Publications by authors named "Kekun Zhang"

20 Publications

  • Page 1 of 1

Expressional diversity of grapevine 3-Hydroxy-3-methylglutaryl-CoA reductase (VvHMGR) in different grapes genotypes.

BMC Plant Biol 2021 Jun 19;21(1):279. Epub 2021 Jun 19.

College of Horticulture, Nanjing Agricultural University, Jiangsu Province, Nanjing City, 210095, PR China.

Background: 3-Hydroxy-3-methylglutaryl-CoA reductase (HMGR) is a key enzyme in the mevalonate (MVA) pathway, which regulates the metabolism of terpenoids in the cytoplasm and determines the type and content of downstream terpenoid metabolites.

Results: Results showed that grapevine HMGR family has three members, such as VvHMGR1, VvHMGR2, and VvHMGR3. The expression of VvHMGRs in 'Kyoho' has tissue specificity, for example, VvHMGR1 keeps a higher expression, VvHMGR2 is the lowest, and VvHMGR3 gradually decreases as the fruit development. VvHMGR3 is closely related to CsHMGR1 and GmHMGR9 and has collinearity with CsHMGR2 and GmHMGR4. By the prediction of interaction protein, it can interact with HMG-CoA synthase, MVA kinase, FPP/GGPP synthase, diphosphate mevalonate decarboxylase, and participates in the synthesis and metabolism of terpenoids. VvHMGR3 have similar trends in expression with some of the genes of carotenoid biosynthesis and MEP pathways. VvHMGR3 responds to various environmental and phytohormone stimuli, especially salt stress and ultraviolet (UV) treatment. The expression level of VvHMGRs is diverse in grapes of different colors and aroma. VvHMGRs are significantly higher in yellow varieties than that in red varieties, whereas rose-scented varieties showed significantly higher expression than that of strawberry aroma. The expression level is highest in yellow rose-scented varieties, and the lowest in red strawberry scent varieties, especially 'Summer Black' and 'Fujiminori'.

Conclusion: This study confirms the important role of VvHMGR3 in the process of grape fruit coloring and aroma formation, and provided a new idea to explain the loss of grape aroma and poor coloring during production. There may be an additive effect between color and aroma in the HMGR expression aspect.
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http://dx.doi.org/10.1186/s12870-021-03073-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8214791PMC
June 2021

Metabolomic profile combined with transcriptomic analysis reveals the value of UV-C in improving the utilization of waste grape berries.

Food Chem 2021 Jun 4;363:130288. Epub 2021 Jun 4.

College of Enology, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling 712100, China. Electronic address:

Table grape is a popular fruit worldwide. The quality of the appearance of table grapes directly affects their commercial value. Table grape bunches are usually carefully managed during production. At different developmental stages, a large number of grape berries are pruned as waste for commercial appearance, which leads to wasted resources. Ultraviolet-C (UV-C) can regulate the accumulation of secondary metabolites in fruits. In this study, metabolomic profile was combined with transcriptomic analysis technology to explore the value of UV-C in improving the utilization of waste grapes. The berries of the 'Jumeigui' grape were subjected to UV-C radiation treatment in the green-berry stage, veraison stage, and maturation stage. The results showed that UV-C could brown grape berries and decrease their sugar content at different developmental stages. Compared with other samples, those treated with UV-C in the veraison stage had the most upregulated metabolites, while samples in the green-berry stage had the most down-regulated metabolites. UV-C promoted the accumulation of stilbenes and some flavonoids in the berries at each developmental stage (especially at the green-berry and veraison stages). Compared with other stages, UV-C treatment during the veraison stage led to the highest number of upregulated genes related to transcription factors, protein modification, indole-3-acetic acid (IAA), abscisic acid (ABA), gibberellin acid (GA), receptor kinases, and Ascorbic acid/Glutathione (Ascorb/Gluath). UV-C might promote the accumulation of phenolic components by upregulating the expression of their biosynthesis related genes. UV-C may be an effective in vitro approach for improving the application value of waste grape berries by enhancing the accumulation of the nutritious phenolic components.
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http://dx.doi.org/10.1016/j.foodchem.2021.130288DOI Listing
June 2021

Transcriptomic and Metabolomic Basis of Short- and Long-Term Post-Harvest UV-C Application in Regulating Grape Berry Quality Development.

Foods 2021 Mar 16;10(3). Epub 2021 Mar 16.

College of Enology, Northwest A&F University, Yangling 712100, China.

