Zonghuan Ma

Clonal selection is essential for adapting wine production to specific terroirs. To characterize clonal variation in berry quality, five ‘Merlot’ clones (M343, VCR1, VCR3, VCR13, and VCR101) grown in the Hexi Corridor region of Gansu Province, China, were evaluated during the 2024 growing season. An integrated analysis of morphological, physicochemical, phenolic, metabolomic, and volatile traits was conducted to provide a multidimensional assessment of clone-specific berry quality under the arid conditions of this region. VCR1 exhibited the highest total soluble solids and anthocyanin contents, alongside the largest number of annotated metabolites. VCR101 had the highest titratable acidity and the most diverse flavonoid profile, whereas VCR13 showed the highest total soluble sugar content. VCR3 had the highest tannin and total phenolic contents and also exhibited the greatest number and total semi-quantitative relative abundance of volatile compounds. These findings demonstrate that, under arid conditions, the clones differ in their accumulation patterns of sugars, organic acids, phenolics, and aroma-related metabolites. Exploratory principal component analysis identified VCR3 and VCR1 as promising candidates for production objectives emphasizing different quality attributes. These findings provide practical information for clonal selection, germplasm evaluation, wine grape breeding, and region-specific cultivation under arid environmental conditions.

The calcium ion-transporting ATPase (Ca²⁺-ATPase) gene family maintains plant intracellular Ca²⁺ homeostasis and regulates growth, development and stress immunity; however, its functions remain poorly characterized in Malus domestica. Here, we performed a genome-wide identification of apple Ca²⁺-ATPase genes and obtained 45 members, which were classified into MdACA (39) and MdECA (6) subfamilies and unevenly distributed on 14 chromosomes. Phylogenetic analysis of Ca²⁺-ATPase genes from Malus domestica, Arabidopsis thaliana, and Oryza sativa classified these proteins into five subgroups. The ACA and ECA subfamilies were highly conserved across species, whereas Group D was apple-specific. Collinearity and Ka/Ks analyses indicated that segmental duplication and purifying selection dominated the evolution of apple Ca²⁺-ATPase genes. Promoter cis-element prediction uncovered numerous regulatory elements related to phytohormone signaling, growth, development and stress defense. Codon usage bias analysis indicated that AUG (methionine) was the dominant codon. Tissue expression profiles showed differential expression of apple Ca²⁺-ATPase genes in various organs. Quantitative real-time PCR (qRT-PCR) assays demonstrated widespread responses of Ca²⁺-ATPase genes to Alternaria alternata infection, exogenous CaCl₂, salicylic acid (SA) and methyl jasmonate (MeJA), among which MdACA39 was strongly induced under all treatments. Subcellular localization verified that MdACA39 resides on the plasma membrane. Moreover, transient overexpression of MdACA39 significantly enhanced apple resistance to A. alternata, likely due to the activation of SA, MeJA and Ca²⁺ signaling-mediated immune pathways, the induction of disease resistance-related genes, and elevated antioxidant enzyme activity. Collectively, this study systematically characterizes the apple Ca²⁺-ATPase family and identifies MdACA39 as a key regulator of fungal resistance, providing valuable gene resources for dissecting Ca²⁺ signaling-mediated disease resistance in apple.

