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grape transcriptome

Qian Ma, Jingli Yang
The length of berry lag phase determines the overall time needed for grape berries to get mature, but the functional gene networks in this phase have not been well documented. In order to reveal the origin of the somatic variation and regulation mechanism of grape berry development and ripening, an early ripening mutant of Vitis vinifera with a shorter lag phase was used for transcriptome profiling. The RNA-seq results revealed that 2021 and 2470 genes were up- and down-regulated, respectively, in the early ripening mutant compared to the wild type...
September 23, 2018: Gene
Xudong Zhu, Xiaopeng Li, Songtao Jiu, Kekun Zhang, Chen Wang, Jinggui Fang
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...
June 2018: Royal Society Open Science
Feng Leng, Jinping Cao, Shiping Wang, Ling Jiang, Xian Li, Chongde Sun
Phytohormones strongly influence growth, development and nutritional quality of agricultural products by modulating molecular and biochemical changes. The purpose of the present study was to investigate the influence of root restriction (RR) treatment on the dynamic changes of main phytohormones during the berry development and ripening of "Summer Black" early ripening seedless grape ( Vitis vinifera × V. labrusca ), and to analyze the changes in the biosynthesis and signal transduction pathways of phytohormones by transcriptomics...
August 6, 2018: International Journal of Molecular Sciences
Priyanka Das, Arun Lahiri Majumder
The negative effects of soil salinity towards grape yield depend upon salt concentration, cultivar type, developmental stage, and rootstock. Thompson Seedless variety of grape plant is considered moderately sensitive to salinity when grown upon its own root stock. In recent epoch, identification of key genes responsive to salinity offers hope to generate salinity-tolerant crop plants by their overexpression through genetic manipulation. In the present report, salt responsive transcriptome analysis of Thompson Seedless grape variety was done to identify vital genes involved in salinity tolerance which could be used further to generate salt liberal grape plant or other crop plants...
July 19, 2018: Functional & Integrative Genomics
Ya-Ling Zhang, Zhi-Zhen Fang, Xin-Fu Ye, Shao-Lin Pan
Jaboticaba is a grape-like fruit that accumulates high levels of anthocyanins in the peel and is proposed as a good source of functional pigments. However, the molecular mechanisms underlying anthocyanin accumulation in jaboticaba peel remains to be elucidated. In this study, we employed RNA-seq technique to compare the transcriptomic differences between green-colored and black-colored jaboticaba peels. Over 5 million high-quality reads were assembled into 62,190 unigenes with an average length of 737 bp, 29,320 (47...
November 15, 2018: Gene
Qianyu Yue, Lili Xu, Guangqing Xiang, Xin Yu, Yuxin Yao
Gene expression profile, phenolic composition, and antioxidant capacity were evaluated in red-fleshed berries and their wines (RF berries and wines) from new grape genotypes. Transcriptomic analysis revealed that ten metabolic pathways involved in polyphenol synthesis and catabolism were significantly altered, and 13 genes related to the biosynthesis and transport of phenolics were largely upregulated in RF berries compared to that of Cabernet Sauvignon (CS). Expression of MybA1 was associated with anthocyanin accumulation in red flesh...
July 11, 2018: Journal of Agricultural and Food Chemistry
Anuradha Upadhyay, Smita Maske, Satisha Jogaiah, Narendra Y Kadoo, Vidya S Gupta
In grapes (Vitis vinifera L.), exogenous gibberellic acid (GA3 ) is applied at different stages of bunch development to achieve desirable bunch shape and berry size in seedless grapes used for table purpose. RNA sequence-based transcriptome analysis was used to understand the mechanism of GA3 action at cluster emergence, full bloom, and berry stage in table grape variety Thompson Seedless. At cluster emergence, rachis samples were collected at 6 and 24 h after application of GA3 , whereas flower clusters and berry samples were collected at 6, 24, and 48 h after application at full bloom and 3-4 mm berry stages...
July 2018: Functional & Integrative Genomics
Shinichi Enoki, Yu Hamaguchi, Shunji Suzuki, Hiroyuki Fujisawa, Tomoki Hattori, Kayo Arita, Chiho Yamaguchi, Masachika Mikami, Shu Nagasaka, Keisuke Tanaka
Koshu is indigenous to Japan and considered the most important wine grape in Japan. Koshu grape berry possesses characteristics that make it unique from European V. vinifera as wine grape. However, the physiological characteristics of Koshu leaf and internode remain unknown. An understanding of those characteristics would contribute to improvements in Koshu cultivation, thereby enhancing grape berry and wine quality. To identify the genes responsible for the physiological characteristics of Koshu, we comprehensively analyzed leaf and internode differences at the transcriptome level between Koshu and Pinot Noir by RNA sequencing...
