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| 1 | Optimizing the CRISPR/Cas9 system for genome editing in grape by using grape promoters显示文摘The efficacy of the CRISPR/Cas9 system in grapevine(Vitis vinifera L.)has been documented,but the optimization of this system,as well as CRISPR/Cas9-mediated multiplex genome editing,has not been explored in this species.Herein,we identified four VvU3 and VvU6 promoters and two ubiquitin(UBQ)promoters in grapevine and demonstrated that the use of the identified VvU3/U6 and UBQ2 promoters could significantly increase the editing efficiency in grape by improving the expression of sgRNA and Cas9,respectively.Furthermore,we conducted multiplex genome editing using the optimized CRISPR/Cas9 vector that contained the conventional multiple sgRNA expression cassettes or the polycistronic tRNA-sgRNA cassette(PTG)by targeting the sugar-related tonoplastic monosaccharide transporter(TMT)family members TMT1 and TMT2,and the overall editing efficiencies were higher than 10%.The simultaneous editing of TMT1 and TMT2 resulted in reduced sugar levels,which indicated the role of these two genes in sugar accumulation in grapes.Moreover,the activities of the VvU3,VvU6,and UBQ2 promoters in tobacco genome editing were demonstrated by editing the phytoene desaturase(PDS)gene in Nicotiana benthamiana leaves.Our study provides materials for the optimization of the CRISPR/Cas9 system.To our knowledge,our simultaneous editing of the grape TMT family genes TMT1 and TMT2 constitutes the first example of multiplex genome editing in grape.The multiplex editing systems described in this manuscript expand the toolbox of grape genome editing,which would facilitate basic research and molecular breeding in grapevine. | Chong Ren Yanfei Liu Yuchen Guo Wei Duan Peige Fan Shaohua Li Zhenchang Liang | 2021 | Horticulture Research2021，8，1： | 6 |
| 2 | A key‘foxy’aroma gene is regulated by homologyinduced promoter indels in the iconic juice grape‘Concord’显示文摘‘Concord’,the most well-known juice grape with a parentage of the North American grape species Vitis labrusca L.,possesses a special‘foxy’aroma predominantly resulted from the accumulation of methyl anthranilate(MA)in berries.This aroma,however,is often perceived as an undesirable attribute by wine consumers and rarely noticeable in the common table and wine grape species V.vinifera.Here we discovered homology-induced promoter indels as a major genetic mechanism for species-specific regulation of a key‘foxy’aroma gene,anthraniloyl-CoA:methanol acyltransferase(AMAT),that is responsible for MA biosynthesis.We found the absence of a 426-bp and/or a 42-bp sequence in AMAT promoters highly associated with high levels of AMAT expression and MA accumulation in‘Concord’and other V.labrusca-derived grapes.These promoter variants,all with direct and inverted repeats,were further confirmed in more than 1,300 Vitis germplasm.Moreover,functional impact of these indels was validated in transgenic Arabidopsis.Superimposed on the promoter regulation,large structural changes including exonic insertion of a retrotransposon were present at the AMAT locus in some V.vinifera grapes.Elucidation of the AMAT genetic regulation advances our understanding of the‘foxy’aroma trait and makes it genetically trackable and amenable in grapevine breeding. | Yingzhen Yang JoséCuenca Nian Wang Zhenchang Liang Honghe Sun Benjamin Gutierrez Xiaojun Xi Jie Arro YiWang Peige Fan Jason Londo Peter Cousins Shaohua Li Zhangjun Fei Gan-Yuan Zhong | 2020 | Horticulture Research2020，7，1： | 3 |
| 3 | SCUBE2 mediates bone metastasis of luminal breast cancer by modulating immune-suppressive osteoblastic niches显示文摘Estrogen receptor (ER)-positive luminal breast cancer is a subtype with generally lower risk of metastasis to most distant organs. However, bone recurrence occurs preferentially in luminal breast cancer. The mechanisms of this subtype-specific organotropism remain elusive. Here we show that an ER-regulated secretory protein SCUBE2 contributes to bone tropism of luminal breast cancer. Single-cell RNA sequencing analysis reveals osteoblastic enrichment by SCUBE2 in early bone-metastatic niches. SCUBE2 facilitates release of tumor membrane-anchored SHH to activate Hedgehog signaling in mesenchymal stem cells, thus promoting