To elucidate promoting and inhibiting effects of hydrogen cynamide (HC) and abscisic acid (ABA) on quiescence release of grape buds, physiological and molecular approaches were used to explore the mechanisms of quiescence based on metabolic and gene expression analysis. Physiological and molecular mechanisms involved in bud quiescence of grape were studied before and after application of HC, ABA and ABA-HC. The data showed that ABA inhibited quiescence release in grape buds and attenuated the effect of HC. Bud quiescence was promoted and regulated by HC and ABA pre-treatment on buds of grape cultivar “Shine Muscat” with 5% HC ,100 μM ABA and combination of ABA-HC(5% HC+100 μM ABA) during quiescence under forcing condition. Exogenous application of ABA enhanced the activities of ascorbate peroxidase (APX), peroxidase (POD) and superoxide dismutase (SOD) while activity of catalase (CAT) increased during initial period of forcing and then decreased. The concentration of plant growth hormones including gibberellins (GA) and indole acetic acid (IAA) increased by HC application but decreased the ABA contents under forcing condition. ABA increased the fructose content during quiescence under forcing condition while sucrose and total soluble sugars peaked in HC treated buds as compared to control. Genes related to ABA pathway, protein phosphatase 2C (PP2C family) were down regulated in the buds treated with HC, ABA and ABA-HC as compared to control while two genes related to GA pathway (GID1 family), out of which one gene showed down regulation during initial period of forcing while other gene was up regulated in response to HC and ABA-HC treatments as compared to control. Exogenous ABA application up regulated genes related to antioxidant enzymes as compared to control. The gene probable fructose-bisphosphate aldolase 1, chloroplastic-like, was up regulated in response to ABA treatment as compared to control. Analysis of metabolites and related gene expression pattern would provide a comprehensive view of quiescence after HC, ABA and ABA-HC treatments in grape buds which may helpful for ultimate improvement in table grape production.

DNAs from the cytoplasmic genomes often communicate with the nuclear genome during regulation, development, and evolution. However, the dynamics of cytonuclear interaction during crop domestication have still been rarely investigated. Here, we examine cytonuclear interactions during grapevine domestication using pan‐mitogenome, pan‐plastome, and haplotype‐resolved nuclear genomes, all assembled from long‐read sequences across 33 wild and domesticated grapevine accessions. Structural variation shaped the mitogenomic variation in gene contents, leading to duplications of three specific genes during grapevine domestication (one cox and two rpl genes). Extensive genomic signals of cytonuclear interactions were detected, including a total of 212–431 nuclear–mitochondrial segments (NUMTs) and 95–205 nuclear–plastid segments (NUPTs). These results showed that NUMTs were under strong selection and were more abundant in cultivated grapes, whereas NUPTs dominated in wild grapes, indicating the evolutionary trajectories of cytonuclear interactions during grape domestication. Through Genome‐Wide Association Study (GWAS), we identified 84 candidate genes associated with mitochondrial–nuclear genome interactions. Among these, the PFD1 gene acts as a signaling regulator, modulating specific signaling pathways regulated by the mitochondria. Interestingly, there are significantly more cytonuclear interaction genes near NUMTs than in other genomic regions, suggesting NUMT‐mediated interactions between the nuclear and mitochondrial genomes. Overall, our study provides evidence that NUMTs promote cytonuclear interaction during grapevine domestication, offering new insight into the impact of cytonuclear interactions on plant evolution, genetics, and breeding.