2018: PloS One
Sagar Patel, Zhixiu Lu, Xiaozhu Jin, Padmapriya Swaminathan, Erliang Zeng, Anne Y Fennell
BACKGROUND: De novo heterozygous assembly is an ongoing challenge requiring improved assembly approaches. In this study, three strategies were used to develop de novo Vitis vinifera 'Sultanina' genome assemblies for comparison with the inbred V. vinifera (PN40024 12X.v2) reference genome and a published Sultanina ALLPATHS-LG assembly (AP). The strategies were: 1) a default PLATANUS assembly (PLAT_d) for direct comparison with AP assembly, 2) an iterative merging strategy using METASSEMBLER to combine PLAT_d and AP assemblies (MERGE) and 3) PLATANUS parameter modifications plus GapCloser (PLAT*_GC)...
January 17, 2018: BMC Genomics
Iván Balic, Paula Vizoso, Ricardo Nilo-Poyanco, Dayan Sanhueza, Patricio Olmedo, Pablo Sepúlveda, Cesar Arriagada, Bruno G Defilippi, Claudio Meneses, Reinaldo Campos-Vargas
Ripening is one of the key processes associated with the development of major organoleptic characteristics of the fruit. This process has been extensively characterized in climacteric fruit, in contrast with non-climacteric fruit such as grape, where the process is less understood. With the aim of studying changes in gene expression during ripening of non-climacteric fruit, an Illumina based RNA-Seq transcriptome analysis was performed on four developmental stages, between veraison and harvest, on table grapes berries cv Thompson Seedless...
2018: PloS One
Michael K Y Ting, Yi-Min She, William C Plaxton
Phosphoenolpyruvate carboxylase (PEPC) is an important regulatory enzyme situated at a key branch point of central plant metabolism. Plant genomes encode several plant-type PEPC (PTPC) isozymes, along with a distantly related bacterial-type PEPC (BTPC). BTPC is expressed at high levels in developing castor oil seeds where it tightly interacts with co-expressed PTPC polypeptides to form unusual hetero-octameric Class-2 PEPC complexes that are desensitized to allosteric inhibition by L-malate. Analysis of RNA-Seq and microarray transcriptome datasets revealed two distinct patterns of tissue-specific BTPC expression in vascular plants...
December 16, 2017: Journal of Experimental Botany
Giorgio Gambino, Alessandra Dal Molin, Paolo Boccacci, Andrea Minio, Walter Chitarra, Carla Giuseppina Avanzato, Paola Tononi, Irene Perrone, Stefano Raimondi, Anna Schneider, Mario Pezzotti, Franco Mannini, Ivana Gribaudo, Massimo Delledonne
'Nebbiolo' (Vitis vinifera) is among the most ancient and prestigious wine grape varieties characterised by a wide genetic variability exhibited by a high number of clones (vegetatively propagated lines of selected mother plants). However, limited information is available for this cultivar at the molecular and genomic levels. The whole-genomes of three 'Nebbiolo' clones (CVT 71, CVT 185 and CVT 423) were re-sequenced and a de novo transcriptome assembly was produced. Important remarks about the genetic peculiarities of 'Nebbiolo' and its intra-varietal variability useful for clonal identification were reported...
December 11, 2017: Scientific Reports
Wei-Kai Chen, Xian-Jin Bai, Mu-Ming Cao, Guo Cheng, Xiong-Jun Cao, Rong-Rong Guo, Yu Wang, Lei He, Xiao-Hui Yang, Fei He, Chang-Qing Duan, Jun Wang
A double cropping system has been commercially adopted in southern China, where there is abundant sunshine and heat resources. In this viticulture system, the first growing season normally starts as a summer cropping cycle; then, the vine is pruned and forced, resulting in a second crop in winter. Due to climate differences between the summer and winter growing seasons, grape ripening progression and flavonoid metabolism vary greatly. Here, the metabolites and transcriptome of flavonoid pathways were analyzed in grapes grown under two growing seasons at different stages...
2017: Frontiers in Plant Science
Yingying Gao, Yi Wang, Haiping Xin, Shaohua Li, Zhenchang Liang
Ubiquitin-conjugating (UBC) E2 enzyme plays crucial roles in plant growth and development. Limited information can describe the function of UBC enzyme E2 in grapes. A total of 43 UBC enzyme E2 genes with conserved UBC domain were identified in grapes. These genes were divided into five groups based on phylogenetic tree with tomatoes. Sequence analyses indicated that VvUBCs in the same group possessed similar gene structures and conserved motifs. Gene distribution in chromosomes was uneven, and gene duplication existed in 36 VvUBCs...