osteoblast differentiation. Osteoblasts deposit collagens to suppress NK cells via the inhibitory LAIR1 signaling and promote tumor colonization. SCUBE2 expression and secretion are associated with osteoblast differentiation and bone metastasis in human tumors. Targeting Hedgehog signaling with Sonidegib and targeting SCUBE2 with a neutralizing antibody both effectively suppress bone metastasis in multiple metastasis models. Overall, our findings provide a mechanistic explanation for bone preference in luminal breast cancer metastasis and new approaches for metastasis treatment. | Qiuyao Wu Pu Tian Dasa He Zhenchang Jia Yunfei He Wenqian Luo Xianzhe Lv Yuan Wang Peiyuan Zhang Yajun Liang Wenjin Zhao Jun Qin Peng Su Yi-Zhou Jiang Zhi-Ming Shao Qifeng Yang Guohong Hu | 2023 | Cell Research2023，33，6： | 1 |
| 4 | Volatiles of grape berries evaluated at the germplasm level by headspace-SPME with GC–MS显示文摘 | Chunxiang Yang Yiju Wang Zhenchang Liang Peige Fan Benhong Wu Liu Yang Younian Wang Shaohua Li | 2008 | Food Chemistry2008，，3： | 1 |
| 5 | Adventist Health; differentweight during valproate dose of blood concentration and clinical resultsof 显示文摘 | Liu Yuxi Pang Feng Liang Zhenchang | 2008 | Shanxi medical journal2008，，2： | 1 |
| 6 | Polypbenofic composition and content in the ripe berries of wild Vitis species显示文摘 | Liang Zhenchang Yang Yingzhen Cheng Lailiang | 2012 | Food Chemistry2012，132，2： | 1 |
| 7 | Gene body demethylation increases expression and is associated with self-pruning during grape genome duplication显示文摘A colchicine-induced autotetraploid grapevine exhibiting potentially valuable agronomic traits for grape production and breeding,including self-pruning,was identified.This study investigated DNA methylation variation and its role in gene expression during self-pruning in the autotetraploid grapevine.We used RNA-Seq to estimate differentially expressed genes between diploid and autotetraploid grapevine shoot tips.The genes showing increases in the autotetraploid were mainly related to stress response pathways,whereas those showing decreases in the autotetraploid were related to biological metabolism and biosynthesis.Whole-genome bisulfite sequencing was performed to produce single-base methylomes for the diploid and autotetraploid grapevines.Comparison between the methylomes revealed that they were conserved in CG and CHG contexts.In the autotetraploid grapevine,hypodifferentially methylated regions(DMRs)and hyper-DMRs in the gene body increased or decreased gene expression,respectively.Our results indicated that a hypo-DMR in the ACO1 gene body increased its expression and might promote self-pruning.This study reports that hypo-DMRs in the gene body increase gene expression in plants and reveals the mechanism underlying the changes in the modifications affecting gene expression during genome duplication.Overall,our results provide valuable information for understanding the relationships between DNA methylation,gene expression,and autotetraploid breeding in grape. | Luming Zou Wenwen Liu Zhan Zhang Everard J.Edwards Elias Kirabi Gathunga Peige Fan Wei Duan Shaohua Li Zhenchang Liang | 2020 | Horticulture Research2020，7，1： | 1 |
| 8 | Volatiles of grape berries evaluated at the germplasm level by headspace-SPME with GC-MS显示文摘 | YANG Chunxiang WANG Yiju LIANG Zhenchang | 2009 | Food Chemistry2009，114，3： | 1 |
| 9 | Changes ofpolyphenols, sugars, and organic acid in 5 vitis genotypes during berryripening显示文摘 | LIANG Zhenchang SANG Min FAN Peige | 2011 | Journal of Food Science2011，76，9： | 1 |
| 10 | Data Comparison and Software Design for Easy Selection and Application of CRISPR-based Genome Editing Systems in Plants显示文摘CRISPR-based genome editing systems have been successfully and effectively used in many organisms.However,only a few studies have reported the comparison between CRISPR/Cas9 and CRISPR/Cpf1 systems in the whole-genome applications.Although many web-based toolkits are available,there is still a shortage of comprehensive,user-friendly,and plant-specific CRISPR databases and desktop software.In this study,we identified and analyzed the similarities and differences between CRISPR/Cas9 and CRISPR/Cpf1 systems by considering the abundance of proto-spacer adjacent motif(PAM)sites,the effects of GC content,optimal proto-spacer