In this study, ultraviolet-C (UV-C) was utilized to improve the quality of post-harvest grape berries, and the transcriptomic and metabolomic basis of this improvement was elucidated. Berries of the red grape variety 'Zicui' and the white variety 'Xiangfei' were chosen to evaluate the effect of short- and long-term UV-C irradiation. Post-harvest UV-C application promoted malondialdehyde (MDA) and proline accumulation, and reduced the soluble solid content in berries. Both the variety and duration of irradiation could modulate the transcriptomic and metabolomic responses of berries to UV-C. Compared with the control, the differentially expressed genes (DEGs) identified under UV-C treatment were enriched in pathways related to metabolite accumulation, hormone biosynthesis and signal transduction, and reactive oxygen species (ROS) homeostasis. Flavonoid biosynthesis and biosynthesis of other secondary metabolites were the shared pathways enriched with differential metabolites. After long-term UV-C irradiation, cis-resveratrol accumulated in the berries of the two varieties, while the differential chalcone, dihydroflavone, flavonoid, flavanol, and tannin components primarily accumulated in 'Xiangfei', and some flavonols and anthocyanins primarily accumulated in 'Zicui'. Based on an exhaustive survey, we made a summary for the effect of UV-C in regulating the quality development of post-harvest grape berries. The results of this study may help to elucidate the mechanism by which UV-C functions and support its efficient application.
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http://dx.doi.org/10.3390/foods10030625DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8001394PMC
March 2021

Postharvest Dehydration Temperature Modulates the Transcriptomic Programme and Flavonoid Profile of Grape Berries.

Foods 2021 Mar 23;10(3). Epub 2021 Mar 23.

College of Enology, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling 712100, China.

Raisins are a popular and nutritious snack that is produced through the dehydration of postharvest grape berries under high temperature (HT). However, the response of the endogenous metabolism of white grape varieties to postharvest dehydration under different temperature have not been fully elucidated to date. In this study, the white grape cultivar 'Xiangfei' was chosen to investigate the effect of dehydration at 50 °C, 40 °C, and 30 °C on the transcriptomic programme and metabolite profiles of grape berries. Postharvest dehydration promoted the accumulation of soluble sugar components and organic acids in berries. The content of gallic acid and its derivatives increased during the dehydration process and the temperature of 40 °C was the optimal for flavonoids and proanthocyanidins accumulation. High-temperature dehydration stress might promote the accumulation of gallic acid by increasing the expression levels of their biosynthesis related genes and regulating the production of NADP and NADPH. Compared with that at 30 °C, dehydration at 40 °C accelerated the transcription programme of 7654 genes and induced the continuous upregulation of genes related to the heat stress response and redox homeostasis in each stage. The results of this study indicate that an appropriate dehydration temperature should be selected and applied when producing polyphenols-rich raisins.
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http://dx.doi.org/10.3390/foods10030687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8005005PMC
March 2021

Effect of foliar application of fulvic acid antitranspirant on sugar accumulation, phenolic profiles and aroma qualities of Cabernet Sauvignon and Riesling grapes and wines.

Food Chem 2021 Jul 18;351:129308. Epub 2021 Feb 18.

College of Enology, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling 712100, China. Electronic address:

This study investigated the effects of foliar application of fulvic acid antitranspirant (FA-AT) on Cabernet Sauvignon (CS) and Riesling grapes and wines in a warm viticulture region of China. FA-AT controlled the contents of total soluble solids, fructose and glucose in mature grapes and alcohol in wines. FA-AT improved total phenols and flavonoids in Riesling grapes, and total tannin and individual flavanols in CS grapes and wine, while reducing total individual phenolic acids and flavonols in CS wine. Increased volatiles in CS grapes (hexyl acetate, linalool) and wine (isoamyl alcohol, 1-hexanol, 2-phenylethanol) detected by SPME-GC-MS can contribute to the fruity and floral aroma. FA-AT reduced the accumulation of anthocyanins in CS grapes and wine without an eventual reduction in the tonality of wine by sensory analysis, and improved the taste and balance of Riesling wine. Overall, FA-AT can improve the quality of grapes and wines produced in warm viticulture regions.
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http://dx.doi.org/10.1016/j.foodchem.2021.129308DOI Listing
July 2021

The role of VvMYBA2r and VvMYBA2w alleles of the MYBA2 locus in the regulation of anthocyanin biosynthesis for molecular breeding of grape (Vitis spp.) skin coloration.

