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Bhattarai A, Nimmakayala P, Davenport B, Natarajan P, Tonapi K, Kadiyala SS, Lopez-Ortiz C, Ibarra-Muñoz L, Chakrabarti M, Benedito V, Adjeroh DA, Balagurusamy N, Reddy UK. Genetic tapestry of Capsicum fruit colors: a comparative analysis of four cultivated species. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:130. [PMID: 38744692 DOI: 10.1007/s00122-024-04635-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/17/2024] [Indexed: 05/16/2024]
Abstract
KEY MESSAGE Genome-wide association study of color spaces across the four cultivated Capsicum spp. revealed a shared set of genes influencing fruit color, suggesting mechanisms and pathways across Capsicum species are conserved during the speciation. Notably, Cytochrome P450 of the carotenoid pathway, MYB transcription factor, and pentatricopeptide repeat-containing protein are the major genes responsible for fruit color variation across the Capsicum species. Peppers (Capsicum spp.) rank among the most widely consumed spices globally. Fruit color, serving as a determinant for use in food colorants and cosmeceuticals and an indicator of nutritional contents, significantly influences market quality and price. Cultivated Capsicum species display extensive phenotypic diversity, especially in fruit coloration. Our study leveraged the genetic variance within four Capsicum species (Capsicum baccatum, Capsicum chinense, Capsicum frutescens, and Capsicum annuum) to elucidate the genetic mechanisms driving color variation in peppers and related Solanaceae species. We analyzed color metrics and chromatic attributes (Red, Green, Blue, L*, a*, b*, Luminosity, Hue, and Chroma) on samples cultivated over six years (2015-2021). We resolved genomic regions associated with fruit color diversity through the sets of SNPs obtained from Genotyping by Sequencing (GBS) and genome-wide association study (GWAS) with a Multi-Locus Mixed Linear Model (MLMM). Significant SNPs with FDR correction were identified, within the Cytochrome P450, MYB-related genes, Pentatricopeptide repeat proteins, and ABC transporter family were the most common among the four species, indicating comparative evolution of fruit colors. We further validated the role of a pentatricopeptide repeat-containing protein (Chr01:31,205,460) and a cytochrome P450 enzyme (Chr08:45,351,919) via competitive allele-specific PCR (KASP) genotyping. Our findings advance the understanding of the genetic underpinnings of Capsicum fruit coloration, with developed KASP assays holding potential for applications in crop breeding and aligning with consumer preferences. This study provides a cornerstone for future research into exploiting Capsicum's diverse fruit color variation.
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Affiliation(s)
- Ambika Bhattarai
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA
| | - Padma Nimmakayala
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA.
| | - Brittany Davenport
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA
| | - Purushothaman Natarajan
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA
| | - Krittika Tonapi
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA
| | - Sai Satish Kadiyala
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA
| | - Carlos Lopez-Ortiz
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA
| | - Lizbeth Ibarra-Muñoz
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, 27275, Torreon, Coahuila, Mexico
| | - Manohar Chakrabarti
- Department of Biology, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Vagner Benedito
- Division of Plant & Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Donald A Adjeroh
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, 26506, USA
| | - Nagamani Balagurusamy
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, 27275, Torreon, Coahuila, Mexico.
| | - Umesh K Reddy
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA.