length,potential universality within the plant kingdom,PAM-rich region(PARR)inhibiting ratio,and the effects of G-quadruplex(G-Q)structures.Using this information,we built a comprehensive CRISPR database(including 138 plant genome data sources,www.grapeworld.cn/pc/index.html),which provides search tools for the identification of CRISPR editing sites in both CRISPR/Cas9 and CRISPR/Cpf1 systems.We also developed a desktop software on the basis of the Perl/Tk tool,which facilitates and improves the detection and analysis of CRISPR editing sites at the whole-genome level on Linux and/or Windows platform.Therefore,this study provides helpful data and software for easy selection and application of CRISPR-based genome editing systems in plants. | Yi Wang Fatma Lecourieux Rui Zhang Zhanwu Dai David Lecourieux Shaohua Li Zhenchang Liang | 2021 | Genomics, Proteomics & Bioinformatics2021，19，6： | 0 |
| 11 | VvBBX44 and VvMYBA1 form a regulatory feedback loop to balance anthocyanin biosynthesis in grape显示文摘Anthocyanins are essential for the quality of perennial horticultural crops,such as grapes.In grapes,ELONGATED HYPOCOTYL 5(HY5)and MYBA1 are two critical transcription factors that regulate anthocyanin biosynthesis.Our previous work has shown that Vitis vinifera B-box protein 44(VvBBX44)inhibits anthocyanin synthesis and represses VvHY5 expression in grape calli.However,the regulatory mechanism underlying this regulation was unclear.In this study,we found that loss of VvBBX44 function resulted in increased anthocyanin accumulation in grapevine callus.VvBBX44 directly represses VvMYBA1,which activates VvBBX44.VvMYBA1,but not VvBBX44,directly modulates the expression of grape UDP flavonoid 3-O-glucosyltransferase(VvUFGT).We demonstrated that VvBBX44 represses the transcriptional activation of VvUFGT and VvBBX44 induced by VvMYBA1.However,VvBBX44 and VvMYBA1 did not physically interact in yeast.The application of exogenous anthocyanin stimulated VvBBX44 expression in grapevine suspension cells and tobacco leaves.These findings suggest that VvBBX44 and VvMYBA1 form a transcriptional feedback loop to prevent overaccumulation of anthocyanin and reduce metabolic costs.Our work sheds light on the complex regulatory network that controls anthocyanin biosynthesis in grapevine. | Wenwen Liu Huayuan Mu Ling Yuan Yang Li Yuting Li Shenchang Li Chong Ren Wei Duan Peige Fan Zhanwu Dai Yongfeng Zhou Zhenchang Liang Shaohua Li Lijun Wang | 2023 | Horticulture Research2023，10，10： | 0 |
| 12 | The class B heat shock factor HSFB1 regulates heat tolerance in grapevine显示文摘Grape is a widely cultivated crop with high economic value.Most cultivars derived from mild or cooler climates may not withstand increasing heat stress.Therefore,dissecting the mechanisms of heat tolerance in grapes is of particular significance.Here,we performed comparative transcriptome analysis of Vitis davidii‘Tangwei’(heat tolerant)and Vitis vinifera‘Jingxiu’(heat sensitive)grapevines after exposure to 25°C,40°C,or 45°C for 2 h.More differentially expressed genes(DEGs)were detected in‘Tangwei’than in‘Jingxiu’in response to heat stress,and the number of DEGs increased with increasing treatment temperatures.We identified a class B Heat Shock Factor,HSFB1,which was significantly upregulated in‘Tangwei’,but not in‘Jingxiu’,at high temperature.VdHSFB1 from‘Tangwei’and VvHSFB1 from‘Jingxiu’differ in only one amino acid,and both showed similar transcriptional repression activities.Overexpression and RNA interference of HSFB1 in grape indicated that HSFB1 positively regulates the heat tolerance.Moreover,the heat tolerance of HSFB1-overexpressing plants was positively correlated to HSFB1 expression level.The activity of the VdHSFB1 promoter is higher than that of VvHSFB1 under both normal and high temperatures.Promoter analysis showed that more TATA-box and AT∼TATA-box cis-elements are present in the VdHSFB1 promoter than the VvHSFB1 promoter.The promoter sequence variations between VdHSFB1 and VvHSFB1 likely determine the HSFB1 expression levels that inf luence heat tolerance of the two grape germplasms with contrasting thermotolerance.Collectively,we validated the role of HSFB1 in heat tolerance,and the knowledge gained will advance our ability to breed heat-tolerant grape cultivars. | Haiyang Chen Xinna Liu Shenchang Li Ling Yuan Huayuan Mu Yi Wang Yang Li Wei Duan Peige Fan Zhenchang Liang Lijun Wang | 2023 | Horticulture Research2023，10，3： | 0 |