Plant Biotechnol J 2021 06 1;19(6):1216-1239. Epub 2021 Mar 1.

Key Laboratory of Genetics and Fruit development, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province, China.

In grape, MYBA1 and MYBA2 at the colour locus are the major genetic determinants of grape skin colour, and the mutation of two functional genes (VvMYBA1 and VvMYBA2) from these loci leads to white skin colour. This study aimed to elucidate the regulation of grape berry coloration by isolating and characterizing VvMYBA2w and VvMYBA2r alleles. The overexpression of VvMYBA2r up-regulated the expression of anthocyanin biosynthetic genes and resulted in higher anthocyanin accumulation in transgenic tobacco than wild-type (WT) plants, especially in flowers. However, the ectopic expression of VvMYBA2w inactivated the expression of anthocyanin biosynthetic genes and could not cause obvious phenotypic modulation in transgenic tobacco. Unlike in VvMYBA2r, CA dinucleotide deletion shortened the C-terminal transactivation region and disrupted the transcriptional activation activity of VvMYBA2w. The results indicated that VvMYBA2r positively regulated anthocyanin biosynthesis by forming the VvMYBA2r-VvMYCA1-VvWDR1 complex, and VvWDR1 enhanced anthocyanin accumulation by interacting with the VvMYBA2r-VvMYCA1 complex; however, R L substitution abolished the interaction of VvMYBA2w with VvMYCA1. Meanwhile, both R L substitution and CA dinucleotide deletion seriously affected the efficacy of VvMYBA2w to regulate anthocyanin biosynthesis, and the two non-synonymous mutations were additive in their effects. Investigation of the colour density and MYB haplotypes of 213 grape germplasms revealed that dark-skinned varieties tended to contain HapC-N and HapE2, whereas red-skinned varieties contained high frequencies of HapB and HapC-Rs. Regarding ploidy, the higher the number of functional alleles present in a variety, the darker was the skin colour. In summary, this study provides insight into the roles of VvMYBA2r and VvMYBA2w alleles and lays the foundation for the molecular breeding of grape varieties with different skin colour.
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http://dx.doi.org/10.1111/pbi.13543DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8196647PMC
June 2021

Characterization and Identification of PpEIN3 during the Modulation of Fruit Ripening Process by Ectopic Expressions in Tomato.

Plant Genome 2019 11;12(3):1-12

College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, China.

Core Ideas: First study of PpEIN3 by transgenic experiments to verify its function in the maturity process PpEIN3 is a positive regulator of ethylene signal transduction pathway to promote fruits ripening Ethylene is one of the most important phytohormone in plants and plays a critical role during growth, development, maturity, and aging. The framework of the ethylene signaling pathway is well reported. Nevertheless, studies on Ethylene Insensitive 3 (EIN3), the downstream regulator of the ethylene signaling pathway, need to be investigated, especially in peach [Prunus persica (L.) Batsch]. In this study, we cloned PpEIN3 from peach and characterized it in tomato (Solanum lycopersicum L.). Our results depicted that the open-reading frame of PpEIN3 was 1875 bp, encoding a protein with 624 amino acid residues that contained a conserved EIN3 domain, a highly conserved N-terminal region, and seven DNA-binding sites. PpEIN3 showed very close association with homologous EIN genes from apple (Malus domestica Borkh.) and grapevine (Vitis vinifera L.). All investigated EIN proteins shared similar domains and structures. The PpEIN3 promoter possessed several motifs related to hormones that affect fruit development and ripening. Spatial-temporal expression analysis revealed that PpEIN3 was expressed at high levels in the late stage of fruit development vs. the early stage. In transgenic tomato, PpEIIN3 showed overexpression and the key ethylene biosynthesis genes SlACO1, SlACS1, and SlSAMS1 were upregulated and promoted early maturation in fruit. By contrast, PpEIIN3 silencing delayed ripening and reduced SlEIN3 expression in tomato. The results confirmed that PpEIN3 is a positive regulator of the ethylene signal transduction pathway, which promoted fruit ripening. Our findings provide valuable insight to the roles in ethylene signal components in the modulation of peach fruit ripening.
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http://dx.doi.org/10.3835/plantgenome2018.11.0089DOI Listing
November 2019

Chitinase family genes in grape differentially expressed in a manner specific to fruit species in response to Botrytis cinerea.

Mol Biol Rep 2020 Oct 10;47(10):7349-7363. Epub 2020 Sep 10.

College of Horticulture, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, People's Republic of China.

