International Journal of Molecular Sciences

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15 pages, 587 KiB

Open AccessArticle

Development of Rapid Detection Methods for Fusarium oysporum f. sp. melonis in Melon Seeds

by Tsai-De Chang, Ya-Zhen Xu, Yu-Fen Wang, Xing-Ru Wang, Shang-Han Tsai, Zhong-Bin Wu, Yuh Tzean and Ying-Hong Lin

Int. J. Mol. Sci. 2024, 25(10), 5371; https://doi.org/10.3390/ijms25105371 - 14 May 2024

Cited by 1 | Viewed by 952

Abstract

Melon (Cucumis melo L.) is a global commercial crop that is sensitive to seed-borne wilt infections caused by Fusarium oxysporum f. sp. melonis (Fom). To address the challenge of detecting Fom contamination, we designed a probe-based real-time PCR method, TDCP2, in combination [...] Read more.

Melon (Cucumis melo L.) is a global commercial crop that is sensitive to seed-borne wilt infections caused by Fusarium oxysporum f. sp. melonis (Fom). To address the challenge of detecting Fom contamination, we designed a probe-based real-time PCR method, TDCP2, in combination with rapid or column-based DNA extraction protocols to develop reliable molecular detection methods. Utilizing TDCP2, the detection rate reached 100% for both artificially Fom-inoculated (0.25–25%) and pod-inoculated melon seeds in conjunction with DNA samples from either the rapid or column-based extraction protocol. We performed analyses of precision, recall, and F1 scores, achieving a maximum F1 score of 1 with TDCP2, which highlights the robustness of the method. Additionally, intraday and interday assays were performed, which revealed the high reproducibility and stability of column-based DNA extraction protocols combined with TDCP2. These metrics confirm the reliability of our developed protocols, setting a foundation for future enhancements in seed pathology diagnostics and potentially broadening their applicability across various Fom infection levels. In the future, we hope that these methods will reduce food loss by improving the control and management of melon diseases. Full article

(This article belongs to the Special Issue Molecular Research in Fruit Crop)

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18 pages, 5142 KiB

Open AccessArticle

Characterization and Potential Action Mode Divergences of Homologous ACO1 Genes during the Organ Development and Ripening Process between Non-Climacteric Grape and Climacteric Peach

by Linjia Luo, Pengcheng Zhao, Ziwen Su, Yuqing Huang, Yanping Zhang, Qian Mu, Xuxian Xuan, Ziyang Qu, Mucheng Yu, Ziyang Qi, Rana Badar Aziz, Peijie Gong, Zhenqiang Xie, Jinggui Fang and Chen Wang

Int. J. Mol. Sci. 2024, 25(2), 789; https://doi.org/10.3390/ijms25020789 - 8 Jan 2024

Viewed by 1186

Abstract

Ethylene is one crucial phytohormone modulating plants’ organ development and ripening process, especially in fruits, but its action modes and discrepancies in non-climacteric grape and climacteric peach in these processes remain elusive. This work is focused on the action mode divergences of ethylene [...] Read more.

Ethylene is one crucial phytohormone modulating plants’ organ development and ripening process, especially in fruits, but its action modes and discrepancies in non-climacteric grape and climacteric peach in these processes remain elusive. This work is focused on the action mode divergences of ethylene during the modulation of the organ development and ripening process in climacteric/non-climacteric plants. We characterized the key enzyme genes in the ethylene synthesis pathway, VvACO1 and PpACO1, and uncovered that their sequence structures are highly conserved, although their promoters exhibit important divergences in the numbers and types of the cis-elements responsive to hormones, implying various responses to hormone signals. Subsequently, we found the two have similar expression modes in vegetative organ development but inverse patterns in reproductive ones, especially in fruits. Then, VvACO1 and PpACO1 were further validated in promoting fruit ripening functions through their transient over-expression/RNAi-expression in tomatoes, of which the former possesses a weaker role than the latter in the fruit ripening process. Our findings illuminated the divergence in the action patterns and function traits of the key VvACO1/PpACO1 genes in the tissue development of climacteric/non-climacteric plants, and they have implications for further gaining insight into the interaction mechanism of ethylene signaling during the modulation of the organ development and ripening process in climacteric/non-climacteric plants. Full article

(This article belongs to the Special Issue Molecular Research in Fruit Crop)