October 16, 2017: Scientific Reports
Yunduan Li, Yanxun Zhu, Jin Yao, Songlin Zhang, Li Wang, Chunlei Guo, Steve van Nocker, Xiping Wang
Seedless grapes are of considerable importance for the raisin and table grape industries. Previous transcriptome analyses of seed development in grape revealed that genes encoding homeobox transcription factors were differentially regulated in seedless compared with seeded grape during seed development. In the present study, we identified a total of 73 homeobox-like genes in the grapevine genome and analyzed the genomic content and expression profiles of these genes. Based on domain architecture and phylogenetic analyses grape homeobox genes can be classified into eleven subfamilies...
October 3, 2017: Scientific Reports
Alejandra Serrano, Carmen Espinoza, Grace Armijo, Claudio Inostroza-Blancheteau, Evelyn Poblete, Carlos Meyer-Regueiro, Anibal Arce, Francisca Parada, Claudia Santibáñez, Patricio Arce-Johnson
Grapevine fruit development is a dynamic process that can be divided into three stages: formation (I), lag (II), and ripening (III), in which physiological and biochemical changes occur, leading to cell differentiation and accumulation of different solutes. These stages can be positively or negatively affected by multiple environmental factors. During the last decade, efforts have been made to understand berry development from a global perspective. Special attention has been paid to transcriptional and metabolic networks associated with the control of grape berry development, and how external factors affect the ripening process...
2017: Frontiers in Plant Science
Camille Duc, Martine Pradal, Isabelle Sanchez, Jessica Noble, Catherine Tesnière, Bruno Blondin
Yeast cell death can occur during wine alcoholic fermentation. It is generally considered to result from ethanol stress that impacts membrane integrity. This cell death mainly occurs when grape musts processing reduces lipid availability, resulting in weaker membrane resistance to ethanol. However the mechanisms underlying cell death in these conditions remain unclear. We examined cell death occurrence considering yeast cells ability to elicit an appropriate response to a given nutrient limitation and thus survive starvation...
2017: PloS One
Lili Xu, Qianyu Yue, Feng'e Bian, Hong Sun, Heng Zhai, Yuxin Yao
This study assessed the primary impacts of exogenous melatonin (MT) treatment on grape berry metabolism. Exogenous MT treatment increased the endogenous MT content and modified berry ripening. Transcriptomic analysis revealed that the processes of polyphenol metabolism, carbohydrate metabolism and ethylene biosynthesis and signaling were the three most significantly altered biological processes upon MT treatment. Further experiments verified that MT treatment increased the contents of total anthocyanins, phenols, flavonoids and proanthocyanidins in berries...
2017: Frontiers in Plant Science
Wu Wang, Muhammad Khalil-Ur-Rehman, Jiao Feng, Jianmin Tao
Grapevine (Vitis vinifera L.) is considered to be one of the most popular and widespread fruit crops in the world. Numerous value added products are prepared from grape fruit and investments are being made to establish new viticulture region (Hoff et al., 2017; Imran et al., 2017). CPPU [forchlorfenuron N-(2-chloro-4-pyridyl)-N-phenylurea] is a synthetic cytokine-like plant regulator which promotes grape berry set and development. The influence of CPPU [forchlorfenuron N-(2-chloro-4-pyridyl)-N-phenylurea] on berry development of 'Shine Muscat' (Vitis labruscana Bailey×V vinifera L...
November 2017: Journal of Plant Physiology
Maryline Magnin-Robert, Marielle Adrian, Sophie Trouvelot, Alessandro Spagnolo, Lucile Jacquens, Patricia Letousey, Fanja Rabenoelina, Mourad Harir, Chloé Roullier-Gall, Christophe Clément, Philippe Schmitt-Kopplin, Armelle Vallat, Eliane Abou-Mansour, Florence Fontaine
Esca disease is one of the major grapevine trunk diseases in Europe and the etiology is complex, since several inhabiting fungi are identified to be associated with this disease. Among the foliar symptom expressions, the apoplectic form may be distinguished and characterized by sudden dieback of shoots, leaf drop, and shriveling of grape clusters in a few days that can ultimately induce the plant death. To further understand this drastic event, we conducted transcriptomic and metabolomic analyses to characterize responses of leaves during the period preceding symptom appearance (20 and 7 days before foliar symptom expression) and at the day of apoplexy expression...
December 2017: Molecular Plant-microbe Interactions: MPMI
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