Flesh mealiness, a textural disorder in apples, reduces storage quality and consumer acceptance. The ‘Delicious’ and ‘Fuji’, prominent apple cultivars in China, exhibit contrasting susceptibility to mealiness, though the underlying mechanisms remain unclear. This study compared cytological, physiological and cell wall metabolic changes between mealy ‘Oregon Spur II Delicious’ and non-mealy ‘Miyazaki Spur Fuji’ during ambient storage. Toluidine blue staining and scanning electron microscopy revealed that ‘Delicious’ exhibited larger intercellular spaces and cell separation in contrast to ‘Fuji’. This observation aligns with the earlier onset of mealiness in ‘Delicious’: its mealiness degree increased from 3.06% at harvest to 19.62% after 28 d of storage (a 6.4-fold rise), whereas that of ‘Fuji’ only increased from 2.13% to 3.90% (1.8-fold). This pronounced increase in ‘Delicious’ was accompanied by a significant increase in air space volume and a reduction in expressible juice. Furthermore, the occurrence of mealiness in ‘Delicious’ involved a sharp increase in respiration rate and ethylene production, alongside rapid declines in firmness and starch content. Notably, there was a substantial accumulation of water-soluble pectin (WSP) and chelator-soluble pectin (CSP) in ‘Delicious’, whereas the content of Na₂CO₃-soluble pectin (NSP) remained consistently lower. Monosaccharide composition analysis confirmed significantly reduced arabinose and galactose levels across pectin fractions (WSP, CSP, and NSP) in ‘Delicious’. Correspondingly, immunofluorescence labeling showed a pronounced degradation of arabinan and galactan within the side chains of rhamnogalacturonan-I (RG-I). In addition, the activities of pectin methylesterase, α-L-Arabinofuranosidase, and β-D-Galactosidase remained significantly elevated in ‘Delicious’. Collectively, these findings demonstrate that cultivar differences in flesh mealiness are attributable to divergent physiological senescence and cell wall disassembly processes.

WD40 proteins play important roles in the synthesis and regulation of anthocyanin, the regulation of plant morphology and development, and the response to various abiotic stresses. However, the role of WD40 in Fragaria vesca (F. vesca) has not been studied. In this study, a total of 216 FvWD40 family members were identified, which were divided into four subfamilies based on evolutionary tree analysis. Subcellular localization predictions show that FvWD40 family members are mainly localized in chloroplasts, nuclei, and cytoplasm. An analysis of collinearity revealed a total of eight pairs of intraspecific collinearity of the FvWD40 gene family, and interspecific collinearity showed that the FvWD40 gene family covaried more gene pairs with Arabidopsis thaliana (Arabidopsis) than with rice (Oryza sativa). Promoter cis-acting elements revealed that the FvWD40 gene family contains predominantly light, hormone, and abiotic stress response elements. Tissue-specific expression analysis showed that a number of members including FvWD40-111 and FvWD40-137 were highly expressed in all tissues, and a number or members including FvWD40-97 and FvWD40-102 were lowly expressed in all tissues. The FvWD40 gene family was found to be expressed at all four different coloring stages of F. vesca by qRT-PCR, with lower expression at the 50% coloring stage (S3). FvWD40-24, FvWD40-50, and FvWD40-60 showed the highest expression during the white fruit stage (S1) period, suggesting that these genes play a potential regulatory role in the pre-fruit coloring stage. FvWD40-62, FvWD40-88 and FvWD40-103 had the highest expression at the 20% coloration stage (S2), and FvWD40-115, FvWD40-170, FvWD40-184 and FvWD40-195 had the highest expression at the full coloration stage (S4). These results suggest a potential role for these genes during fruit coloration. This study lays a foundation for further research on the function of the WD40 gene family.

Dihydroflavonol 4-reductase (DFR) significantly influences the modification of flower color. To explore the role of DFR in the synthesis of strawberry anthocyanins, in this study, we downloaded the CDS sequences of the DFR gene family from the Arabidopsis genome database TAIR; the DFR family of forest strawberry was compared; then, a functional domain screen was performed using NCBI; the selected strawberry DFR genes were analyzed; and the expression characteristics of the family members were studied by qRT-PCR. The results showed that there are 57 members of the DFR gene family in strawberry, which are mainly expressed in the cytoplasm and chloroplast; most of them are hydrophilic proteins; and the secondary structure of the protein is mainly composed of α-helices and random coils. The analysis revealed that FvDFR genes mostly contain light, hormone, abiotic stress, and meristem response elements. From the results of the qRT-PCR analysis, the relative expression of each member of the FvDFR gene was significantly different, which was expressed throughout the process of fruit coloring. Most genes had the highest expression levels in the full coloring stage (S4). The expression of FvDFR30, FvDFR54, and FvDFR56 during the S4 period was 8, 2.4, and 2.4 times higher than during the S1 period, indicating that the DFR gene plays a key role in regulating the fruit coloration of strawberry. In the strawberry genome, 57 members of the strawberry DFR gene family were identified. The higher the DFR gene expression, the higher the anthocyanin content, and the DFR gene may be the key gene in anthocyanin synthesis. Collectively, the DFR gene is closely related to fruit coloring, which lays a foundation for further exploring the function of the DFR gene family.