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17 pages, 2888 KiB

Open AccessArticle

An LcMYB111-LcHY5 Module Differentially Activates an LcFLS Promoter in Different Litchi Cultivars

by Zhidan Xiao, Jing Wang, Nonghui Jiang, Chao Fan, Xu Xiang and Wei Liu

Int. J. Mol. Sci. 2023, 24(23), 16817; https://doi.org/10.3390/ijms242316817 - 27 Nov 2023

Viewed by 1078

Abstract

Flavonol synthase (FLS) is the crucial enzyme of the flavonol biosynthetic pathways, and its expression is tightly regulated in plants. In our previous study, two alleles of LcFLS, LcFLS-A and LcFLS-B, have been identified in litchi, with extremely early-maturing (EEM) cultivars [...] Read more.

Flavonol synthase (FLS) is the crucial enzyme of the flavonol biosynthetic pathways, and its expression is tightly regulated in plants. In our previous study, two alleles of LcFLS, LcFLS-A and LcFLS-B, have been identified in litchi, with extremely early-maturing (EEM) cultivars only harboring LcFLS-A, while middle-to-late-maturing (MLM) cultivars only harbor LcFLS-B. Here, we overexpressed both LcFLS alleles in tobacco, and transgenic tobacco produced lighter-pink flowers and showed increased flavonol levels while it decreased anthocyanin levels compared to WT. Two allelic promoters of LcFLS were identified, with EEM cultivars only harboring proLcFLS-A, while MLM cultivars only harbor proLcFLS-B. One positive and three negative R2R3-MYB transcription regulators of LcFLS expression were identified, among which only positive regulator LcMYB111 showed a consistent expression pattern with LcFLS, which both have higher expression in EEM than that of MLM cultivars. LcMYB111 were further confirmed to specifically activate proLcFLS-A with MYB-binding element (MBE) while being unable to activate proLcFLS-B with mutated MBE (MBEm). LcHY5 were also identified and can interact with LcMYB111 to promote LcFLS expression. Our study elucidates the function of LcFLS and its differential regulation in different litchi cultivars for the first time. Full article

(This article belongs to the Special Issue Molecular Research in Fruit Crop)

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18 pages, 18567 KiB

Open AccessArticle

Effects of Coverlys TF150^® on the Photosynthetic Characteristics of Grape

by Zhonghan Li, Enshun Jiang, Minghui Liu, Qinghua Sun, Zhen Gao and Yuanpeng Du

Int. J. Mol. Sci. 2023, 24(23), 16659; https://doi.org/10.3390/ijms242316659 - 23 Nov 2023

Cited by 1 | Viewed by 1031

Abstract

Grape rain-shelter cultivation is a widely employed practice in China. At present, the most commonly used rain shelter film materials are polyvinyl chloride (PVC), polyethylene (PE), ethylene-vinyl acetate copolymer (EVA), and polyolefin (PO). Coverlys TF150^® is a woven fabric with an internal [...] Read more.

Grape rain-shelter cultivation is a widely employed practice in China. At present, the most commonly used rain shelter film materials are polyvinyl chloride (PVC), polyethylene (PE), ethylene-vinyl acetate copolymer (EVA), and polyolefin (PO). Coverlys TF150^® is a woven fabric with an internal antifoggy PE coating that has not yet been popularized as a rain shelter film for grapes in China. To investigate the effects of Coverlys TF150^® on grapes, we measured the microdomain environment, leaf development, and photosynthetic characteristics of ‘Miguang’ (Vitis vinifera × V. labrusca) under rain-shelter cultivation and performed transcriptome analysis. The results showed that Coverlys TF150^® significantly reduced (p < 0.05) the light intensity, temperature, and humidity compared with PO film, increased the chlorophyll content and leaf thickness (particularly palisade tissue thickness), and increased stomatal density and stomatal opening from 10:00 to 14:00. Coverlys TF150^® was observed to improve the maximum efficiency of photosystem II (F_v/F_m), photochemical quenching (qP), the electron transfer rate (ETR), and the actual photochemical efficiency (Φ_PSII) from 10:00 to 14:00. Moreover, the net photosynthetic rate (P_n), intercellular CO₂ concentration (C_i), stomatal conductance (G_s), and transpiration rate (T_r) of grape leaves significantly increased (p < 0.05) from 10:00 to 14:00. RNA-Seq analysis of the grape leaves at 8:00, 10:00, and 12:00 revealed 1388, 1562, and 1436 differential genes at these points in time, respectively. KEGG enrichment analysis showed the occurrence of protein processing in the endoplasmic reticulum. Plant hormone signal transduction and plant-pathogen interaction were identified as the metabolic pathways with the highest differential gene expression enrichment. The psbA encoding D1 protein was significantly up-regulated in both CO10vsPO10 and CO12vsPO12, while the sHSPs family genes were significantly down-regulated in all time periods, and thus may play an important role in the maintenance of the photosystem II (PSII) activity in grape leaves under Coverlys TF150^®. Compared with PO film, the PSI-related gene psaB was up-regulated, indicating the ability of Coverlys TF150^® to better maintain PSI activity. Compared with PO film, the abolic acid receptacle-associated gene PYL1 was down-regulated at all time periods under the Coverlys TF150^® treatment, while PP2C47 was significantly up-regulated in CO10vsPO10 and CO12vsPO12, inducing stomatal closure. The results reveal that Coverlys TF150^® alleviates the stress of high temperature and strong light compared with PO film, improves the photosynthetic capacity of grape leaves, and reduces the midday depression of photosynthesis. Full article