Chitinases (Chi), an important resistance-related protein, act against fungal pathogens by catalyzing the fungal cell wall, whereas are involved in different biological pathways in grape. In this study, we found 42 Chi family genes in Vitis vinifera L. (VvChis) and evaluated their expression levels after Botrytis infection, stress hormones like ethylene (ETH) and methyl-jasmonate (MeJA), and abiotic stresses like salinity and temperature changes in ripened fruits. VvChis were categorized into five groups including A, B, C, D, and E belonged to glycoside hydrolase family 18 and 19 (GH18 and GH19) according to genes structure, which expression analysis showed distinct temporal and spatial expression patterns changed in different tissues and various development stages. Different responsive elements to biotic and abiotic stresses were determined in the promoter regions of VvChis, specially elicitor-responsive element that was conserved among all VvChis genes. The expression levels of VvChis in groups A, B, and E increased after Botrytis cinerea infection in leaves and berries. Meanwhile, VvChis in glycoside hydrolase family 18 (GH18) were up-regulated under MeJA and ETH treatment, although the induction of VvChis by low temperature was more significant than high temperature. The expression of VvChis was also positively correlated with the concentration of NaCl treatment. Furthermore, differential gene-overexpression of VvChi5, VvChi17, VvChi22, VvChi26, and VvChi31 in strawberry and tomato fruits demonstrated the involvement of various isoforms in resistance to Botrytis infection through antioxidant system and lignin accumulation, which led to a reduction of damage. Among different isoforms of VvChis, we confirmed the interaction of Chi17 with Metallothionein (MTL) as oxidative stress protection, which suggests VvChis can modulate oxidative stress during postharvest storage in ripened fruits.
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http://dx.doi.org/10.1007/s11033-020-05791-yDOI Listing
October 2020

Characterization of the regulation mechanism of grapevine microRNA172 family members during flower development.

BMC Plant Biol 2020 Sep 3;20(1):409. Epub 2020 Sep 3.

College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.

Background: Grapevine (Vitis vinifera L.), which has important nutritional values and health benefits, is one of the most economically important fruit crops cultivated worldwide. Several studies showed a large number of microRNAs (VvmiRNAs) involved in the modulation of grape growth and development, and many VvmiRNA families have multiple members. However, the way by which various members from the same miRNA family work is unclear, particularly in grapes.

Results: In this study, an important conserved VvmiR172 family (VvmiR172s) and their targets were set as a good example for elucidating the interaction degree, mechanism, and spatio-temporal traits of diverse members from the same miRNA family. miR-RACE and Stem-loop RT-PCR were used to identify the spatio-temporal expressions of various members of VvmiR172s; together with RLM-RACE, PPM-RACE, Western blot, transgenic technologies, their interaction degree, and regulation mechanism were further validated. The expression of VvmiR172c was significantly higher than that of VvmiR172a, b, and d and showed a positive correlation with the abundance of VvAP2 cleavage products. These findings indicated that VvmiR172c might be one of the main action factors of the VvmiR172 family in flower development. The ability of VvmiR172c to cleave target genes differed due to divergence in complementary degree with VvAP2 and expression levels of various members. In VvmiR172 transgenic lines, we observed that 35S::VvmiR172c resulted in the earliest and abundant flowering, indicating the strong function of VvmiR172c. In contrast, the non-significant phenotypic changes were detected in the VvAP2 transgenic lines. The qRT-PCR and Western bolt results demonstrated that VvmiR172c plays a major role in targeting VvAP2.

Conclusions: VvmiR172 up-regulated the expression of NtFT and decreased the expression of NtFLC. The up/down regulation of VvmiR172c was the most pronounced. The functions of four VvmiR172 members in grape differed, and miR172c had the strongest regulation on AP2.
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http://dx.doi.org/10.1186/s12870-020-02627-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7650276PMC
September 2020

Using foliar nitrogen application during veraison to improve the flavor components of grape and wine.

J Sci Food Agric 2021 Mar 25;101(4):1288-1300. Epub 2020 Sep 25.

College of Enology, Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, No. 22 Xinong Road, Yangling, shaanxi, 712100, China.

