Ta-Na Wuyun

Camellia hainanica is an endemic woody oil species from Hainan Island, but the phenotypic and genomic bases of its agronomic and ornamental variation remain poorly understood. Here, 31 phenotypic traits were evaluated in 100 accessions from Changjiang, Hainan, and flower-diameter variation guided the selection of 30 accessions for whole-genome resequencing and genome-wide association analysis. Coefficients of variation ranged from 8.81% to 56.85%, with flower density and first-branch height showing the greatest variation. Cluster analysis separated five groups with contrasting phenotypic characteristics, including groups characterized by large fruits and thick pericarps and ornamental groups characterized by dense flowering and large flowers. Flow cytometry classified the 30 selected accessions as decaploid, and resequencing showed that most variants occurred in non-coding regions. Genome-wide association analysis identified 9 significant SNPs (−log10(P) > 8.63) associated with petal number, flower diameter, locule number, and flower density (3, 1, 3, and 2 SNPs, respectively), including a flower-diameter signal on GWHERBT00000039 and signals on GWHERBT00000008 and GWHERBT00000036. These results integrate phenotypic and genomic evidence for C. hainanica and provide germplasm resources and preliminary candidate regions for further validation and ornamental improvement alongside fruit-trait evaluation.

Tubulins are essential cytoskeletal components involved in plant cell division and expansion, yet their evolutionary dynamics across plant lineages and potential roles in horticultural seed/kernel development remain insufficiently understood. Here, we identified 2535 tubulin-related genes from 97 plant genomes and performed an integrated phylogenomic analysis. Phylogenetic and synteny network analyses resolved four ancient clades, including α-, β-,γ-tubulin and FtsZ, all of which were predominantly subjected to purifying selection. The α- and β-tubulin subfamilies exhibited lineage-specific expansion in angiosperms, particularly in eudicots, and these expansions were associated with ancient WGD and WGT events while retaining relatively conserved chromosomal contexts. By employing a pyramid-structured microsynteny framework across 12 Rosaceae genomes, we further traced the orthologous conservation and lineage-specific rearrangements of tubulin loci, with Prunus armeniaca as a reference. Spatiotemporal transcriptome profiling of Siberian apricot and kernel apricot revealed a group of tubulin genes highly expressed during key stages of kernel development, highlighting PaTUA1 as a priority candidate gene. Transient overexpression of PaTUA1 in wounded developing apricot kernels was associated with short-term increases in average phytohormone concentrations, including IAA, GA₃, BR, and cytokinins. Together, these results suggest that PaTUA1 represents a promising candidate gene associated with hormone-related responses during apricot kernel development, providing a basis for future functional validation rather than direct evidence of kernel-size determination.

The APETALA2/Ethylene Responsive Factor (AP2/ERF transcription factor) family plays pivotal roles in plant growth, stress responses, and metabolic regulation. Here, we identified 118 AP2/ERF family members in the apricot (Prunus armeniaca L.) genome, which were classified into four major subfamilies (AP2, DREB, ERF, and RAV) and Soloists (few unclassified factors), through phylogenetic analysis. The ERF subfamily exhibited the largest expansion (55 members), driven predominantly by 10 tandem and 14 segmental duplication events. Gene structures and conserved motifs exhibited similar patterns within each subfamily. Chromosomal distribution was uneven, with chromosome 1 harboring the highest gene density. PaWRI1 was specifically expressed in apricot kernel and positively correlated with oil accumulation. A total of 47 lipid-related genes were predicted as potential targets of PaWRI1 through correlation analysis, which covers the entire three-stage process of plant oil synthesis. These results advance our understanding of how core AP2/ERF transcription factors modulate oil accumulation pathways in apricot, offering potential targets for metabolic engineering.

Studying the evolutionary history of plants in the Qinghai-Tibetan Plateau region provides a theoretical basis for the conservation and use of plant genetic resources. In this study, we analyzed five chloroplast gene fragments to examine the genetic diversity and phylogeography of Prunus mira in 577 individuals from 32 populations. The results indicated that P. mira populations exhibit high genetic diversity and significant phylogeographic structure (NST > GST). High genetic differentiation (FST = 0.979) and limited gene flow were detected among populations, likely due to geographic isolation. Neutrality tests and mismatch analysis indicated that the P. mira population has not experienced significant expansion during the historical period and remains relatively stable. Additionally, based on haplotype distribution and genetic diversity levels, we propose that P. mira had three refugia during the glacial period. Considering the genetic diversity of P. mira populations, we propose dividing all populations into two conservation units and prioritizing in situ conservation of populations with high genetic diversity within each unit. Furthermore, ex situ conservation of specific populations could prevent the loss of unique genes, such as those in populations with low genetic diversity but distinct haplotypes.