(This article belongs to the Special Issue Molecular Research in Fruit Crop)

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22 pages, 9472 KiB

Open AccessArticle

Characterization of VvmiR166s-Target Modules and Their Interaction Pathways in Modulation of Gibberellic-Acid-Induced Grape Seedless Berries

by Yunhe Bai, Zhuangwei Wang, Linjia Luo, Xuxian Xuan, Wei Tang, Ziyang Qu, Tianyu Dong, Ziyang Qi, Mucheng Yu, Weimin Wu, Jinggui Fang and Chen Wang

Int. J. Mol. Sci. 2023, 24(22), 16279; https://doi.org/10.3390/ijms242216279 - 14 Nov 2023

Cited by 3 | Viewed by 997

Abstract

Exogenous GA is widely used to efficiently induce grape seedless berry development for significantly improving berry quality. Recently, we found that VvmiR166s are important regulators of response to GA in grapes, but its roles in GA-induced seedless grape berry development remain elusive. Here, [...] Read more.

Exogenous GA is widely used to efficiently induce grape seedless berry development for significantly improving berry quality. Recently, we found that VvmiR166s are important regulators of response to GA in grapes, but its roles in GA-induced seedless grape berry development remain elusive. Here, the precise sequences of VvmiR166s and their targets VvREV, VvHB15 and VvHOX32 were determined in grape cv. ‘Rosario Bianco’, and the cleavage interactions of VvmiR166s-VvHB15/VvHOX32/VvREV modules and the variations in their cleavage roles were confirmed in grape berries. Exogenous GA treatment significantly induced a change in their expression correlations from positive to negative between VvmiR166s and their target genes at the seeds during the stone-hardening stages (32 DAF–46 DAF) in grape berries, indicating exogenous GA change action modes of VvmiR166s on their targets in this process, in which exogenous GA mainly enhanced the negative regulatory roles of VvmiR166s on VvHB15 among all three VvmiR166s-target pairs. The transient OE-VvmiR166a-h/OE-VvHB15 in tobacco confirmed that out of the VvmiR166 family, VvmiR166h/a/b might be the main factors in modulating lignin synthesis through inhibiting VvHB15, of which VvmiR166h-VvHB15-NtPAL4/NtCCR1/NtCCR2/NtCCoAMT5/NtCOMT1 and VvmiR166a/b-VvHB15-NtCAD1 are the potential key regulatory modules in lignin synthesis. Together with the GA-induced expression modes of VvmiR166s-VvHB15 and genes related to lignin synthesis in grape berries, we revealed that GA might repress lignin synthesis mainly by repressing VvCAD1/VvCCR2/VvPAL2/VvPAL3/Vv4CL/VvLac7 levels via mediating VvmiR166s-VvHB15 modules in GA-induced grape seedless berries. Our findings present a novel insight into the roles of VvmiR66s that are responsive to GA in repressing the lignin synthesis of grape seedless berries, with different lignin-synthesis-enzyme-dependent action pathways in diverse plants, which have important implications for the molecular breeding of high-quality seedless grape berries. Full article