Nitrogen is involved in the winemaking process from grapevine growth to wine fermentation, and its precise utilization in vineyards can regulate grape and wine quality. Foliar nitrogen application during veraison (FNAV) could prevent nitrogen deficiency in grape and must in nitrogen-deficient vineyards. Moreover, FNAV also could improve certain flavor components of grape and wine, but little attention has been paid to FNAV. Therefore, this paper mainly reviews the difficulties encountered in current applications of nitrogen in vineyards and wineries, and the advantages of FNAV over the addition of nitrogen in soil and wineries. And it discusses that FNAV can increase yeast-assimilable nitrogen and phenolics, and scarcely affect volatile components of grape (must and wine), and points out the existing problems including the core issue and then puts forward future research directions. This information may indicate future directions for research, and provide a reference for viticulturists and winemakers on the precise application of nitrogen on grapevine and must to further improve grape and wine quality in nitrogen-deficient vineyards. © 2020 Society of Chemical Industry.
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http://dx.doi.org/10.1002/jsfa.10782DOI Listing
March 2021

Characterization of DNA methylation variations during fruit development and ripening of (cv. 'Fujiminori').

Physiol Mol Biol Plants 2020 Apr 3;26(4):617-637. Epub 2020 Feb 3.

1Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu Province, China.

The fruit is the most important economical organ in the grape; accordingly, to investigate the grapevine genomic methylation landscape and examine its functional significance during fruit development, we generated whole genome DNA methylation maps for various developmental stages in the fruit of grapevine. In this study, thirteen DNA methylation-related genes and their expression profiles were identified and analyzed. The methylation levels for mC, mCG, mCHG, and mCHH contexts in 65 days after flowering (65DAF) fruit (véraison stage) were higher than those in 40DAF (green stage) and 90DAF (mature stage) fruits. Relative to methylation in the mC context, methylation levels in the mCHH context were higher than those of mCG and mCHG. The DNA methylation level in the ncRNA regions was significantly higher than that in exon, gene, intron, and mRNA regions. The differentially methylated regions (DMRs) and differentially methylated promoters (DMPs) in 65DAF_vs_40DAF were both higher than those in 90DAF_vs_65DAF and 90DAF_vs_40DAF. Most DMRs (or DMPs) were involved in metabolic processes and cell processes, binding, and catalytic activity. These results indicated that DNA methylation represses gene expression during grape fruit development, and it broadens our understanding of the landscape and function of DNA methylation in grapevine genomes.
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http://dx.doi.org/10.1007/s12298-020-00759-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7113366PMC
April 2020

Comparative study of , , and gene families in fourteen species and their expression in .

3 Biotech 2020 Feb 27;10(2):72. Epub 2020 Jan 27.

1Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu People's Republic of China.

Bud dormancy is one of the most important defensive mechanisms through which plants resist cold stress during harsh winter weather. , , and have been reported to be involved in many biological processes, including bud dormancy. In the present study, grapevine () and other thirteen plants (six woody plants and seven herbaceous plants) were analyzed for the quantity, sequence structure, and evolution patterns of their , , and gene family members. Moreover, the expression of , , and genes was also investigated. Thus, 51 , 1,205 , and 489 genes were isolated from selected genomes, while 5 , 114 , and 50 duplicate gene pairs were identified in 10 genomes. Moreover, WGD and segmental duplication events were associated with the majority of the expansions of and gene families. The , , and genes significantly differentially expressed throughout bud dormancy outnumbered those significantly differentially expressed throughout fruit development or under abiotic stresses. Interestingly, multiple stress responsive genes were identified, such as (VIT_00s0313g00070), two genes (VIT_18s0001g11310 and VIT_02s0025g02250), and two genes (VIT_07s0031g01710 and VIT_11s0052g00450). These data provide candidate genes for molecular biology research investigating bud dormancy and responses to abiotic stresses (namely salt, drought, copper, and waterlogging).
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http://dx.doi.org/10.1007/s13205-019-2039-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6985326PMC
February 2020

Integrated metatranscriptome and transcriptome reveals the microbial community composition and physiological function of xylem sap on grapevine during bleeding period.

Genes Genomics 2019 09 24;41(9):1095-1111. Epub 2019 Jun 24.

College of Horticulture, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, Jiangsu, China.

Background: The xylem sap of fruit trees ensures the survival during the dormant period, and its flow during the bleeding period is correlated with the start of a new life cycle. Though the simple exploration on ingredients in the sap was carried out in the early years, the specific life activities and physiology functions of the sap during bleeding period have not been reported yet and the bleeding period is still a fruit tree development period worthy of attention.

Objectives: In this study, the microbial community composition during bleeding period were revealed by metatranscriptome and transcriptomic data. For the first time, the microorganism genome and grape genome in xylem sap were analyzed on transcriptional level, based on which the main physiological functions of the sap were also determined.