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2
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Li H, Yang Y, Zhang W, Zheng H, Xu X, Li H, Sun C, Hu H, Zhao W, Ma R, Tao J. Promoter replication of grape MYB transcription factor is associated with a new red flesh phenotype. PLANT CELL REPORTS 2024; 43:136. [PMID: 38709311 DOI: 10.1007/s00299-024-03225-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 04/30/2024] [Indexed: 05/07/2024]
Abstract
KEY MESSAGE In our study, we discovered a fragment duplication autoregulation mechanism in 'ZS-HY', which may be the reason for the phenotype of red foliage and red flesh in grapes. In grapes, MYBA1 and MYBA2 are the main genetic factors responsible for skin coloration which are located at the color loci on chromosome 2, but the exact genes responsible for color have not been identified in the flesh. We used a new teinturier grape germplasm 'ZhongShan-HongYu' (ZS-HY) which accumulate anthocyanin both in skin and flesh as experimental materials. All tissues of 'ZS-HY' contained cyanidin 3-O-(6″-p-coumaroyl glucoside), and pelargonidins were detected in skin, flesh, and tendril. Through gene expression analysis at different stage of flesh, significant differences in the expression levels of VvMYBA1 were found. Gene amplification analysis showed that the VvMYBA1 promoter is composed of two alleles, VvMYBA1a and 'VvMYBA1c-like'. An insertion of a 408 bp repetitive fragment was detected in the allele 'VvMYBA1c-like'. In this process, we found the 408 bp repetitive fragment was co-segregated with red flesh and foliage phenotype. Our results revealed that the 408 bp fragment replication insertion in promoter of 'VvMYBA1c-like' was the target of its protein, and the number of repeat fragments was related to the increase of trans-activation of VvMYBA1 protein. The activation of promoter by VvMYBA1 was enhanced by the addition of VvMYC1. In addition, VvMYBA1 interacted with VvMYC1 to promote the expression of VvGT1 and VvGST4 genes in 'ZS-HY'. The discovery of this mutation event provides new insights into the regulation of VvMYBA1 on anthocyanin accumulation in red-fleshed grape, which is of great significance for molecular breeding of red-fleshed table grapes.
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Affiliation(s)
- Hui Li
- College of Horticulture, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
- College of Seed and Facility Agricultural Engineering, Weifang University, Weifang, 261061, China
| | - Yaxin Yang
- College of Horticulture, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wen Zhang
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Science, Urumqi, 830001, Xinjiang, China
| | - Huan Zheng
- College of Horticulture, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xianbin Xu
- College of Horticulture, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haoran Li
- College of Horticulture, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chenxu Sun
- College of Horticulture, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haipeng Hu
- College of Horticulture, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wanli Zhao
- College of Horticulture, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruiyang Ma
- College of Horticulture, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianmin Tao
- College of Horticulture, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China.
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Science, Urumqi, 830001, Xinjiang, China.
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3
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Piarulli L, Pirolo C, Roseti V, Bellin D, Mascio I, La Notte P, Montemurro C, Miazzi MM. Breeding new seedless table grapevines for a more sustainable viticulture in Mediterranean climate. FRONTIERS IN PLANT SCIENCE 2024; 15:1379642. [PMID: 38645394 PMCID: PMC11027070 DOI: 10.3389/fpls.2024.1379642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/14/2024] [Indexed: 04/23/2024]
Abstract
The growing demand for sustainable and environmentally friendly viticulture is leading to a multiplication of breeding programs aimed at obtaining vines that are resistant to powdery mildew (PM) and downy mildew (DM), the two most damaging vine diseases. In Puglia, the most important Italian region for the production of table grapes, an extensive crossing program was launched in 2015 with 113 crosses, including elite table varieties, seedless varieties, and resistant varieties. The main seedling production parameters were measured for each cross. In particular, berries harvested as well as the number of seeds and seedlings obtained were considered. Approximately 103,119 seedlings were obtained and subjected to marker-assisted selection for seedlessness using the marker VvAGL11 and for resistance to PM and DM with appropriate markers. Approximately one third (32,638) of the progenies were selected as putative seedless and seventeen thousand five hundred-nine (17,509) were transferred to the field for phenotypic evaluation, including 527 seedless individuals putatively resistant, of which 208 confirmed to be resistant to DM, 22 resistant to PM, and 20 individuals that combined resistance and seedlessness traits. The work discusses the effects of parental combinations and other variables in obtaining surviving progeny and pyramiding genes in table grapes and provides useful information for selecting genotypes and increasing the efficiency of breeding programs for seedless disease-resistant grapes.