(This article belongs to the Special Issue Molecular Research in Fruit Crop)

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14 pages, 7549 KiB

Open AccessArticle

Comparative Metabolomic and Transcriptomic Analyses Reveal Distinct Ascorbic Acid (AsA) Accumulation Patterns between PCA and PCNA Persimmon Developing Fruit

by Yiru Wang, Songfeng Diao, Huawei Li, Lingshuai Ye, Yujing Suo, Yanhao Zheng, Peng Sun, Weijuan Han and Jianmin Fu

Int. J. Mol. Sci. 2023, 24(20), 15362; https://doi.org/10.3390/ijms242015362 - 19 Oct 2023

Cited by 1 | Viewed by 1286

Abstract

Persimmon fruit has a high nutritional value and significantly varies between pollination-constant astringent (PCA) and pollination-constant non-astringent (PCNA) persimmons. The astringency type affects sugar, flavonoids, and tannin accumulation and is well known in persimmon fruit. However, the impact of the fruit astringency type [...] Read more.

Persimmon fruit has a high nutritional value and significantly varies between pollination-constant astringent (PCA) and pollination-constant non-astringent (PCNA) persimmons. The astringency type affects sugar, flavonoids, and tannin accumulation and is well known in persimmon fruit. However, the impact of the fruit astringency type on ascorbic acid (AsA) accumulation is limited. In this study, typical PCA varieties (‘Huojing’ and ‘Zhongshi5’) and PCNA varieties (‘Yohou’ and ‘Jiro’) of persimmon fruit were sampled at four developing stages (S1–S4) to provide valuable information on AsA content variation in PCA and PCNA persimmon. Persimmon fruit is rich in ascorbic acid; the AsA content of the four varieties ‘Zhongshi5’, ‘Huojing’, ‘Jiro’, and ‘Youhou’ mature fruit reached 104.49, 48.69, 69.69, and 47.48 mg/100 g. Fruit of the same astringency type persimmon showed a similar AsA accumulation pattern. AsA content was significantly higher in PCA than PCNA fruit at S1–S3. The initial KEGG analysis of metabolites showed that galactose metabolism is the major biosynthetic pathway of AsA in persimmon fruit. There were significant differences in galactose pathway-related metabolite content in developing PCA and PCNA fruit, such as Lactose, D-Tagatose, and D-Sorbitol content in PCA being higher than that of PCNA. Combined gene expression and WGCNA analyses showed that the expression of the GME (evm.TU.contig4144.37) gene was higher in PCA-type than in PCNA-type fruit in S1–S3 and exhibited the highest correlation with AsA content (r = 690 **, p < 0.01). Four hub genes, including the DNA methylation gene, methyltransferase gene, F-box, and Actin-like Protein, were identified as potential regulators of the GME gene. These results provide basic information on how astringency types affect AsA accumulation and will provide valuable information for further investigation on AsA content variation in persimmon fruit. Full article

(This article belongs to the Special Issue Molecular Research in Fruit Crop)

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16 pages, 3587 KiB

Open AccessArticle

Interaction of VvDELLA2 and VvCEB1 Mediates Expression of Expansion-Related Gene during GA-Induced Enlargement of Grape Fruit

by Zhenhua Liu, Yan Wang, Pingyin Guan, Jianfang Hu and Lei Sun

Int. J. Mol. Sci. 2023, 24(19), 14870; https://doi.org/10.3390/ijms241914870 - 3 Oct 2023

Viewed by 1430

Abstract

Exogenous gibberellin treatment can promote early growth of grape fruit, but the underlying regulatory mechanisms are not well understood. Here, we show that VvDELLA2 directly regulates the activity of the VvCEB1 transcription factor, a key regulator in the control of cell expansion in [...] Read more.