| 13 | A transcriptome analysis of two grapevine populations segregating for tendril phyllotaxy显示文摘The shoot structure of cultivated grapevine Vitis vinifera L.typically exhibits a three-node modular repetitive pattern,two sequential leaf-opposed tendrils followed by a tendril-free node.In this study,we investigated the molecular basis of this pattern by characterizing differentially expressed genes in 10 bulk samples of young tendril tissue from two grapevine populations showing segregation of mutant or wild-type shoot/tendril phyllotaxy.One population was the selfed progeny and the other one,an outcrossed progeny of a Vitis hybrid,‘Roger’s Red’.We analyzed 13375 expressed genes and carried out in-depth analyses of 324 of them,which were differentially expressed with a minimum of 1.5-fold changes between the mutant and wild-type bulk samples in both selfed and cross populations.A significant portion of these genes were direct cis-binding targets of 14 transcription factor families that were themselves differentially expressed.Network-based dependency analysis further revealed that most of the significantly rewired connections among the 10 most connected hub genes involved at least one transcription factor.TCP3 and MYB12,which were known important for plant-form development,were among these transcription factors.More importantly,TCP3 and MYB12 were found in this study to be involved in regulating the lignin gene PRX52,which is important to plant-form development.A further support evidence for the roles of TCP3-MYB12-PRX52 in contributing to tendril phyllotaxy was the findings of two other lignin-related genes uniquely expressed in the mutant phyllotaxy background. | Jie Arro Jose Cuenca Yingzhen Yang Zhenchang Liang Peter Cousins Gan-Yuan Zhong | 2017 | Horticulture Research2017，4，1： | 0 |
| 14 | Basic leucine zipper gene VvbZIP61 is expressed at a quantitative trait locus for high monoterpene content in grape berries显示文摘The widely appreciated muscat flavor of grapes and wine is mainly attributable to the monoterpenes that accumulate in ripe grape berries.To identify quantitative trait loci(QTL)for grape berry monoterpene content,an F1 mapping population was constructed by a cross between two grapevine genotypes,one with neutral aroma berries(cv.‘Beifeng’)and the other with a pronounced muscat aroma(elite Vitis vinifera line‘3–34’).A high-density genetic linkage map spanning 1563.7 cM was constructed using 3332 SNP markers that were assigned to 19 linkage groups.Monoterpenes were extracted from the berry of the F1 progeny,then identified and quantified by gas chromatography–mass spectrometry.Twelve stable QTLs associated with the amounts of 11 monoterpenes in berries were thus identified.In parallel,the levels of RNA in berries from 34 diverse cultivars were estimated by RNA sequencing and compared to the monoterpene content of the berries.The expression of five genes mapping to stable QTLs correlated well with the monoterpene content of berries.These genes,including the basic leucine zipper VvbZIP61 gene on chromosome 12,are therefore considered as potentially being involved in monoterpene metabolism.Overexpression of VvbZIP61 in Vitis amurensis callus through Agrobacterium-mediated transformation significantly increased the accumulation of several monoterpenes in the callus,including nerol,linalool,geranial,geraniol,β-myrcene,and D-limonene.It is hypothesized that VvbZIP61 expression acts to increase muscat flavor in grapes.These results advance our understanding of the genetic control of monoterpene biosynthesis in grapes and provide important information for the marker-assisted selection of aroma compounds in grape breeding. | Yuyu Zhang Cuixia Liu Xianju Liu Zemin Wang Yi Wang Gan-yuan Zhong Shaohua Li Zhanwu Dai Zhenchang Liang Peige Fan | 2023 | Horticulture Research2023，10，9： | 0 |