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Affiliation(s)
- Luciana Piarulli
- SINAGRI S.r.l. – Spin-Off of the University of Bari Aldo Moro, Bari, Italy
- Rete Italian Variety Club (IVC), Locorotondo, Italy
| | - Costantino Pirolo
- SINAGRI S.r.l. – Spin-Off of the University of Bari Aldo Moro, Bari, Italy
- Rete Italian Variety Club (IVC), Locorotondo, Italy
| | | | - Diana Bellin
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Isabella Mascio
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | | | - Cinzia Montemurro
- SINAGRI S.r.l. – Spin-Off of the University of Bari Aldo Moro, Bari, Italy
- Rete Italian Variety Club (IVC), Locorotondo, Italy
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Monica Marilena Miazzi
- Rete Italian Variety Club (IVC), Locorotondo, Italy
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
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4
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Zhao K, Lan Y, Shi Y, Duan C, Yu K. Metabolite and transcriptome analyses reveal the effects of salinity stress on the biosynthesis of proanthocyanidins and anthocyanins in grape suspension cells. FRONTIERS IN PLANT SCIENCE 2024; 15:1351008. [PMID: 38576780 PMCID: PMC10993317 DOI: 10.3389/fpls.2024.1351008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/07/2024] [Indexed: 04/06/2024]
Abstract
Proanthocyanidins (PAs) and anthocyanins are flavonoids that contribute to the quality and health benefits of grapes and wine. Salinity affects their biosynthesis, but the underlying mechanism is still unclear. We studied the effects of NaCl stress on PA and anthocyanin biosynthesis in grape suspension cells derived from berry skins of Vitis vinifera L. Cabernet Sauvignon using metabolite profiling and transcriptome analysis. We treated the cells with low (75 mM NaCl) and high (150 mM NaCl) salinity for 4 and 7 days. High salinity inhibited cell growth and enhanced PA and anthocyanin accumulation more than low salinity. The salinity-induced PAs and anthocyanins lacked C5'-hydroxylation modification, suggesting the biological significance of delphinidin- and epigallocatechin-derivatives in coping with stress. The genes up-regulated by salinity stress indicated that the anthocyanin pathway was more sensitive to salt concentration than the PA pathway, and WGCNA analysis revealed the coordination between flavonoid biosynthesis and cell wall metabolism under salinity stress. We identified transcription factors potentially involved in regulating NaCl dose- and time-dependent PA and anthocyanin accumulation, showing the dynamic remodeling of flavonoid regulation network under different salinity levels and durations. Our study provides new insights into regulator candidates for tailoring flavonoid composition and molecular indicators of salt stress in grape cells.
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Affiliation(s)
- Kainan Zhao
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Yibin Lan
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Ying Shi
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Changqing Duan
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Keji Yu
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
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5
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Guo S, Zhang M, Feng M, Liu G, Torregrosa L, Tao X, Ren R, Fang Y, Zhang Z, Meng J, Xu T. miR156b-targeted VvSBP8/13 functions downstream of the abscisic acid signal to regulate anthocyanins biosynthesis in grapevine fruit under drought. HORTICULTURE RESEARCH 2024; 11:uhad293. [PMID: 38371638 PMCID: PMC10873574 DOI: 10.1093/hr/uhad293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/20/2023] [Indexed: 02/20/2024]
Abstract
Anthocyanins are the primary color components of grapevine berries and wines. In cultivation practices, a moderate water deficit can promote anthocyanin accumulation in red grape skins. Our previous study showed that abscisic acid (ABA) plays a key role in this process. Herein, we identified a microRNA, vv-miR156b, that is generated in grapevine berries in response to drought stress, along with increasing anthocyanin content and biosynthetic structural gene transcripts. In contrast, vv-miR156b short tandem target mimic (STTM) function-loss callus exhibits the opposite phenotype. Results from in vivo and in vitro experiments revealed that the ABA-signaling-regulated transcription factor VvAREB2 binds directly to the ABA-responsive element (ABRE) of the MIR156b promoter and activates miR156b expression. Furthermore, two miR156b downstream targets, VvSBP8 and VvSBP13, exhibited reduced grape anthocyanin content in their overexpressors but there was a contrary result in their CRISPR-edited lines, the decrease in anthocyanin content was rescued in miR156b and SBP8/13 double overexpressors. We further demonstrated that both VvSBP8 and VvSBP13, encoding transcriptional repressors, displayed sufficient ability to interact with VvMYC1 and VvMYBA1, thereby interfering with MYB-bHLH-WD (MBW) repeat transcriptional complex formation, resulting in the repression of anthocyanin biosynthesis. Our findings demonstrate a direct functional relationship between ABA signaling and the miR156-SBP-MBW complex regulatory module in driving drought-induced anthocyanin accumulation in grape berries.