Exogenous gibberellin treatment can promote early growth of grape fruit, but the underlying regulatory mechanisms are not well understood. Here, we show that VvDELLA2 directly regulates the activity of the VvCEB1 transcription factor, a key regulator in the control of cell expansion in grape fruit. Our results show that VvCEB1 binds directly to the promoters of cell expansion-related genes in grape fruit and acts as a transcriptional activator, while VvDELLA2 blocks VvCEB1 function by binding to its activating structural domain. The exogenous gibberellin treatment relieved this inhibition by promoting the degradation of VvDELLA2 protein, thus, allowing VvCEB1 to transcriptionally activate the expression of cell expansion-related genes. In conclusion, we conclude that exogenous GA₃ treatment regulates early fruit expansion by affecting the VvDELLA-VvCEB1 interaction in grape fruit development. Full article

(This article belongs to the Special Issue Molecular Research in Fruit Crop)

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14 pages, 6101 KiB

Open AccessArticle

Effects of Exogenous Application of Glycine Betaine Treatment on ‘Huangguoggan’ Fruit during Postharvest Storage

by Zhendong Zheng, Tie Wang, Miaoyi Liu, Xiaozhu Xu, Jun Wang, Guochao Sun, Siya He, Ling Liao, Bo Xiong, Xun Wang, Jiaxian He, Zhihui Wang and Mingfei Zhang

Int. J. Mol. Sci. 2023, 24(18), 14316; https://doi.org/10.3390/ijms241814316 - 20 Sep 2023

Cited by 3 | Viewed by 1672

Abstract

Loss of quality in citrus fruit is a common occurrence during postharvest storage due to oxidative stress and energy consumption. In recent years, glycine betaine (GB) has been widely applied to postharvest horticulture fruit. This study aimed to investigate the effect of GB [...] Read more.

Loss of quality in citrus fruit is a common occurrence during postharvest storage due to oxidative stress and energy consumption. In recent years, glycine betaine (GB) has been widely applied to postharvest horticulture fruit. This study aimed to investigate the effect of GB treatment (10 mM and 20 mM) on the quality and antioxidant activity of ‘Huangguogan’ fruit during postharvest storage at room temperature. Our results indicated that both 10 mM and 20 mM treatments effectively reduced weight and firmness losses and maintained total soluble solid (TSS), titratable acidity (TA), and ascorbic acid contents. Additionally, GB treatment significantly increased the activity of antioxidant enzymes, maintained higher levels of total phenols and total flavonoids, and led to slower accumulation of H₂O₂. A transcriptome analysis conducted at 28 days after treatment (DAT)identified 391 differentially expressed genes (DEGs) between 20 mM GB (GB-2) and the control (CK) group. These DEGs were enriched in various pathways, particularly related to oxygen oxidoreductase, peroxidase activity, and flavonoid biosynthesis. Overall, the application of GB proved beneficial in enhancing the storability and extending the shelf life of ‘Huangguogan’ fruit. Full article

(This article belongs to the Special Issue Molecular Research in Fruit Crop)

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15 pages, 3218 KiB

Open AccessArticle

Genome-Wide Identification and Characterization Analysis of WUSCHEL-Related Homeobox Family in Melon (Cucumis melo L.)

by Lingli Tang, Yuhua He, Bin Liu, Yongyang Xu and Guangwei Zhao

Int. J. Mol. Sci. 2023, 24(15), 12326; https://doi.org/10.3390/ijms241512326 - 1 Aug 2023

Cited by 8 | Viewed by 1971

Abstract

WUSCHEL-related homeobox (WOX) proteins are very important in controlling plant development and stress responses. However, the WOX family members and their role in response to abiotic stresses are largely unknown in melon (Cucumis melo L.). In this study, 11 WOX (CmWOX) transcript [...] Read more.

WUSCHEL-related homeobox (WOX) proteins are very important in controlling plant development and stress responses. However, the WOX family members and their role in response to abiotic stresses are largely unknown in melon (Cucumis melo L.). In this study, 11 WOX (CmWOX) transcript factors with conserved WUS and homeobox motif were identified and characterized, and subdivided into modern clade, ancient clade and intermediate clade based on bioinformatic and phylogenetic analysis. Evolutionary analysis revealed that the CmWOX family showed protein variations in Arabidopsis, tomato, cucumber, melon and rice. Alignment of protein sequences uncovered that all CmWOXs had the typical homeodomain, which consisted of conserved amino acids. Cis-element analysis showed that CmWOX genes may response to abiotic stress. RNA-seq and qRT-PCR results further revealed that the expression of partially CmWOX genes are associated with cold and drought. CmWOX13a and CmWOX13b were constitutively expressed under abiotic stresses, CmWOX4 may play a role in abiotic processes during plant development. Taken together, this study offers new perspectives on the CmWOX family’s interaction and provides the framework for research on the molecular functions of CmWOX genes. Full article