Sucrose phosphate synthase (SPS) is an important link in the process of sugar metabolism. In addition, it is also involved in abiotic stresses in plants. In order to study the SPS gene family and its role in abiotic stress, we identified the MdSPS gene family members by bioinformatics methods such as correlation analysis, the HMM method, and the Clustering method, and analyzed the transient expression of MdSPS genes by quantitative real-time fluorescence analysis (qRT-PCR). The MdSPS gene family consists of a total of 19 members divided into three subfamilies distributed on 14 chromosomes in apples. The MdSPS gene family has 12 collinearity gene pairs, indicating significant duplication. Most members of this family contain a large number of plant hormone response elements, light-inducible elements, and abiotic stress response elements 2kb upstream of the promoter. Codon bias analysis shows that there are 28 high-frequency codons and no codons with strong preference in this family. Gene chip results showed that only MdSPS2, MdSPS3, MdSPS11, and MdSPS17 were up-regulated in roots, and they were all members of subfamily C. The qRT-PCR analysis showed that all members of this family responded significantly to drought stress, salt stress, and low temperature stress. Interestingly, the relative expression of MdSPS12 was significantly down-regulated under salt stress and low temperature stress. In addition, the expression of MdSPS3, MdSPS8, MdSPS11, and MdSPS17 was more than 20 fold higher than that of the control under drought stress, salt stress, and low temperature stress. These four genes could be candidates for molecular breeding in the MdSPS family.

To explore the impact of shade treatment on grape berries, ‘Marselan’ grape berries were bagged under different light transmission rates (100% (CK), 75% (A), 50% (B), 25% (C), 0% (D)). It was observed that this treatment delayed the ripening of the grape berries. The individual weight of the grape berries, as well as the content of fructose, glucose, soluble sugars, and organic acids in the berries, was measured at 90, 100, and 125 days after flowering (DAF90, DAF100, DAF125). The results revealed that shading treatment reduced the sugar content in grape berries; the levels of fructose and glucose were higher in the CK treatment compared to the other treatments, and they increased with the duration of the shading treatment. Conversely, the sucrose content exhibited the opposite trend. Additionally, as the weight of the grape berries increased, the content of soluble solids and soluble sugars in the berries also increased, while the titratable acidity decreased. Furthermore, 16 differentially expressed genes (DEGs) were identified in the photosynthesis-antenna protein pathway from the transcriptome sequencing data. Correlation analysis revealed that the expression levels of genes VIT_08s0007g02190 (Lhcb4) and VIT_15s0024g00040 (Lhca3) were positively correlated with sugar content in the berries at DAF100, but negatively correlated at DAF125. qRT-PCR results confirmed the correlation analysis. This indicates that shading grape clusters inhibits the expression of genes in the photosynthesis-antenna protein pathway in the grape berries, leading to a decrease in sugar content. This finding contributes to a deeper understanding of the impact mechanisms of grape cluster shading on berry quality, providing important scientific grounds for improving grape berry quality.

In this study, we obtained and cloned VvSnRK2.7 by screening transcriptomic data to investigate the function of the grape sucrose non-fermenting kinase 2 (SnRK2) gene under stress conditions. A yeast two-hybrid (Y2H) assay was used to further screen for interaction proteins of VvSnRK2.7. Ultimately, VvSnRK2.7 was heterologously expressed in Arabidopsis thaliana, and the relative conductivity, MDA content, antioxidant enzyme activity, and sugar content of the transgenic plants were determined under drought treatment. In addition, the expression levels of VvSnRK2.7 in Arabidopsis were analyzed. The results showed that the VvSnRK2.7-EGFP fusion protein was mainly located in the cell membrane and nucleus of tobacco leaves. In addition, the VvSnRK2.7 protein had an interactive relationship with the VvbZIP protein during the Y2H assay. The expression levels of VvSnRK2.7 and the antioxidant enzyme activities and sugar contents of the transgenic lines were higher than those of the wild type under drought treatment. Moreover, the relative conductivity and MDA content were lower than those of the wild type. The results indicate that VvSnRK2.7 may activate the enzyme activity of the antioxidant enzyme system, maintain normal cellular physiological metabolism, stabilize the berry sugar metabolism pathway under drought stress, and promote sugar accumulation to improve plant resistance.