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Affiliation(s)
- Shuihuan Guo
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Meng Zhang
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingxin Feng
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Guipeng Liu
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Laurent Torregrosa
- UMR LEPSE, Université de Montpellier , CIRAD, INRAE, Institut Agro, 34060 Montpellier, France
| | - Xiaoqing Tao
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ruihua Ren
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yulin Fang
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhenwen Zhang
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiangfei Meng
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tengfei Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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6
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Zhang C, Dai Z, Ferrier T, Orduña L, Santiago A, Peris A, Wong DCJ, Kappel C, Savoi S, Loyola R, Amato A, Kozak B, Li M, Liang A, Carrasco D, Meyer-Regueiro C, Espinoza C, Hilbert G, Figueroa-Balderas R, Cantu D, Arroyo-Garcia R, Arce-Johnson P, Claudel P, Errandonea D, Rodríguez-Concepción M, Duchêne E, Huang SSC, Castellarin SD, Tornielli GB, Barrieu F, Matus JT. MYB24 orchestrates terpene and flavonol metabolism as light responses to anthocyanin depletion in variegated grape berries. THE PLANT CELL 2023; 35:4238-4265. [PMID: 37648264 PMCID: PMC10689149 DOI: 10.1093/plcell/koad228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 08/13/2023] [Accepted: 08/30/2023] [Indexed: 09/01/2023]
Abstract
Variegation is a rare type of mosaicism not fully studied in plants, especially fruits. We examined red and white sections of grape (Vitis vinifera cv. 'Béquignol') variegated berries and found that accumulation of products from branches of the phenylpropanoid and isoprenoid pathways showed an opposite tendency. Light-responsive flavonol and monoterpene levels increased in anthocyanin-depleted areas in correlation with increasing MYB24 expression. Cistrome analysis suggested that MYB24 binds to the promoters of 22 terpene synthase (TPS) genes, as well as 32 photosynthesis/light-related genes, including carotenoid pathway members, the flavonol regulator HY5 HOMOLOGUE (HYH), and other radiation response genes. Indeed, TPS35, TPS09, the carotenoid isomerase gene CRTISO2, and HYH were activated in the presence of MYB24 and MYC2. We suggest that MYB24 modulates ultraviolet and high-intensity visible light stress responses that include terpene and flavonol synthesis and potentially affects carotenoids. The MYB24 regulatory network is developmentally triggered after the onset of berry ripening, while the absence of anthocyanin sunscreens accelerates its activation, likely in a dose-dependent manner due to increased radiation exposure. Anthocyanins and flavonols in variegated berry skins act as effective sunscreens but for different wavelength ranges. The expression patterns of stress marker genes in red and white sections of 'Béquignol' berries strongly suggest that MYB24 promotes light stress amelioration but only partly succeeds during late ripening.