Methods: The genomic RNA in the sap was isolated and sequenced. Kyoto Encyclopedia of Gene and Genome (KEGG), Evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) and Carbohydrate-Active enzymes Database (CAZy) functional annotation were used to analysis the function of micro-organisms in xylem sap. DEGs were analyzed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The genes responsive to biotic and abiotic stresses were finally screened by transcriptome screening, stress data analysis and vitro validation experiments.

Results: The analysis exhibited 36,144,564 micro-related clean reads and 244,213 unigene. KEGG, eggNOG and CAZy functional annotation analysis indicated that signal transduction and material metabolism were the most important function of xylem sap. DEGs analysis were mainly about disease resistance, carbon source metabolism and hormone signal transduction, especially in P3 vs P1, enriched in the plant-pathogen interaction pathway. Analysis on grape genome information revealed xylem sap had little RNA with weak life activity. Metabolic pathways, biosynthesis of secondary metabolites, plant hormone signal transduction and plant-pathogen interaction were the four pathways with the largest number of enriched genes. Moreover, 16 genes responsive to biotic and abiotic stresses were screened out.

Conclusion: Promoting plant growth and resisting pathogens were the most important function of xylem sap during the bleeding period, and the function of microbial community were closely related to microorganisms growth and disease resistance. The 16 stress-related genes might be used for the future grape resistance research.
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http://dx.doi.org/10.1007/s13258-019-00841-7DOI Listing
September 2019

Transcriptome Sequence Analysis Elaborates a Complex Defensive Mechanism of Grapevine ( L.) in Response to Salt Stress.

Int J Mol Sci 2018 Dec 12;19(12). Epub 2018 Dec 12.

College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.

Salinity is ubiquitous abiotic stress factor limiting viticulture productivity worldwide. However, the grapevine is vulnerable to salt stress, which severely affects growth and development of the vine. Hence, it is crucial to delve into the salt resistance mechanism and screen out salt-resistance prediction marker genes; we implicated RNA-sequence (RNA-seq) technology to compare the grapevine transcriptome profile to salt stress. Results showed 2472 differentially-expressed genes (DEGs) in total in salt-responsive grapevine leaves, including 1067 up-regulated and 1405 down-regulated DEGs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations suggested that many DEGs were involved in various defense-related biological pathways, including ROS scavenging, ion transportation, heat shock proteins (HSPs), pathogenesis-related proteins (PRs) and hormone signaling. Furthermore, many DEGs were encoded transcription factors (TFs) and essential regulatory proteins involved in signal transduction by regulating the salt resistance-related genes in grapevine. The antioxidant enzyme analysis showed that salt stress significantly affected the superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and glutathione S-transferase (GST) activities in grapevine leaves. Moreover, the uptake and distribution of sodium (Na⁺), potassium (K⁺) and chlorine (Cl) in source and sink tissues of grapevine was significantly affected by salt stress. Finally, the qRT-PCR analysis of DE validated the data and findings were significantly consistent with RNA-seq data, which further assisted in the selection of salt stress-responsive candidate genes in grapevine. This study contributes in new perspicacity into the underlying molecular mechanism of grapevine salt stress-tolerance at the transcriptome level and explore new approaches to applying the gene information in genetic engineering and breeding purposes.
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http://dx.doi.org/10.3390/ijms19124019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6321183PMC
December 2018

Genome-wide Characterization and Expression Analysis of Sugar Transporter Family Genes in Woodland Strawberry.

Plant Genome 2018 11;11(3)

In higher plants, sugars are nutrients and important signal molecules. Sugar transporters (STs) facilitate sugar transport across membranes and are associated with loading and unloading of the conducting complex. Strawberry ( Duchesne ex Rozier) is one of the most economically important and widely cultivated fruit crop and a model plant among fleshy fruits worldwide. In this study, 66 woodland strawberry ( L.) ST (FvST) genes were identified and further classified into eight distinct subfamilies in the woodland strawberry genome based on the phylogenetic analysis. In the promoter sequences of FvST gene families, a search for -regulatory elements suggested that some of them might probably be regulated by plant hormones (e.g., salicylic acid, abscisic acid, and auxin), abiotic (e.g., drought, excessive cold, and light), and biotic stress factors. Exon-intron analysis showed that each subfamily manifested closely associated gene architectural features based on similar number or length of exons. Moreover, to comprehend the potential evolution mechanism of FvST gene family, the analysis of genome duplication events was performed. The segmental and tandem duplication analysis elucidated that some of ST genes arose through whole-genome duplication (WGD) or segmental duplication, accompanied by tandem duplications. The expression analysis of 24 FvST genes in vegetative and during fruit development has shown that the expression of several ST genes was tissue and developmental stage specific. Generally, our findings are important in understanding of the allocation of photo assimilates from source to sink cell and provide insights into the genomic organization and expression profiling of FvST gene families in woodland strawberry.
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http://dx.doi.org/10.3835/plantgenome2017.11.0103DOI Listing
November 2018