The nuclear factor Y (NF-Y) gene family plays important roles in regulating many of the biological processes of plants, including oil accumulation. The apricot (Prunus armeniaca) is one of the most commercially traded plants, and apricot kernel oil has a high nutritional value owing to its richness in fatty acids and bioactive compounds. However, the systematic characterization of the PaNF-Y family in the apricot and the underlying regulatory mechanisms involved in oil biosynthesis remain unclear. In this study, a total of 28 PaNF-Y members from the apricot genome were identified and divided into three subfamilies (6 PaNF-YAs, 15 PaNF-YBs, and 7 PaNF-YCs) based on phylogenetic analysis results. The types and distributions of the gene structures and conserved motifs were similar in the clustered PaNF-Ys of the same subfamily. Gene duplication analysis results revealed that segmental duplication events were important for the expansion of the PaNF-Y family. Importantly, transcriptome data analysis results showed that most genes of the PaNF-YA subfamily and PaNF-YB4 of the PaNF-YB subfamily were specifically expressed in the apricot kernel. Furthermore, highly positive correlations were observed between apricot oil content and the transcript levels of PaNF-YA2, PaNF-YA6, and PaNF-YB4. In conclusion, our results provide insights into the molecular mechanisms of the key PaNF-Y genes regulating apricot oil biosynthesis.

Fruit color affects its commercial value. β-carotene is the pigment that provides color for many fruits and vegetables. However, the molecular mechanism of β-carotene metabolism during apricot ripening is largely unknown. Here, we investigated whether β-carotene content affects apricot fruit color. First, the differences in β-carotene content between orange apricot ‘JTY’ and white apricot ‘X15’ during nine developmental stages (S1–S9) were compared. β-carotene contents highly significantly differed between ‘JTY’ and ‘X15’ from S5 (color transition stage) onwards. Whole-transcriptome analysis showed that the β-carotene synthesis genes 15-cis-phytoene desaturase (PaPDS) and 15-cis-phytoene synthase (PaPSY) significantly differed between the two cultivars during the color transition stage. There was a 5 bp deletion in exon 11 of PaPDS in ‘X15’, which led to early termination of amino acid translation. Gene overexpression and virus-induced silencing analysis showed that truncated PaPDS disrupted the β-carotene biosynthesis pathway in apricot pulp, resulting in decreased β-carotene content and a white phenotype. Furthermore, virus-induced silencing analysis showed that PaPSY was also a key gene in β-carotene biosynthesis. These findings provide new insights into the molecular regulation of apricot carotenoids and provide a theoretical reference for breeding new cultivars of apricot.

Prunasin and amygdalin are important factors that influence the kernel taste of apricots, however, the regulatory mechanisms underlying this are unclear. In this study, we analyzed the phenotype and transcriptome of kernels during development in Prunus sibirica (bitter kernels) and Prunus armeniaca × Prunus sibirica (kernel consumption apricot, sweet kernels). Prunasin and amygdalin content was significantly higher in bitter kernels compared with that in sweet kernels. Prunasin content exhibited a decreasing trend in both bitter and sweet kernels. The fastest decline was observed in bitter and sweet kernels during S3–S4 (82.21%) and S2–S3 (59.65%), respectively. The amygdalin content in the bitter kernels exhibited the fastest increase between 45–60 d after flowering, and reached a peak at 6.22% on 60 d after flowering. In contrast, the peak in sweet kernels occurred at 60 d after flowering, with a much lower content of 0.18%. Transcriptome analysis revealed 6,942 differentially expressed genes (DEGs), with a subset of 38 DEGs specifically enriched in the cyanoamino acid metabolic pathway. Among these, the ten candidate genes, including CYP79, CYP71, UGT1, AH, and PH, were identified as crucial in regulating prunasin and amygdalin metabolism. Furthermore, a weighted gene co-expression network analysis (WGCNA) unveiled two modules that exhibited significant correlation with prunasin and amygdalin content. Five DEGs were located at the center of the co-expression network, and were identified as hub genes, with four positively regulating prunasin content and one negatively regulating amygdalin content. Our results provide novel insights into the molecular-level regulation of the apricot kernel taste.

The apricot (Prunus armeniaca L.) is a fruit that belongs to the Rosaceae family; it has a unique flavor and is of important economic and nutritional value. The composition and content of soluble sugars and organic acids in fruit are key factors in determining the flavor quality. However, the molecular mechanism of sugar and acid accumulation in apricots remains unclear. We measured sucrose, fructose, glucose, sorbitol, starch, malate, citric acid, titratable acid, and pH, and investigated the transcriptome profiles of three apricots (the high-sugar cultivar ‘Shushanggan’, common-sugar cultivar ‘Sungold’, and low-sugar cultivar ‘F43’) at three distinct developmental phases. The findings indicated that ‘Shushanggan’ accumulates a greater amount of sucrose, glucose, fructose, and sorbitol, and less citric acid and titratable acid, resulting in a better flavor; ‘Sungold’ mainly accumulates more sucrose and less citric acid and starch for the second flavor; and ‘F43’ mainly accumulates more titratable acid, citric acid, and starch for a lesser degree of sweetness. We investigated the DEGs associated with the starch and sucrose metabolism pathways, citrate cycle pathway, glycolysis pathway, and a handful of sugar transporter proteins, which were considered to be important regulators of sugar and acid accumulation. Additionally, an analysis of the co-expression network of weighted genes unveiled a robust correlation between the brown module and sucrose, glucose, and fructose, with VIP being identified as a hub gene that interacted with four sugar transporter proteins (SLC35B3, SLC32A, SLC2A8, and SLC2A13), as well as three structural genes for sugar and acid metabolism (MUR3, E3.2.1.67, and CSLD). Furthermore, we found some lncRNAs and miRNAs that regulate these genes. Our findings provide clues to the functional genes related to sugar metabolism, and lay the foundation for the selection and cultivation of high-sugar apricots in the future.