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Affiliation(s)
- Chen Zhang
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
| | - Zhanwu Dai
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Thilia Ferrier
- EGFV, Bordeaux Sciences Agro, University of Bordeaux, INRAE, ISVV, 210 Chemin de Leysotte, 33140 Villenave d'Ornon, France
| | - Luis Orduña
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
| | - Antonio Santiago
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
| | - Arnau Peris
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
| | - Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm 14476, Germany
| | - Stefania Savoi
- Department of Agricultural, Forest and Food Sciences, University of Turin, Turin 10124, Italy
| | - Rodrigo Loyola
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Alessandra Amato
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Bartosz Kozak
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia V1V 1V7, Canada
| | - Miaomiao Li
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Akun Liang
- Departamento de Física Aplicada-ICMUV-MALTA Consolider Team, Universitat de València, Burjassot 46100, Valencia, Spain
| | - David Carrasco
- Centre for Plant Biotechnology and Genomics (CBGP), Universidad Politécnica de Madrid-INIA, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Carlos Meyer-Regueiro
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Carmen Espinoza
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago 8380453, Chile
| | - Ghislaine Hilbert
- EGFV, Bordeaux Sciences Agro, University of Bordeaux, INRAE, ISVV, 210 Chemin de Leysotte, 33140 Villenave d'Ornon, France
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Rosa Arroyo-Garcia
- Centre for Plant Biotechnology and Genomics (CBGP), Universidad Politécnica de Madrid-INIA, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Patricio Arce-Johnson
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería Universidad Autónoma deChile
| | | | - Daniel Errandonea
- Departamento de Física Aplicada-ICMUV-MALTA Consolider Team, Universitat de València, Burjassot 46100, Valencia, Spain
| | - Manuel Rodríguez-Concepción
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-Universitat Politècnica de València, Valencia 46022, Spain
| | - Eric Duchêne
- SVQV, University of Strasbourg, INRAE, Colmar 68000, France
| | - Shao-shan Carol Huang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Simone Diego Castellarin
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia V1V 1V7, Canada
| | | | - Francois Barrieu
- EGFV, Bordeaux Sciences Agro, University of Bordeaux, INRAE, ISVV, 210 Chemin de Leysotte, 33140 Villenave d'Ornon, France
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
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7
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Rodríguez-Lorenzo M, Mauri N, Royo C, Rambla JL, Diretto G, Demurtas O, Hilbert G, Renaud C, Tobar V, Huete J, Delrot S, Granell A, Martínez-Zapater JM, Carbonell-Bejerano P. The flavour of grape colour: anthocyanin content tunes aroma precursor composition by altering the berry microenvironment. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6369-6390. [PMID: 37294268 PMCID: PMC10627162 DOI: 10.1093/jxb/erad223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 06/07/2023] [Indexed: 06/10/2023]
Abstract
Anthocyaninless (white) instead of black/red (coloured) fruits develop in grapevine cultivars without functional VviMYBA1 and VviMYBA2 genes, and this conditions the colour of wines that can be produced. To evaluate whether this genetic variation has additional consequences on fruit ripening and composition, we performed comparisons of microenvironment, transcriptomics, and metabolomics of developing grapes between near-isogenic white- and black-berried somatic variants of Garnacha and Tempranillo cultivars. Berry temperature was as much as 3.5 ºC lower in white- compared to black-berried Tempranillo. An RNA-seq study combined with targeted and untargeted metabolomics revealed that ripening fruits of white-berried variants were characterized by the up-regulation of photosynthesis-related and other light-responsive genes and by their higher accumulation of specific terpene aroma precursors, fatty acid-derived aldehyde volatiles, and phenylpropanoid precursor amino acids. MYBA1-MYBA2 function proved essential for flavonol trihydroxylation in black-berried somatic variants, which were also characterized by enhanced expression of pathogen defence genes in the berry skin and increased accumulation of C6-derived alcohol and ester volatiles and γ-aminobutyric acid. Collectively, our results indicate that anthocyanin depletion has side-effects on grape composition by altering the internal microenvironment of the berry and the partitioning of the phenylpropanoid pathway. Our findings show how fruit colour can condition other fruit features, such as flavour potential and stress homeostasis.
