Introduction: Flavonoids, as secondary metabolites in plants, play important roles in many biological processes and responses to environmental factors.Methods: Apricot fruits are rich in flavonoid compounds, and in this study, we performed a combined metabolomic and transcriptomic analysis of orange flesh (JN) and white flesh (ZS) apricot fruits.Results and discussion: A total of 222 differentially accumulated flavonoids (DAFs) and 15855 differentially expressed genes (DEGs) involved in flavonoid biosynthesis were identified. The biosynthesis of flavonoids in apricot fruit may be regulated by 17 enzyme-encoding genes, namely PAL (2), 4CL (9), C4H (1), HCT (15), C3’H (4), CHS (2), CHI (3), F3H (1), F3’H (CYP75B1) (2), F3’5’H (4), DFR (4), LAR (1), FLS (3), ANS (9), ANR (2), UGT79B1 (6) and CYP81E (2). A structural gene-transcription factor (TF) correlation analysis yielded 3 TFs (2 bHLH, 1 MYB) highly correlated with 2 structural genes. In addition, we obtained 26 candidate genes involved in the biosynthesis of 8 differentially accumulated flavonoids metabolites in ZS by weighted gene coexpression network analysis. The candidate genes and transcription factors identified in this study will provide a highly valuable molecular basis for the in-depth study of flavonoid biosynthesis in apricot fruits.

As the wild progenitor of cultivated apricot, Xinjiang wild apricot is a key resource for ecosystem stability and germplasm conservation. We analyzed its phylogeography in the Ili wild fruit forests using two chloroplast DNA regions ( rpl32‐trnL , ndhC‐trnV ) and one single‐copy nuclear locus (DXH). Genetic variation was mainly within populations, with weak among‐population differentiation. cpDNA and nuclear data showed discordant spatial patterns, indicating different demographic signals from seed‐mediated versus pollen‐mediated processes. cpDNA neutrality and mismatch analyses did not support recent overall expansion and were more consistent with contraction/bottleneck dynamics, although the dominant cpDNA lineage (h4) retained a post‐LGM expansion signal (~19.6 ka). In contrast, DXH supported recent expansion, strongest in the Yining County population. Isolation‐by‐distance was significant for cpDNA but weak and nonsignificant for DXH, consistent with stronger geographic structuring of maternally inherited variation. MaxEnt models identified precipitation in the wettest season (100–135 mm), precipitation in the warmest season (90–120 mm), and soil sand content (6%–38%) as key predictors of distribution. Suitable habitat is currently concentrated in the Ili Kazakh Autonomous Prefecture, with projected expansion under future climate scenarios. These results provide an integrated view of historical demography and contemporary habitat suitability, and offer a basis for conservation planning and sustainable use of Xinjiang wild apricot genetic resources.

Sweet cherry (Prunus avium L.) is a high-value horticultural crop; however, winter freezing injury significantly limits its introduction and stable production in cold-temperate regions. In this study, annual shoots of 16 major sweet cherry cultivars were collected during the dormancy phase and subjected to a simulated low-temperature gradient. Eight physiological indicators, namely, relative electrolyte conductivity (REC), malondialdehyde (MDA) content, osmoregulatory substances, and antioxidant enzyme activities, were systematically measured along with the poststress recovery growth rate (RR). The semilethal temperature (LT₅₀) was calculated using a logistic equation, and a multidimensional comprehensive evaluation system for cold tolerance was constructed using the membership function method, principal component analysis (PCA), and cluster analysis. The results indicated that low-temperature stress significantly induced membrane lipid peroxidation and osmotic compensation in the shoots. PCA revealed four principal components—osmoregulation potential, cell membrane damage threshold, cold-protective protein synthesis, and membrane stability—with a cumulative variance contribution rate of 79.47%. Correlation analysis revealed no significant correlation between LT₅₀ (reflecting thermodynamic survival capacity) and the recovery growth rate (reflecting poststress regenerative capacity), suggesting that “passive endurance” and “active recovery” in sweet cherries are two relatively independent physiological processes. The comprehensive evaluation model classified the 16 cultivars into four cold-tolerance tiers: High Tolerance (Russia 8, Reid, Pacific Red, and Brooks); Moderate-High Tolerance (Tieton, Jiahong, Sandra Rose, and Early Lory); Moderate-Low Tolerance (Luyu, Rocket, Tamara, Lapins, Frisco, and Taisho-nishiki); and Sensitive (Summit and Kordia). The four-dimensional evaluation model developed in this study provides a scientific basis for cultivar selection in cold regions and offers a theoretical reference for the trade-off of traits in future molecular breeding for cold resistance in cherries.

