Ancient structural variants control sex-specific flowering time morphs in walnuts and hickories

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.

Combined transcriptional and metabolomic analysis of flavonoids in the regulation of female flower bud differentiation in Juglans sigillata Dode

Juglans sigillata Dode is rich in flavonoids, but the low ratio of female to male flower buds limits the development of the J. sigillata industry. While the abundance of flavonoids in J. sigillata is known, whether flavonoids influence female flower bud differentiation has not been reported. In this study, we explored the regulatory mechanisms of gene expression and metabolite accumulation during female flower bud differentiation through integrated transcriptomic and metabolomic analyses. Our findings revealed that flavonoid biosynthesis is a key pathway influencing female flower bud differentiation, with metabolites primarily shifting towards the isoflavonoid, flavone, and flavonol branches. Structural genes such as chalcone synthase, dihydroflavonol 4-reductase, flavonol synthase, and flavonoid 3',5'-hydroxylase were identified as playing crucial regulatory roles. The expression of these genes promoted the accumulation of flavonoids, which in turn influenced female flower bud differentiation by modulating key regulatory genes including Suppressor of Overexpression of Constans1, Constans, Flowering Locus T, and APETALA1. Furthermore, transcription factors (TFs) highly expressed during the physiological differentiation of female flower buds, particularly M-type MADS, WRKY, and MYB, were positively correlated with flavonoid biosynthesis genes, indicating their significant role in the regulation of flavonoid production. These results offer valuable insights into the mechanisms of female flower bud differentiation in J. sigillata and highlight the regulatory role of flavonoids in plant bud differentiation.