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Affiliation(s)
- Maite Rodríguez-Lorenzo
- Instituto de Ciencias de la Vid y del Vino, ICVV, CSIC - Universidad de La Rioja - Gobierno de La Rioja, 26007 Logroño, Spain
| | - Nuria Mauri
- Instituto de Ciencias de la Vid y del Vino, ICVV, CSIC - Universidad de La Rioja - Gobierno de La Rioja, 26007 Logroño, Spain
| | - Carolina Royo
- Instituto de Ciencias de la Vid y del Vino, ICVV, CSIC - Universidad de La Rioja - Gobierno de La Rioja, 26007 Logroño, Spain
| | - José L Rambla
- Instituto de Biología Molecular y Celular de Plantas, IBMCP, CSIC - Universidad Politécnica de Valencia, 46011 Valencia, Spain
- Universitat Jaume I, Departamento de Biología, Bioquímica y Ciencias Naturales, 12071 Castellón de la Plana, Spain
| | - Gianfranco Diretto
- Italian National Agency for New Technologies Energy and Sustainable Development, Casaccia Research Centre, 00123 Rome, Italy
| | - Olivia Demurtas
- Italian National Agency for New Technologies Energy and Sustainable Development, Casaccia Research Centre, 00123 Rome, Italy
| | - Ghislaine Hilbert
- EGFV, Bordeaux Sciences Agro, INRA - Université de Bordeaux, ISVV, 33140 Villenave d’Ornon, France
| | - Christel Renaud
- EGFV, Bordeaux Sciences Agro, INRA - Université de Bordeaux, ISVV, 33140 Villenave d’Ornon, France
| | - Vanessa Tobar
- Servicio de Información Agroclimática de La Rioja (SIAR). Consejería de Agricultura, Ganadería y Medio Ambiente, Gobierno de La Rioja, 26007 Logroño, Spain
| | - Joaquín Huete
- Servicio de Información Agroclimática de La Rioja (SIAR). Consejería de Agricultura, Ganadería y Medio Ambiente, Gobierno de La Rioja, 26007 Logroño, Spain
| | - Serge Delrot
- EGFV, Bordeaux Sciences Agro, INRA - Université de Bordeaux, ISVV, 33140 Villenave d’Ornon, France
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas, IBMCP, CSIC - Universidad Politécnica de Valencia, 46011 Valencia, Spain
| | - José Miguel Martínez-Zapater
- Instituto de Ciencias de la Vid y del Vino, ICVV, CSIC - Universidad de La Rioja - Gobierno de La Rioja, 26007 Logroño, Spain
| | - Pablo Carbonell-Bejerano
- Instituto de Ciencias de la Vid y del Vino, ICVV, CSIC - Universidad de La Rioja - Gobierno de La Rioja, 26007 Logroño, Spain
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8
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Blois L, de Miguel M, Bert PF, Ollat N, Rubio B, Voss-Fels KP, Schmid J, Marguerit E. Dissecting the genetic architecture of root-related traits in a grafted wild Vitis berlandieri population for grapevine rootstock breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:223. [PMID: 37838631 PMCID: PMC10576685 DOI: 10.1007/s00122-023-04472-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/25/2023] [Indexed: 10/16/2023]
Abstract
In woody perennial plants, quantitative genetics and association studies remain scarce for root-related traits, due to the time required to obtain mature plants and the complexity of phenotyping. In grapevine, a grafted cultivated plant, most of the rootstocks used are hybrids between American Vitis species (V. rupestris, V. riparia, and V. berlandieri). In this study, we used a wild population of an American Vitis species (V. berlandieri) to analyze the genetic architecture of the root-related traits of rootstocks in a grafted context. We studied a population consisting of 211 genotypes, with one to five replicates each (n = 846 individuals), plus four commercial rootstocks as control genotypes (110R, 5BB, Börner, and SO4). After two independent years of experimentation, the best linear unbiased estimates method revealed root-related traits with a moderate-to-high heritability (0.36-0.82) and coefficient of genetic variation (0.15-0.45). A genome-wide association study was performed with the BLINK model, leading to the detection of 11 QTL associated with four root-related traits (one QTL was associated with the total number of roots, four were associated with the number of small roots (< 1 mm in diameter), two were associated with the number of medium-sized roots (1 mm < diameter < 2 mm), and four were associated with mean diameter) accounting for up to 25.1% of the variance. Three genotypes were found to have better root-related trait performances than the commercial rootstocks and therefore constitute possible new candidates for use in grapevine rootstock breeding programs.
