Comparative transcriptome analysis of genes involved in paradormant bud release response in ‘Summer Black’ grape

Grapevines possess a hierarchy of buds, and the fruitful winter bud forms the foundation of the two-crop-a-year cultivation system, yielding biannual harvests. Throughout its developmental stages, the winter bud sequentially undergoes paradormancy, endodormancy, and ecodormancy to ensure survival in challenging environmental conditions. Releasing the endodormancy of winter bud results in the first crop yield, while breaking the paradormancy of winter bud allows for the second crop harvest. Hydrogen cyanamide serves as an agent to break endodormancy, which counteracting the inhibitory effects of ABA, while H2O2 and ethylene function as signaling molecules in the process of endodormancy release. In the context of breaking paradormancy, common agronomic practices include short pruning and hydrogen cyanamide treatment. However, the mechanism of hydrogen cyanamide contributes to this process remains unknown. This study confirms that hydrogen cyanamide treatment significantly improved both the speed and uniformity of bud sprouting, while short pruning proved to be an effective method for releasing paradormancy until August. This observation highlights the role of apical dominance as a primary inhibitory factor in suppressing the sprouting of paradormant winter bud. Comparative transcriptome analysis revealed that the sixth node winter bud convert to apical tissue following short pruning and established a polar auxin transport canal through the upregulated expression of VvPIN3 and VvTIR1. Moreover, short pruning induced the generation of reactive oxygen species, and wounding, ethylene, and H2O2 collectively acted as stimulating signals and amplified effects through the MAPK cascade. In contrast, hydrogen cyanamide treatment directly disrupted mitochondrial function, resulting in ROS production and an extended efficacy of the growth hormone signaling pathway induction

Integrated Transcriptome and Metabolome Analysis Revealed the Causal Agent of Primary Bud Necrosis in ‘Summer Black’ Grape

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

Comparison among ‘Benitaka’ grape, ABA-treated ‘Benitaka’, and its deeper-colored bud mutation revealed the coloring mechanisms on grapes

To investigate the deeper coloring mechanism of berry, the ‘Benitaka’ (Be) grape, ABA treatment on ‘Benitaka’ (Be (ABA)), and its deeper coloring bud mutation ‘Brasil’ (Br) grape were compared three weeks post-ABA treatment (11 weeks post-flowering, 200 mg/g ABA). Firstly, the ABA-treated group exhibited a deeper coloring at three weeks post-ABA treatment than the ‘Brasil’. Deeper color in ‘Brasil’ was caused by higher content of peonidin-3-O-monoglucoside, malvidin-3-O-monoglucoside, and malvidin-3-O-coumarylglucoside, while the deeper color in ABA-treated group was mainly caused by higher content of cyanidin-3-O-monoglucoside and peonidin-3-O-monoglucoside. In addition, the results revealed that ‘Brasil’ showed deeper coloring than ‘Benitaka’ was probably due to the higher expression of the VvmybA1 and VvmybA1-1 genes, similar with ABA-treated group. Compared with ‘Benitaka’, the distinction between the ABA-treated group and ‘Brasil’ was the expression of VvmybA1 gene. The gene expression was delayed in the ABA-treated group until three weeks post treatment. The VvmybA1 gene and transcription factor play an important role in the anthocyanin biosynthesis, and showed the difference in expressions of the VvmybA1 and VvmybA1-1 gene during different period of time probably due to different kind of anthocyanins. Based on these results, a possible mechanism of anthocyanins biosynthesis was established to elaborate the reason for the deeper coloring in ABA-treated ‘Benitaka’ and ‘Brasil’ grapes

Genome-Wide Detection of SNP and SV Variations to Reveal Early Ripening-Related Genes in Grape.

Early ripening in grape (Vitis vinifera L.) is a crucial agronomic trait. The fruits of the grape line 'Summer Black' (SBBM), which contains a bud mutation, can be harvested approximately one week earlier than the 'Summer Black' (SBC)control. To investigate the molecular mechanism of the bud mutation related to early ripening, we detected genome-wide genetic variations based on re-sequencing. In total, 3,692,777 single nucleotide polymorphisms (SNPs) and 81,223 structure variations (SVs) in the SBC genome and 3,823,464 SNPs and 85,801 SVs in the SBBM genome were detected compared with the reference grape sequence. Of these, 635 SBC-specific genes and 665 SBBM-specific genes were screened. Ripening and colour-associated unigenes with non-synonymous mutations (NS), SVs or frame-shift mutations (F) were analysed. The results showed that 90 unigenes in SBC, 76 unigenes in SBBM and 13 genes that mapped to large fragment indels were filtered. The expression patterns of eight genes were confirmed using quantitative reverse transcription-polymerase chain reaction (qRT-PCR).The re-sequencing data showed that 635 SBC-specific genes and 665 SBBM-specific genes associated with early ripening were screened. Among these, NCED6 expression appears to be related to NCED1 and is involved in ABA biosynthesis in grape, which might play a role in the onset of anthocyanin accumulation. The SEP and ERF genes probably play roles in ethylene response

