Prunus zhengheensis, an extremely rare population of apricots, originated in warm South-East China and is an excellent material for genetic breeding. However, most apricots and two related species (P. sibirica, P. mandshurica) are found in the cold northern regions in China and the mechanism of their distribution is still unclear. In addition, the classification status of P. zhengheensis is controversial. Thus, we generated a high-quality haplotype-resolved genome for P. zhengheensis, exploring key genetic variations in its adaptation and the causes of phylogenetic incongruence. We found extensive phylogenetic discordances between the nuclear and organelle phylogenies of P. zhengheensis, which could be explained by incomplete lineage sorting. A 242.22-Mb pan-genome of the Armeniaca section was developed with 13 chromosomal genomes. Importantly, we identified a 566-bp insertion in the promoter of the HSFA1d gene in apricot and showed that the activity of the HSFA1d promoter increased under low temperatures. In addition, HSFA1d overexpression in Arabidopsis thaliana indicated that HSFA1d positively regulated plant growth under chilling. Therefore, we hypothesized that the insertion in the promoter of HSFA1d in apricot improved its low-temperature adaptation, allowing it to thrive in relatively cold locations. The findings help explain the weather adaptability of Armeniaca plants.

ALMT (aluminum-activated malate transporter) proteins play crucial roles in the transport of organic acids and have significant implications for plant stress responses and development. While extensively studied in some plants, the characteristics and functional divergence of the ALMT gene family have not yet been thoroughly explored in Prunus mume and some other Rosaceae species. In this study, we systematically analyzed the ALMT gene family across nine Rosaceae species to explore their evolutionary relationships, structural characteristics, and functional roles. A total of 138 ALMT genes were identified and categorized into four groups based on a phylogenetic analysis. The motif analysis confirmed the accuracy of the phylogenetic grouping. The collinearity analysis indicated that whole-genome duplication events were the primary drivers of ALMT gene expansion in these species. Furthermore, the cis-acting element analysis revealed diverse regulatory elements associated with environmental responses, including abscisic acid, light, and jasmonic acid. The gene expression correlation analysis showed that PmALMT1 is primarily associated with malic acid accumulation, whereas PmALMT8 is related to citric acid accumulation. Further transient expression in Nicotiana benthamiana validated the above conclusion. This comprehensive analysis provides valuable insights into the evolution, function, and regulation of the ALMT gene family in Rosaceae species.

KANADI (KAN) transcription factors are pivotal regulators of lateral organ polarity establishment in plants. Although extensively studied in herbaceous plants, the role of KAN genes in woody plant development remains unclear. This study conducts the first comprehensive analysis of 26 PmKAN genes in Prunus mume, elucidating their evolutionary trajectories, structural configurations, tissue-specific expression patterns and potential roles in root and fruit development. Phylogenetic analysis of four Rosaceae species and Arabidopsis thaliana clustered these PmKANs into five subfamilies, with conserved motif patterns supporting this classification. Chromosomal localization revealed that all PmKAN members are distributed across eight chromosomes, with tandem duplications events and syntenic relationships indicating functional diversification driven by gene family expansion. Cis-regulatory element analysis identified light-responsive, hormone-associated, stress-related, and developmental motifs, suggesting PmKAN genes are involved in regulating plant physiological processes and development. The qRT-PCR analysis revealed tissue-specific expression heterogeneity among PmKAN genes, with markedly elevated expression particularly observed in roots and fruits. Further expression profiling across fruit developmental stages suggests potential stage-specific functional divergence of PmKAN genes during fruit development. This study provides a theoretical foundation for further investigating the evolutionary relationships and molecular regulatory mechanisms of the PmKAN gene family.

Organic acid accumulation is a key determinant of fruit flavor and processing quality in Prunus mume, yet its underlying molecular mechanisms remain poorly understood. P-type ATPases are membrane proteins that drive the active transport of ions and molecules via ATP hydrolysis and play important roles in organic acid accumulation However, their genome-wide features and functions in P. mume remain poorly understood. Here, 49 P-type ATPase genes were identified from the P. mume pan-genome, including 29 core, 6 near-core, 11 dispensable, and 3 private genes, and classified into six subfamilies. Dispersed and whole-genome duplication were the major force driving gene family expansion, and most genes experienced strong negative selection. Expression profiling identified the P3A-type gene PmAHA3 as highly expressed in fruit, with vacuolar membrane localization. Both transient RNAi silencing in fruit and CRISPR/Cas9 knockout in callus significantly reduced the contents of malic and citric acid, demonstrating their roles in organic acid accumulation. These results provide insight into the evolution and function of P-type ATPases, offering potential targets for improving fruit quality.

The aroma and nutrition of Japanese apricot fruit change continuously as the fruit ripens. The differences in fruit aroma and nutrition can affect the resulting wine, which is produced by steeping the Japanese apricot fruit. In this study, we used HS-SPME-GC-MS to examine the aromatic compositions of Japanese apricot fruit and wine produced from its macerated fruit at different levels of ripeness. We employed UPLC to examine the nutritional components such as organic acids, amygdalin, and phenolics to support the identification of the optimal ripening time. The microwave aging technology was also used to treat the steeped mume wine in order to explore the optimal conditions for microwave aging. We found that the optimum aroma period for the ‘Nannong Longxia’ fruit was 81 d after flowering. Furthermore, the changes in the aroma of mume wine after steeping in 65%vol base wine were closer to those of the fruit than those of 42%vol base wine, and the optimum period for the aroma of mume wine after steeping was the same as the fruit. Analysis showed that the optimum nutritional period for the fruit coincided with the optimum aromatic period. The best aromatic and nutritional components of the finished wine were obtained when the fruit was picked 81 days after flowering and the steeped mume wine was made with a 65%vol base wine. Microwave aging technology can significantly increase the proportion of esters in the aroma composition and reduce the content of acids. Among them, 500 W treatment at 50 °C for 80 min had the best effect on improving aroma components. These findings represent a theoretical foundation for exploring the aroma optimum period for Japanese apricot fruit and steeped mume wine, and for determining the optimum harvest periods for production.