| 15 | Grapevine plantlets respond to different monochromatic lights by tuning photosynthesis and carbon allocation显示文摘The quality of planting materials is the foundation for productivity,longevity,and berry quality of perennial grapevines with a long lifespan.Manipulating the nursery light spectrum may speed up the production of healthy and high-quality planting vines but the underlying mechanisms remain elusive.Herein,the effects of different monochromatic lights(green,blue,and red)on grapevine growth,leaf photosynthesis,whole-plant carbon allocation,and transcriptome reprograming were investigated with white light as control.Results showed that blue and red lights were favorable for plantlet growth in comparison with white light.Blue light repressed excessive growth,significantly increased the maximum net photosynthetic rate(Pn)of leaves by 39.58%and leaf specific weight by 38.29%.Red light increased the dry weight of the stem by 53.60%,the starch content of the leaf by 53.63%,and the sucrose content of the stem by 230%.Green light reduced all photosynthetic indexes of the grape plantlet.Photosynthetic photon flux density(PPFD)/Ci–Pn curves indicated that blue light affected photosynthetic rate depending on the light intensity and CO2 concentration.RNA-seq analysis of different organs(leaf,stem,and root)revealed a systematic transcriptome remodeling and VvCOP1(CONSTITUTIVELY PHOTOMORPHOGENIC 1),VvHY5(ELONGATED HYPOCOTYL5),VvHYH(HY5 HOMOLOG),VvELIP(early light-induced protein)and VvPIF3(PHYTOCHROME INTERACTING FACTOR 3)may play important roles in this shoot-to-root signaling.Furthermore,the correlation network between differential expression genes and physiological traits indicated that VvpsbS(photosystem II subunit S),Vvpsb28(photosystem II subunit 28),VvHYH,VvSUS4(sucrose synthase 4),and VvALDA(fructose-bisphosphate aldolase)were pertinent candidate genes in responses to different light qualities.Our results provide a foundation for optimizing the light recipe of grape plantlets and strengthen the understanding of light signaling and carbon metabolism under different monochromatic lights. | Menglong Liu Yan Zhao Peige Fan Junhua Kong Yongjian Wang Xiaobo Xu Meilong Xu Lijun Wang Shaohua Li Zhenchang Liang Wei Duan Zhanwu Dai | 2023 | Horticulture Research2023，10，9： | 0 |
| 16 | CRISPR/Cas genome editing in grapevine:recent advances,challenges and future prospects显示文摘The development of clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9(CRISPR/Cas9)system has revolutionized genome editing and plant breeding.Applications of CRISPR/Cas9 technology in fruit crops,including grapevine,enable precise improvement of agronomically important traits.In this review,we first describe genome editing based on the most widely used CRISPR/Cas9 system and recently developed CRISPR technologies.We then focus on applications of CRISPR/Cas9 in improvement of disease resistance,optimization of CRISPR/Cas9 systems,multiplex genome editing and off-target effect analysis in grapevine.We also discuss the challenges facing genome editing that should be overcome to realize the potential of CRISPR technology in grapevine.Finally,we highlight possible future experimental considerations for more precise and efficient genome editing in grapevine. | Chong Ren Yanping Lin Zhenchang Liang | 2022 | Fruit Research2022，2，1： | 0 |
| 17 | VitisGDB: The Multifunctional Database for Grapevine Breeding and Genetics显示文摘Grapevine cultivation has been gaining commercial popularity in many parts of the world due to the high yield and versatility of this horticultural crop.A recent survey from the International Organization of Vine and Wine(OIV)estimated that the global area under vine cultivation in 2018 was about 7.4 million hectares and that the world production of grapes was about 77.8 million tons in total(OIV,2019).The majority of the global grape yield is used for producing wines,fresh fruit,and raisins,bringing in annual revenue of billions of US dollars(Alston and Sambucci,2019).In addition to its economic value,the grapevine is also a useful model for the study of the genetic basis of clonality,fruit development,sex determination,grafting,evolution,and domestication(This et al.,2006).Furthermore,for many countries in the world traditional viniculture and viticulture are important emblems of cultural identity.All these factors have made grapevine one of the most heavily invested plants in horticultural research. | Xiao Dong Wei Chen Zhenchang Liang Xuzhen Li Peter Nick Shanshan Chen Yang Dong Shaohua Li Jun Sheng | 2020 | Molecular Plant2020，13，8： | 0 |
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