Study on russet-related enzymatic activity and gene expression in ‘Shine Muscat’ grape treated with GA3 and CPPU

Physiological (metabolite analysis) and molecular (gene expression) approaches were used to understand the mechanism underlying russet formation in response to the application of GA3 and CPPU (Forchlorfenuron) in a Japanese table grape cultivar ‘Shine Muscat’. Several different concentrations of GA3 and GA3 + CPPU [25 mg L−1 GA3 (A), 25 mg L−1 GA3 + 5 mg L−1 CPPU (B), 25 mg L−1 GA3 + 10 mg L−1 CPPU (C), and 25 mg L−1 GA3 + 15 mg L−1 CPPU (D)] were applied to grape berry clusters at two weeks after flowering (WAF). No russet was observed on the berries treated with the ‘C’ combination. Lower levels of phenylalanine ammonia-lyase (PAL) activity was observed in the treated samples, relative to the untreated material. Reduced peroxide (POD) activity was also observed in response to different treatments, while the expression of Peroxidase 17 and Phenylalanine ammonia-lyase G1 genes mirrored lignin content. Increased activity of 4-coenzyme A ligase (4CL) may contribute to decreasing the level of russet and help to improve grape berry quality

Image_3_Comparative transcriptome analysis of genes involved in paradormant bud release response in ‘Summer Black’ grape.jpeg

Grapevines possess a hierarchy of buds, and the fruitful winter bud forms the foundation of the two-crop-a-year cultivation system, yielding biannual harvests. Throughout its developmental stages, the winter bud sequentially undergoes paradormancy, endodormancy, and ecodormancy to ensure survival in challenging environmental conditions. Releasing the endodormancy of winter bud results in the first crop yield, while breaking the paradormancy of winter bud allows for the second crop harvest. Hydrogen cyanamide serves as an agent to break endodormancy, which counteracting the inhibitory effects of ABA, while H2O2 and ethylene function as signaling molecules in the process of endodormancy release. In the context of breaking paradormancy, common agronomic practices include short pruning and hydrogen cyanamide treatment. However, the mechanism of hydrogen cyanamide contributes to this process remains unknown. This study confirms that hydrogen cyanamide treatment significantly improved both the speed and uniformity of bud sprouting, while short pruning proved to be an effective method for releasing paradormancy until August. This observation highlights the role of apical dominance as a primary inhibitory factor in suppressing the sprouting of paradormant winter bud. Comparative transcriptome analysis revealed that the sixth node winter bud convert to apical tissue following short pruning and established a polar auxin transport canal through the upregulated expression of VvPIN3 and VvTIR1. Moreover, short pruning induced the generation of reactive oxygen species, and wounding, ethylene, and H2O2 collectively acted as stimulating signals and amplified effects through the MAPK cascade. In contrast, hydrogen cyanamide treatment directly disrupted mitochondrial function, resulting in ROS production and an extended efficacy of the growth hormone signaling pathway induction.</p

Table_1_Comparative transcriptome analysis of genes involved in paradormant bud release response in ‘Summer Black’ grape.xlsx

Grapevines possess a hierarchy of buds, and the fruitful winter bud forms the foundation of the two-crop-a-year cultivation system, yielding biannual harvests. Throughout its developmental stages, the winter bud sequentially undergoes paradormancy, endodormancy, and ecodormancy to ensure survival in challenging environmental conditions. Releasing the endodormancy of winter bud results in the first crop yield, while breaking the paradormancy of winter bud allows for the second crop harvest. Hydrogen cyanamide serves as an agent to break endodormancy, which counteracting the inhibitory effects of ABA, while H2O2 and ethylene function as signaling molecules in the process of endodormancy release. In the context of breaking paradormancy, common agronomic practices include short pruning and hydrogen cyanamide treatment. However, the mechanism of hydrogen cyanamide contributes to this process remains unknown. This study confirms that hydrogen cyanamide treatment significantly improved both the speed and uniformity of bud sprouting, while short pruning proved to be an effective method for releasing paradormancy until August. This observation highlights the role of apical dominance as a primary inhibitory factor in suppressing the sprouting of paradormant winter bud. Comparative transcriptome analysis revealed that the sixth node winter bud convert to apical tissue following short pruning and established a polar auxin transport canal through the upregulated expression of VvPIN3 and VvTIR1. Moreover, short pruning induced the generation of reactive oxygen species, and wounding, ethylene, and H2O2 collectively acted as stimulating signals and amplified effects through the MAPK cascade. In contrast, hydrogen cyanamide treatment directly disrupted mitochondrial function, resulting in ROS production and an extended efficacy of the growth hormone signaling pathway induction.</p