Background: Anthocyanin synthase (ANS) is the enzyme downstream of the anthocyanins synthesis pathway and the rate-limiting enzyme of the synthesis pathway. It catalyzes the conversion of colorless anthocyanins to anthocyanins and plays an important role in plant color presentation and stress resistance. However,ANSgene is rarely studied in grapes.Results: In this study, 121VvANSgenes were identified and distributed on 18 chromosomes, VvANS family members were divided into 8 subgroups. Secondary structure prediction showed mainly irregular coils and α-helices, and subcellular localization indicated that VvANS gene family is mainly located in chloroplast, cytoplasm and nucleus. The promoter region of the VvANS gene family contains multiple cis-acting elements that are associated with light, abiotic stress, and hormones. Intraspecific collinearity analysis showed that there were 13 pairs of collinearity betweenVvANSgenes. Interspecific collinearity analysis showed that there was more collinearity between grape, apple andArabidopsis, but less collinearity between grape and rice. Microarray data analysis showed thatVvANS17,VvANS23andVvANS75had higher expression levels in flesh and peel, whileVvANS25,VvANS64andVvANS106had higher expression levels in flower. The results of qRT-PCR analysis showed thatVvANSgenes were expressed throughout the whole process of fruit coloring, such asVvANS47andVvANS55in the green fruit stage,VvANS3,VvANS64andVvANS90in the initial fruit color turning stage. The expression levels ofVvANS21,VvANS79andVvANS108were higher at 50% coloring stage, indicating that these genes play an important role in the fruit coloring process.VvANS4,VvANS66andVvANS113had the highest expression levels in the full maturity stage.Conclusions: These results indicated that different members of VvANS gene family played a role in different coloring stages, and this study laid a foundation for further research on the function of ANS gene family.

The color of strawberry fruit is an important appearance quality index that affects the marketability of fruit, and the content and type of anthocyanin are two of the main reasons for the formation of fruit color. At present, the research on anthocyanin synthesis mainly focuses on the phenylpropane metabolic pathway, and the F3H gene family is an important member of this metabolic pathway. Therefore, in order to clarify the role of flavanone 3-hydroxylase (F3H) in regulating anthocyanin accumulation in strawberry, we identified F3H gene family members in strawberry and analyzed their bioinformatics and expression at different fruit color stages. The results showed that the strawberry F3H family contains 126 members, which are distributed on seven chromosomes and can be divided into six subgroups. The promoter region of strawberry F3H gene family contains light response elements, abiotic stress response elements and hormone response elements. Intraspecic collinearity analysis showed that there were six pairs of collinearity of the F3H gene. Interspecific collinearity analysis showed that there were more collinearity relationships between strawberry and apple, grape and Arabidopsis, but less collinearity between strawberry and rice. Via tissue-specific expression analysis, we found that the expression levels of FvF3H48, FvF3H120 and FvF3H74 were higher in the stages of germination, growth, flowering and fruit setting. The expression levels of FvF3H42 and FvF3H16 were higher in seeds. The expression levels of FvF3H16 and FvF3H11 were higher in the ovary wall of stage 1, stage 2, stage 3 and stage 5. FvF3H15 and FvF3H48 were highly expressed in the pericardium, anther, receptacle and anther. Real-time fluorescence quantitative PCR showed the expression changes in F3H in the fruit coloring process. The results indicate that the expression levels of most members were higher during the S3 stage, such as FvF3H7, FvF3H16, FvF3H32, FvF3H82, FvF3H89, FvF3H92 and FvF3H112. FvF3H63 and FvF3H104 exhibited particularly high expression levels during the S1 stage, with some genes also showing elevated expression during the S4 stage, including FvF3H13, FvF3H27, FvF3H66 and FvF3H103. FvF3H58, FvF3H69, FvF3H79 and FvF3H80 showed higher expression levels during the S2 stage. These findings lay the groundwork for elucidating the biological functions of the strawberry F3H gene family and the selection of related genes.