Genome-Wide Identification of PIFs in Grapes ( L.) and Their Transcriptional Analysis under Lighting/Shading Conditions.

Genes (Basel) 2018 Sep 7;9(9). Epub 2018 Sep 7.

College of Horticulture, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.

Phytochrome-interacting factors (PIFs), as the basic helix⁻loop⁻helix (bHLH) transcription factors, are the primary signaling partners for phytochromes (PHY) that play a key role in PHY-mediated light signal transduction. At present, there are few studies on PIFs in fruit trees. In order to clarify the status of PIFs in grapevines, we identified members of the grape PIFs family and conducted phylogenetic and expression analysis. We identified PIF1, PIF3, PIF4, and PIF7 in PIFs families of the grapevine ( L.), which were distributed on four different chromosomes with similar gene structures. Except for the closer relationship with PIF1 of citrus, PIFs of grape were distant from the other fruit species such as apple, pear, peach, and strawberry. The (except ) were located in the syntenic block with those from , , or In addition to PIF1, all PIFs in grapevines have conserved active PHYB binding (APB) sequences. VvPIF1 has a conserved PIF1-specific active PHYA binding (APA) sequence, while amino acid mutations occurred in the specific APA sequence in VvPIF3. Interestingly, two specific motifs were found in the PIF4 amino acid sequence. The photoreceptor-related elements in the promoter region were the most abundant. PIF1, LONG HYPOCOTYL 5 (HY5) and PIF3, PIF4, GIBBERELLIC ACID INSENSITIVE 1 (GAI1) may interact with each other and participate together in light signal transduction. The relative expression levels of the showed diverse patterns in the various organs at different developmental stages, of which was most highly expressed. Prior to maturation, the expression of and in the skin of the different cultivars increased, while the expression of all in the flesh decreased. The transcription level of in grape leaves was sensitive to changes in lighting and shading. Shading treatment was beneficial for enhancing the transcription level of , but the effect on and was time-controlled. We concluded that PIFs in grapevines are both conservative and species-specific. The identification and analysis of grape PIFs could provide a theoretical foundation for the further construction of grape light regulation networks.
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http://dx.doi.org/10.3390/genes9090451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6162725PMC
September 2018

Analysis of the regulation networks in grapevine reveals response to waterlogging stress and candidate gene-marker selection for damage severity.

R Soc Open Sci 2018 Jun 27;5(6):172253. Epub 2018 Jun 27.

Nanjing Agricultural University, Nanjing 210095, People's Republic of China.

Owing to the climate change impacts, waterlogging is one of the most hazardous abiotic stresses to crops, which also can result in a serious reduction in the quantity and quality of grape berry and wine production during the rainy season. Therefore, the exploration of the response mechanism of grape to waterlogging is necessary, for which the analysis of the transcriptomic regulation networks of grapevine leaves in response to waterlogging stress was carried out. In this study, 12 634 genes were detected in both waterlogging stress and control grapevine plants, out of which 6837 genes were differentially expressed. A comparative analysis revealed that genes functioning in the antioxidant system, glycolysis and fermentation pathway, chlorophyll metabolism, amino acid metabolism and hormones were activated to reduce injury to grapes under the waterlogging stress. Meanwhile, genes encoding class-2 non-symbiotic haemoglobin were determined as important in waterlogging acclimation. Additionally, the expression variations of three marker genes were found to be informative and can be used to predict the viability of the grapevines subjected to waterlogging. This research not only probes the molecular mechanism underlying grapevine waterlogging tolerance but also puts forward an idea about the application of gene expression information to practical management.
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http://dx.doi.org/10.1098/rsos.172253DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030322PMC
June 2018

Changes of Anthocyanin Component Biosynthesis in 'Summer Black' Grape Berries after the Red Flesh Mutation Occurred.

J Agric Food Chem 2018 Sep 22;66(35):9209-9218. Epub 2018 Aug 22.