Background: The phylogenetic placement and chloroplast-inferred maternal relationships of commercial pluot cultivars remain unclear, largely because plastome-level evidence is limited for assessing their affinities with Prunus salicina and Prunus ussuriensis. Although chloroplast genome structure has been well characterized in angiosperms and in several Prunus species, complete plastome resources and comparative genomic evidence for commercial pluot cultivars remain scarce. Methods: Here, we assembled the complete chloroplast genomes of six commercial pluot cultivars and performed comparative genomic, phylogenomic, and divergence time analyses using representative Prunus species. Results: All genomes exhibited the typical circular quadripartite structure and ranged from 157,865 to 158,138 bp in length. Genome organization, GC content, and gene content were highly conserved, whereas the IR regions showed an elevated GC content of approximately 42.6%, owing to rRNA gene enrichment. IR boundary comparison revealed contraction at the IRb/SSC boundary in P. ussuriensis, while pluot cultivars were structurally more similar to P. salicina. In total, 370 SSR loci and four hypervariable regions, namely rpoB–trnC-GCA, petN–psbM, trnV-UAC–trnM-CAU, and trnP-UGG–psaJ, were identified as candidate molecular markers for Prunus germplasm identification and genetic analysis. Phylogenomic analysis resolved four major clades within Prunus and showed that ‘Flavor King’, ‘Flavor Supreme’, and ‘Flavor Queen’ grouped with P. ussuriensis, whereas ‘Flavorosa’, ‘Dinosaur Egg’, and ‘Flavorich’ grouped with P. salicina. Conclusion: Overall, this study provides the first comparative plastome analysis of six commercial pluot cultivars and offers chloroplast-level evidence for their maternal affinities within Prunus, together with useful marker resources for cultivar identification and germplasm evaluation.

Sweet cherry (Prunus avium L.) is a high-value horticultural crop; however, winter freezing injury significantly limits its introduction and stable production in cold-temperate regions. In this study, annual shoots of 16 major sweet cherry cultivars were collected during the dormancy phase and subjected to a simulated low-temperature gradient. Eight physiological indicators, namely, relative electrolyte conductivity (REC), malondialdehyde (MDA) content, osmoregulatory substances, and antioxidant enzyme activities, were systematically measured along with the poststress recovery growth percentage (RP). The semilethal temperature (LT₅₀) was calculated using a logistic equation, and a multidimensional comprehensive evaluation system for cold tolerance was constructed using the membership function method, principal component analysis (PCA), and cluster analysis. The results indicated that low-temperature stress significantly induced membrane lipid peroxidation and osmotic compensation in the shoots. PCA revealed four principal components—osmoregulation potential, cell membrane damage threshold, cold-protective protein synthesis, and membrane stability—with a cumulative variance contribution rate of 79.47%. Correlation analysis revealed no significant correlation between LT₅₀ (reflecting thermodynamic survival capacity) and the recovery growth percentage (reflecting poststress regenerative capacity), suggesting that “passive endurance” and “active recovery” in sweet cherries are two relatively independent physiological processes. The comprehensive evaluation model classified the 16 cultivars into four cold-tolerance tiers: High Tolerance (Russia 8, Reid, Pacific Red, and Brooks); Moderate-High Tolerance (Tieton, Jiahong, Sandra Rose, and Rivedel); Moderate-Low Tolerance (Luyu, Rocket, Tamara, Lapins, Frisco, and Taisho-nishiki); and Sensitive (Summit and Kordia). The four-dimensional evaluation model developed in this study provides a scientific basis for cultivar selection in cold regions and offers a theoretical reference for the trade-off of traits in future molecular breeding for cold resistance in cherries.