS based on the heterozygosity rate, we successfully identified 11 significant loci and 4 candidate genes. In the analysis of local heterozygosity rate by GWAS, it was found that 63.8% exhibited trans-acting and 36.2% exhibited cis-acting. In addition, with the help of genomic residual heterozygotes, we enriched functional genes from 44 Pfam families related to growth regulation and development. Finally, it is worth mentioning that during the process of walnut improvement, we observed an increase in the heterozygosity rate of genes related to the flowering time. It is speculated that a higher level of whole-genome heterozygosity can enhance the environmental adaptability of plants and improve their growth performance. The results of this study may provide assistance for optimizing the breeding strategies of walnuts.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01572-2.