College of Horticulture , Nanjing Agricultural University , Nanjing City , 210095 Jiangsu Province People's Republic of China.

The coloring process of grape flesh is valuable for research and promotion of the high nutritional quality of anthocyanins. 'Summer Black' and it is new red flesh mutant were used to analyze the changes of anthocyanin biosynthesis during grape berry development. Eighteen kinds of anthocyanins were detected in mature berries of the two cultivars, but the content of most 3'- and 3',5'-substituted anthocyanins was higher in the skin of the mutant. Anthocyanin accumulation occurred simultaneously in the skin and flesh of the mutant, and their types and content were more abundant in the former. For the mutant, there were only CHS, OMT, MYBA3, and MYBPA1 at lower transcriptional level in the flesh during veraison when compared with these in the skin, which might be an important factor to limit the anthocyanin accumulation in the flesh. The occurrence of red flesh might be related the enhancement of anthocyanin biosynthesis in the whole berry.
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http://dx.doi.org/10.1021/acs.jafc.8b02150DOI Listing
September 2018

In silico identification and computational characterization of endogenous small interfering RNAs from diverse grapevine tissues and stages.

Genes Genomics 2018 08 4;40(8):801-817. Epub 2018 Apr 4.

College of Horticulture, Nanjing Agricultural University, Weigang 1 hao, Nanjing, 210095, China.

Small interfering RNAs (siRNAs) are effectors of regulatory pathways underlying plant development, metabolism, and stress- and nutrient-signaling regulatory networks. The endogenous siRNAs are generally not conserved between plants; consequently, it is necessary and important to identify and characterize siRNAs from various plants. To address the nature and functions of siRNAs, and understand the biological roles of the huge siRNA population in grapevine (Vitis vinifera L.). The high-throughput sequencing technology was used to identify a large set of putative endogenous siRNAs from six grapevine tissues/organs. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed to classify the target genes of siRNA. In total, 520,519 candidate siRNAs were identified and their expression profiles exhibited typical temporal characters during grapevine development. In addition, we identified two grapevine trans-acting siRNA (TAS) gene homologs (VvTAS3 and VvTAS4) and the derived trans-acting siRNAs (tasiRNAs) that could target grapevine auxin response factor (ARF) and myeloblastosis (MYB) genes. Furthermore, the GO and KEGG analysis of target genes showed that most of them covered a broad range of functional categories, especially involving in disease-resistance process. The large-scale and completely genome-wide level identification and characterization of grapevine endogenous siRNAs from the diverse tissues by high throughput technology revealed the nature and functions of siRNAs in grapevine.
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http://dx.doi.org/10.1007/s13258-018-0679-zDOI Listing
August 2018

RNA-Sequencing Reveals Biological Networks during Table Grapevine ('Fujiminori') Fruit Development.

PLoS One 2017 24;12(1):e0170571. Epub 2017 Jan 24.

College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, PR China.

Grapevine berry development is a complex and genetically controlled process, with many morphological, biochemical and physiological changes occurring during the maturation process. Research carried out on grapevine berry development has been mainly concerned with wine grape, while barely focusing on table grape. 'Fujiminori' is an important table grapevine cultivar, which is cultivated in most provinces of China. In order to uncover the dynamic networks involved in anthocyanin biosynthesis, cell wall development, lipid metabolism and starch-sugar metabolism in 'Fujiminori' fruit, we employed RNA-sequencing (RNA-seq) and analyzed the whole transcriptome of grape berry during development at the expanding period (40 days after full bloom, 40DAF), véraison period (65DAF), and mature period (90DAF). The sequencing depth in each sample was greater than 12×, and the expression level of nearly half of the expressed genes were greater than 1. Moreover, greater than 64% of the clean reads were aligned to the Vitis vinifera reference genome, and 5,620, 3,381, and 5,196 differentially expressed genes (DEGs) were identified between different fruit stages, respectively. Results of the analysis of DEGs showed that the most significant changes in various processes occurred from the expanding stage to the véraison stage. The expression patterns of F3'H and F3'5'H were crucial in determining red or blue color of the fruit skin. The dynamic networks of cell wall development, lipid metabolism and starch-sugar metabolism were also constructed. A total of 4,934 SSR loci were also identified from 4,337 grapevine genes, which may be helpful for the development of phylogenetic analysis in grapevine and other fruit trees. Our work provides the foundation for developmental research of grapevine fruit as well as other non-climacteric fruits.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170571PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5261597PMC
August 2017
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