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Affiliation(s)
- Louis Blois
- EGFV, Bordeaux Sciences Agro, INRAE, ISVV, Univ. Bordeaux, 33882, Villenave d'Ornon, France.
- Department of Grapevine Breeding, Geisenheim University, Von Lade Str. 1, 65366, Geisenheim, Germany.
| | - Marina de Miguel
- EGFV, Bordeaux Sciences Agro, INRAE, ISVV, Univ. Bordeaux, 33882, Villenave d'Ornon, France
| | - Pierre-François Bert
- EGFV, Bordeaux Sciences Agro, INRAE, ISVV, Univ. Bordeaux, 33882, Villenave d'Ornon, France
| | - Nathalie Ollat
- EGFV, Bordeaux Sciences Agro, INRAE, ISVV, Univ. Bordeaux, 33882, Villenave d'Ornon, France
| | - Bernadette Rubio
- EGFV, Bordeaux Sciences Agro, INRAE, ISVV, Univ. Bordeaux, 33882, Villenave d'Ornon, France
| | - Kai P Voss-Fels
- Department of Grapevine Breeding, Geisenheim University, Von Lade Str. 1, 65366, Geisenheim, Germany
| | - Joachim Schmid
- Department of Grapevine Breeding, Geisenheim University, Von Lade Str. 1, 65366, Geisenheim, Germany
| | - Elisa Marguerit
- EGFV, Bordeaux Sciences Agro, INRAE, ISVV, Univ. Bordeaux, 33882, Villenave d'Ornon, France
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9
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Shi X, Cao S, Wang X, Huang S, Wang Y, Liu Z, Liu W, Leng X, Peng Y, Wang N, Wang Y, Ma Z, Xu X, Zhang F, Xue H, Zhong H, Wang Y, Zhang K, Velt A, Avia K, Holtgräwe D, Grimplet J, Matus JT, Ware D, Wu X, Wang H, Liu C, Fang Y, Rustenholz C, Cheng Z, Xiao H, Zhou Y. The complete reference genome for grapevine ( Vitis vinifera L.) genetics and breeding. HORTICULTURE RESEARCH 2023; 10:uhad061. [PMID: 37213686 PMCID: PMC10199708 DOI: 10.1093/hr/uhad061] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/02/2023] [Indexed: 05/23/2023]
Abstract
Grapevine is one of the most economically important crops worldwide. However, the previous versions of the grapevine reference genome tipically consist of thousands of fragments with missing centromeres and telomeres, limiting the accessibility of the repetitive sequences, the centromeric and telomeric regions, and the study of inheritance of important agronomic traits in these regions. Here, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the cultivar PN40024 using PacBio HiFi long reads. The T2T reference genome (PN_T2T) is 69 Mb longer with 9018 more genes identified than the 12X.v0 version. We annotated 67% repetitive sequences, 19 centromeres and 36 telomeres, and incorporated gene annotations of previous versions into the PN_T2T assembly. We detected a total of 377 gene clusters, which showed associations with complex traits, such as aroma and disease resistance. Even though PN40024 derives from nine generations of selfing, we still found nine genomic hotspots of heterozygous sites associated with biological processes, such as the oxidation-reduction process and protein phosphorylation. The fully annotated complete reference genome therefore constitutes an important resource for grapevine genetic studies and breeding programs.