(This article belongs to the Special Issue Molecular Research in Fruit Crop)

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19 pages, 5228 KiB

Open AccessArticle

VvPL15 Is the Core Member of the Pectate Lyase Gene Family Involved in Grape Berries Ripening and Softening

by Yuying Ma, Chukun Wang, Zhen Gao, Yuxin Yao, Hui Kang and Yuanpeng Du

Int. J. Mol. Sci. 2023, 24(11), 9318; https://doi.org/10.3390/ijms24119318 - 26 May 2023

Cited by 9 | Viewed by 1896

Abstract

The process of ripening and softening in grape begins at veraison and is closely related to the depolymerization of pectin components. A variety of enzymes are involved in pectin metabolism and one class of enzyme, pectin lyases (PLs), have been reported to play [...] Read more.

The process of ripening and softening in grape begins at veraison and is closely related to the depolymerization of pectin components. A variety of enzymes are involved in pectin metabolism and one class of enzyme, pectin lyases (PLs), have been reported to play an important role in softening in many fruits; however, little information is available on the VvPL gene family in grape. In this study, 16 VvPL genes were identified in the grape genome using bioinformatics methods. Among them, VvPL5, VvPL9, and VvPL15 had the highest expression levels during grape ripening, which suggests that these genes are involved in grape ripening and softening. Furthermore, overexpression of VvPL15 affects the contents of water-soluble pectin (WSP) and acid-soluble pectin (ASP) in the leaves of Arabidopsis and significantly changes the growth of Arabidopsis plants. The relationship between VvPL15 and pectin content was further determined by antisense expression of VvPL15. In addition, we also studied the effect of VvPL15 on fruit in transgenic tomato plants, which showed that VvPL15 accelerated fruit ripening and softening. Our results indicate that VvPL15 plays an important role in grape berry softening during ripening by depolymerizing pectin. Full article

(This article belongs to the Special Issue Molecular Research in Fruit Crop)

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20 pages, 6822 KiB

Open AccessArticle

Integrated Metabolome and Transcriptome Analysis Reveals a Potential Mechanism for Water Accumulation Mediated Translucency in Pineapple (Ananas comosus (L.) Merr.) Fruit

by Jing Chen, Yanli Yao, Hui Zeng and Xiumei Zhang

Int. J. Mol. Sci. 2023, 24(8), 7199; https://doi.org/10.3390/ijms24087199 - 13 Apr 2023

Cited by 5 | Viewed by 5383

Abstract

A physiological disease of the pineapple fruit called pineapple translucency causes the pulp to become water-soaked, which affects the fruit’s taste, flavor, shelf life, and integrity. In the present study, we analyzed seven pineapple varieties, of which three were watery and four were [...] Read more.

A physiological disease of the pineapple fruit called pineapple translucency causes the pulp to become water-soaked, which affects the fruit’s taste, flavor, shelf life, and integrity. In the present study, we analyzed seven pineapple varieties, of which three were watery and four were non-watery. There were no apparent macronutritional (K, P, or N) differences in their pulp, but the non-watery pineapple varieties had higher dry matter and soluble sugar content. The metabolomic analysis found 641 metabolites and revealed differential expression of alkaloids, phenolic acids, nucleotide derivatives, lipids, and other metabolites among the seven species. Transcriptome analysis and further KEGG enrichment showed downregulation of ‘flavonoid biosynthesis’ pathways, differential expression of metabolic pathways, secondary metabolites biosynthesis, plant–pathogen interaction, and plant hormone signal transduction. We believe this study will provide critical molecular data supporting a deeper understanding of pineapple translucency formation and greatly benefit future research on this commercially important crop. Full article

(This article belongs to the Special Issue Molecular Research in Fruit Crop)

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16 pages, 4203 KiB

Open AccessArticle

Genome-Wide Identification of the SQUAMOSA Promoter-Binding Protein-like (SPL) Transcription Factor Family in Sweet Cherry Fruit

by Yueting Sun, Yanyan Wang, Yuqin Xiao, Xiang Zhang, Bingyang Du, Maihemuti Turupu, Chao Wang, Qisheng Yao, Shilin Gai, Jing Huang, Shi Tong and Tianhong Li

Int. J. Mol. Sci. 2023, 24(3), 2880; https://doi.org/10.3390/ijms24032880 - 2 Feb 2023

Cited by 10 | Viewed by 2780

Abstract

Plant-specific SQUAMOSA promoter-binding protein-like (SPL) transcription factors play important regulatory roles during plant growth and development, fruit ripening, inflorescence branching, and biotic and abiotic stresses. However, there have been no identification or systematic studies of the SPL gene family in the sweet cherry. [...] Read more.