Primary bud necrosis of grape buds is a physiological disorder that leads to decreased berry yield and has a catastrophic impact on the double cropping system in sub-tropical areas. The pathogenic mechanisms and potential solutions remain unknown. In this study, the progression and irreversibility patterns of primary bud necrosis in ‘Summer Black’ were examined via staining and transmission electron microscopy observation. Primary bud necrosis was initiated at 60 days after bud break and was characterized by plasmolysis, mitochondrial swelling, and severe damage to other organelles. To reveal the underlying regulatory networks, winter buds were collected during primary bud necrosis progression for integrated transcriptome and metabolome analysis. The accumulation of reactive oxygen species and subsequent signaling cascades disrupted the regulation systems for cellular protein quality. ROS cascade reactions were related to mitochondrial stress that can lead to mitochondrial dysfunction, lipid peroxidation causing damage to membrane structure, and endoplasmic reticulum stress leading to misfolded protein aggregates. All these factors ultimately resulted in primary bud necrosis. Visible tissue browning was associated with the oxidation and decreased levels of flavonoids during primary bud necrosis, while the products of polyunsaturated fatty acids and stilbenes exhibited an increasing trend, leading to a shift in carbon flow from flavonoids to stilbene. Increased ethylene may be closely related to primary bud necrosis, while auxin accelerated cell growth and alleviated necrosis by co-chaperone VvP23-regulated redistribution of auxin in meristem cells. Altogether, this study provides important clues for further study on primary bud necrosis.

The most common bud sport trait in grapevines is the change in color of grape berry skin, and the color of grapes is mainly developed by the composition and accumulation of anthocyanins. Many studies have shown that MYBA is a key gene regulates the initiation of bud sport color and anthocyanin synthesis in grape peels. In the current study, we used berry skins of ‘Italia’, ‘Benitaka’, ‘Muscat of Alexandria’, ‘Flame Muscat’, ‘Rosario Bianco’, ‘Rosario Rosso’, and ‘Red Rosario’ at the véraison stage (10 weeks post-flowering and 11 weeks post-flowering) as research materials. The relative expressions of genes related to grape berry bud sport skin color were evaluated utilizing RNA-Seq technology. The results revealed that the expressions of the VvMYBA1/A2 gene in the three red grape varieties at the véraison stage were higher than in the three white grape varieties. The VvMYBA1/A2 gene is known to be associated with UFGT in the anthocyanin synthesis pathway. According to the results, VvMYBA1/A2 gene expression could also be associated with the expression of LDOX. In addition, a single gene (gene ID: Vitvi19g01871) displayed the highest expressions in all the samples at the véraison stage for the six varieties. The expression of this gene was much higher in the three green varieties compared to the three red ones. GO molecular function annotation identified it as a putative metallothionein-like protein with the ability to regulate the binding of copper ions to zinc ions and the role of maintaining the internal stable state of copper ions at the cellular level. High expression levels of this screened gene may play an important role in bud sport color of grape berry skin at the véraison stage.

Anthocyanins and proanthocyanidins are considered to be essential secondary metabolites in grapes and are used to regulate metabolic processes, while miRNAs are involved in their synthesis of anthocyanins and proanthocyanidins to regulate metabolic processes. The present research work was carried out to investigate the underlying regulatory mechanism of target genes in the grape cultivars ‘Italia’ and ‘Benitaka’. miRNA and transnscriptomic sequencing technology were employed to characterize both the profiles of miRNAs and the transcripts of grape peels at 10 and 11 weeks post flowering (10 wpf and 11 wpf). The results revealed that the expression level of vvi-miR828a in ‘Italia’ at 10 and 11 wpf was significantly higher than that in ‘Benitaka’. miRNA-seq analysis predicted MYBPA1 to be the target gene of vvi-miR828a. In transcriptome analysis, the expression level of the VvMYBPA1 gene in ‘Benitaka’ was significantly higher than that in ‘Italia’; in addition, the TPM values (expression levels) of VvMYBPA1 and miR828a also showed an evident negative correlation. The determination of the proanthocyanidin (PA) content in ‘Italia’ and ‘Benitaka’ peels at 11 wpf demonstrated that the PA content of ‘Benitaka’ was significantly higher than that of ‘Italia’. The outcomes of RT-qRCR analysis exhibited that the expression levels of the VdPAL, VdCHS, VdCHI, VdDFR, VdMYB5b, VdANR, and VdMYBPA1 genes related anthocyanin and proanthocyanidin pathways were reduced, while the expression levels of all of the above genes were increased after the transient expression of the VvMYBPA1 vector into grape leaves. The results of the transient overexpression experiment of vvi-miR828a before the veraison period of strawberry fruits showed that vvi-miR828a can significantly slow down the coloration of strawberries. The vvi-miR828a negatively regulates the accumulation of proanthocyanidins in grape fruits by inhibiting the expression of VvMYBPA1.