The texture of fresh jujube fruit is related to its popularity and commercial value. The metabolic networks and essential genes that regulate the texture of jujube (Ziziphus jujuba) fruit are still unknown. In this study, two jujube cultivars with significantly different textures were selected by a texture analyzer. The four developmental stages of the exocarp and mesocarp of jujube fruit were studied separately using metabolomic and transcriptomic analyses. Differentially accumulated metabolites were enriched in several critical pathways related to cell wall substance synthesis and metabolism. Transcriptome analysis confirmed this by finding enriched differential expression genes in these pathways. Combined analysis showed that ‘Galactose metabolism’ was the most overlapping pathway in two omics. Genes such as β-Gal, MYB and DOF may affect fruit texture by regulating cell wall substances. Overall, this study provides an essential reference for the establishment of texture-related metabolic and gene networks of jujube fruit.

The genetic efficiency of seed orchards is crucial for determining seed crops’ genetic gain and diversity. Platycladus orientalis is a conifer tree of important ecological value in China. Here, we assessed the reproductive output (fertility) variation for 166 clones in a first-generation P. orientalis seed orchard over five years and across three years for each gender (female: 2017, 2018, and 2020 and male: 2017, 2019, and 2021). Fertility variation and genetic diversity parameters were estimated for each gender-year combination. The reproductive output (fertility) variation differed among years, provinces, clones nested within provinces, and ramets within clones. We observed asymmetry in the gender reproductive output and parental imbalance and determined their profound effects on the genetic diversity of these seed crops. The maleness index revealed the existence of female-biased or male-biased clones. When seeds from multiple individuals and years were blended, we found an increase in the effective number of parents (N_p) and in genetic diversity (GD), and a reduced fertility variation (Ψ) in the seed orchard. When we set the effective number of parents (N_p) to 30, the GD of the seed orchard could be maintained at more than 95%. Thus, achieving genetic diversity balance in seed production can be accomplished through monitoring the fertility variation of orchards and through the utilization of the thereby generated information for the advanced generation of seed orchards.

The selection of unique and individual-specific SNPs is important as compared with universal SNPs for individual identification. Therefore, the main significance of this research is the selection of specific SNPs in male parent and the identification of offspring with these specific SNPs in their genome by multiplex PCR, which is utilized for genotyping of 332 half-sib plants of Ziziphus jujuba.This cost-effective method makes as much as possible to utilize the same amount of each pair of various targeted loci primers. After PCR amplification of targeted genome parts, the mixed products can be directly used in a next-generation sequencing platform. We concomitantly amplified 10 unique SNP loci at 10 different chromosomes of male JingZao 39 plants in 332 half-sib plants and sequenced them on the Illumina Novaseq 6000 platform. Analysis of SNP genotyping accuracy of 332 half-sib plants showed that all 10 unique SNPs in all 332 plants were correctly amplified in this multiplex PCR method. Furthermore, based on Mendelian inheritance, we identified 124 full-sib plants that have 10 unique SNPs in their genomes. These results were further confirmed by whole genome resequencing of 82 randomly selected half-sib plants, and the identity-by-descent values of all full-sib plants were between 0.4399 to 0.5652. This study displayed a cost-effective multiplex PCR method and proper identification of pollen parent through specific SNPs in half-sib progenies and firstly obtained a full-sib population between ‘Wuhezao’ and ‘JingZao 39’, segregating for stone and stoneless fruit.

Ehretia macrophylla fruit is a traditionally used but underutilized functional resource that is noted for its diverse phytochemical composition, which includes flavonoids and polyphenols. However, the systematic metabolic transformations that occur in the fruit during post-harvest storage—particularly those associated with its traditional processing into dark fruit tea—remain largely unknown, limiting efforts to optimize quality and processing strategies. In the study, to address this gap, we employed a widely targeted metabolomics approach based on ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS) to dynamically profile the fruit metabolome across four storage stages (T0, T4, T8, T12). A total of 1101 metabolites were putatively annotated, and day 8 (T8) emerged as a potential pronounced metabolic inflection point. From T8 onward, 30–40% of metabolites showed differential accumulation, characterized by a gradual rise in nutrition-relevant lipids, amino acids, and vitamins. In contrast, key antioxidant-related metabolites, including phenolics and flavonoids, increased transiently before T8 but declined sharply thereafter. These coordinated shifts correlated with an increased representation of lipid- and alkaloid-related metabolic pathways, whereas flavonoid-associated features showed a relative decline. Collectively, these findings provide insights into the biochemical processes potentially associated with fruit blackening and the marked decline in antioxidant capacity during traditional processing. Our study provides the first metabolic blueprint connecting traditional processing practices with phased metabolic remodeling, offering a scientific foundation for quality assessment and the development of informed post-harvest strategies for processing E. macrophylla fruit.