Plant-specific SQUAMOSA promoter-binding protein-like (SPL) transcription factors play important regulatory roles during plant growth and development, fruit ripening, inflorescence branching, and biotic and abiotic stresses. However, there have been no identification or systematic studies of the SPL gene family in the sweet cherry. In this study, 12 SPL genes were identified in the sweet cherry reference genome, which were distributed over 6 chromosomes and classified into six groups according to phylogenetic relationships with other SPL gene families. Nine PavSPLs were highly expressed at green fruit stages and dramatically decreased at the onset of fruit ripening, which implied that they were important regulators during fruit development and ripening. The expression patterns of PavSPL genes under ABA, GA, and MeJA treatments showed that the PavSPLs were involved in the process of fruit ripening. A subcellular localization experiment proved that PavSPL4 and PavSPL7 proteins were localized in the nucleus. The genome-wide identification of the SPL gene family provided new insights while establishing an important foundation for sweet cherry studies. Full article

(This article belongs to the Special Issue Molecular Research in Fruit Crop)

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22 pages, 5727 KiB

Open AccessArticle

Transcriptome Analysis of the Effects of Grafting Interstocks on Apple Rootstocks and Scions

by Qingshan Li, Yuan Gao, Kun Wang, Jianrong Feng, Simiao Sun, Xiang Lu, Zhao Liu, Deying Zhao, Lianwen Li and Dajiang Wang

Int. J. Mol. Sci. 2023, 24(1), 807; https://doi.org/10.3390/ijms24010807 - 2 Jan 2023

Cited by 9 | Viewed by 2881

Abstract

Apples are a major horticultural crop worldwide. Grafting techniques are widely utilized in apple production to keep the varieties pure. Interstocks are frequently used in Northern China to achieve intensive apple dwarfing cultivation. High-throughput sequencing was used to investigate differentially expressed genes in [...] Read more.

Apples are a major horticultural crop worldwide. Grafting techniques are widely utilized in apple production to keep the varieties pure. Interstocks are frequently used in Northern China to achieve intensive apple dwarfing cultivation. High-throughput sequencing was used to investigate differentially expressed genes in the phloem tissues of two different xenograft systems, M (‘Gala’/‘Mac 9’/Malus baccata (L.) Borkh.) and B (‘Gala’/Malus baccata (L.) Borkh.). The results showed that dwarfing interstocks could significantly reduce the height and diameters of apple trees while have few effects on the growth of annual branches. The interstocks were found to regulate the expression of genes related to hormone metabolism and tree body control (GH3.9, PIN1, CKI1, ARP1, GA2ox1 and GA20ox1), these effects may attribute the dwarf characters for apple trees with interstocks. Besides, the interstocks reduce photosynthesis-related genes (MADH-ME4 and GAPC), promote carbon (C) metabolism gene expression (AATP1, GDH and PFK3), promote the expression of nitrogen (N)-metabolism-related genes (NRT2.7, NADH and GDH) in rootstocks, and improve the expression of genes related to secondary metabolism in scions (DX5, FPS1, TPS21 and SRG1). We also concluded that the interstocks acquired early blooming traits due to promotion of the expression of flowering genes in the scion (MOF1, FTIP7, AGL12 and AGL24). This study is a valuable resource regarding the molecular mechanisms of dwarf interstocks’ influence on various biological processes and transplantation systems in both scions and rootstocks. Full article

(This article belongs to the Special Issue Molecular Research in Fruit Crop)

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18 pages, 3973 KiB

Open AccessArticle

Metabolite and Transcriptome Profiles of Proanthocyanidin Biosynthesis in the Development of Litchi Fruit

by Ruihao Zhong, Junbin Wei, Bin Liu, Honghui Luo, Zhaoqi Zhang, Xuequn Pang and Fang Fang

Int. J. Mol. Sci. 2023, 24(1), 532; https://doi.org/10.3390/ijms24010532 - 28 Dec 2022

Cited by 8 | Viewed by 2069

Abstract

The fruit of Litchi chinensis contains high levels of proanthocyanidins (PAs) in the pericarp. These substances can serve as substrates of laccase-mediated rapid pericarp browning after the fruit is harvested. In this study, we found that the major PAs in litchi pericarp were [...] Read more.

The fruit of Litchi chinensis contains high levels of proanthocyanidins (PAs) in the pericarp. These substances can serve as substrates of laccase-mediated rapid pericarp browning after the fruit is harvested. In this study, we found that the major PAs in litchi pericarp were (−)-epicatechin (EC) and several procyanidins (PCs), primarily PC A2, B2, and B1, and the EC and the PC content decreased with the development of the fruit. RNA-seq analysis showed that 43 early and late structure genes related to flavonoid/PA biosynthesis were expressed in the pericarp, including five ANTHOCYANIDIN REDUCTASE (ANR), two LEUCOANTHOCYANIDIN REDUCTASE (LAR), and two ANTHOCYANIDIN SYNTHASE (ANS) genes functioning in the PA biosynthesis branch of the flavonoid pathway. Among these nine PA biosynthesis-related genes, ANR1a, LAR1/2, and ANS1 were highly positively correlated with changes in the EC/PC content, suggesting that they are the key PA biosynthesis-related genes. Several transcription factor (TF) genes, including MYB, bHLH, WRKY, and AP2 family members, were found to be highly correlated with ANR1a, LAR1/2, and ANS1, and their relevant binding elements were detected in the promoters of these target genes, strongly suggesting that these TF genes may play regulatory roles in PA biosynthesis. In summary, this study identified the candidate key structure and regulatory genes in PA biosynthesis in litchi pericarp, which will assist in understanding the accumulation of high levels of browning-related PA substances in the pericarp. Full article

(This article belongs to the Special Issue Molecular Research in Fruit Crop)

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Open AccessArticle

High-Throughput Sequencing Reveals Novel microRNAs Involved in the Continuous Flowering Trait of Longan (Dimocarpus longan Lour.)

by Saquib Waheed, Fan Liang, Mengyuan Zhang, Dayi He and Lihui Zeng

Int. J. Mol. Sci. 2022, 23(24), 15565; https://doi.org/10.3390/ijms232415565 - 8 Dec 2022

Cited by 5 | Viewed by 2054

Abstract

A major determinant of fruit production in longan (Dimocarpus longan Lour.) is the difficulty of blossoming. In this study, high-throughput microRNA sequencing (miRNA-Seq) was carried out to compare differentially expressed miRNAs (DEmiRNAs) and their target genes between a continuous flowering cultivar ‘Sijimi’ [...] Read more.

A major determinant of fruit production in longan (Dimocarpus longan Lour.) is the difficulty of blossoming. In this study, high-throughput microRNA sequencing (miRNA-Seq) was carried out to compare differentially expressed miRNAs (DEmiRNAs) and their target genes between a continuous flowering cultivar ‘Sijimi’ (SJ), and a unique cultivar ‘Lidongben’ (LD), which blossoms only once in the season. Over the course of our study, 1662 known miRNAs and 235 novel miRNAs were identified and 13,334 genes were predicted to be the target of 1868 miRNAs. One conserved miRNA and 29 new novel miRNAs were identified as differently expressed; among them, 16 were upregulated and 14 were downregulated. Through the KEGG pathway and cluster analysis of DEmiRNA target genes, three critical regulatory pathways, plant–pathogen interaction, plant hormone signal transduction, and photosynthesis-antenna protein, were discovered to be strongly associated with the continuous flowering trait of the SJ. The integrated correlation analysis of DEmiRNAs and their target mRNAs revealed fourteen important flowering-related genes, including COP1-like, Casein kinase II, and TCP20. These fourteen flowering-related genes were targeted by five miRNAs, which were novel-miR137, novel-miR76, novel-miR101, novel-miR37, and csi-miR3954, suggesting these miRNAs might play vital regulatory roles in flower regulation in longan. Furthermore, novel-miR137 was cloned based on small RNA sequencing data analysis. The pSAK277-miR137 transgenic Arabidopsis plants showed delayed flowering phenotypes. This study provides new insight into molecular regulation mechanisms of longan flowering. Full article

(This article belongs to the Special Issue Molecular Research in Fruit Crop)

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