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Affiliation(s)
| | | | | | - Siyang Huang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Yue Wang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, China
| | - Zhongjie Liu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wenwen Liu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiangpeng Leng
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Yanling Peng
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Nan Wang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yiwen Wang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhiyao Ma
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiaodong Xu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Fan Zhang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hui Xue
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Haixia Zhong
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Yi Wang
- Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing 100093, China
| | - Kekun Zhang
- College of Enology, Northwest A&F University, Yangling 712100, China
| | - Amandine Velt
- SVQV, INRAE - University of Strasbourg, 68000 Colmar, France
| | - Komlan Avia
- SVQV, INRAE - University of Strasbourg, 68000 Colmar, France
| | - Daniela Holtgräwe
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Jérôme Grimplet
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), 50059 Zaragoza, Spain
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Systems Biotech Program, Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- USDA ARS NEA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA
| | - Xinyu Wu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Haibo Wang
- Fruit Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization), Ministry of Agriculture/Key Laboratory of Mineral Nutrition and Fertilizers Efficient Utilization of Deciduous Fruit Tree, Liaoning Province, Xingcheng 125100, China
| | - Chonghuai Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450004, China
| | - Yuling Fang
- College of Enology, Northwest A&F University, Yangling 712100, China
| | | | | | - Hua Xiao
- Corresponding authors: E-mail: ; ; ;
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10
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Tello J, Ibáñez J. Review: Status and prospects of association mapping in grapevine. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 327:111539. [PMID: 36410567 DOI: 10.1016/j.plantsci.2022.111539] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
Thanks to current advances in sequencing technologies, novel bioinformatics tools, and efficient modeling solutions, association mapping has become a widely accepted approach to unravel the link between genotype and phenotype diversity in numerous crops. In grapevine, this strategy has been used in the last decades to understand the genetic basis of traits of agronomic interest (fruit quality, crop yield, biotic and abiotic resistance), of special relevance nowadays to improve crop resilience to cope with future climate scenarios. Genome-wide association studies have identified many putative causative loci for different traits, some of them overlapping well-known causal genes identified by conventional quantitative trait loci studies in biparental progenies, and/or validated by functional approaches. In addition, candidate-gene association studies have been useful to pinpoint the causal mutation underlying phenotypic variation for several traits of high interest in breeding programs (like berry color, seedlessness, and muscat flavor), information that has been used to develop highly informative and useful markers already in use in marker-assisted selection processes. Thus, association mapping has proved to represent a valuable step towards high quality and sustainable grape production. This review summarizes current applications of association mapping in grapevine research and discusses future prospects in view of current viticulture challenges.
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Affiliation(s)
- Javier Tello
- Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), Logroño 26007, Spain.
| | - Javier Ibáñez
- Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), Logroño 26007, Spain
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11
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Jia H, Zuo Q, Sadeghnezhad E, Zheng T, Chen X, Dong T, Fang J. HDAC19 recruits ERF4 to the MYB5a promoter and diminishes anthocyanin accumulation during grape ripening. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:127-144. [PMID: 36423230 DOI: 10.1111/tpj.16040] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 11/04/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
DNA acetylation alters the expression of responsive genes during plant development. In grapes (Vitis vinifera), however, little is known about this regulatory mechanism. In the present study, 'Kyoho' grapes treated with trichostatin A (TSA, a deacetylase inhibitor) were used for transcriptome sequencing and quantitative proteomics analysis. We observed that acetylation was associated with anthocyanin accumulation and gene expression. Acetylation positively regulated phenylalanine metabolism and flavonoid biosynthesis pathways. Using omics analysis, we detected an increase in the levels of the AP2/EREBP transcription factor family after TSA treatment, indicating its association with acetylation-deacetylation dynamics in grapes. Furthermore, ethylene response factor 4 (ERF4) physically interacted with VvHDAC19, a histone deacetylase, which synergistically reduced the expression of target genes involved in anthocyanin biosynthesis owing to the binding of VvERF4 to the GCC-box cis-regulatory element in the VvMYB5a promoter. VvHDAC19 and VvERF4 also controlled anthocyanin biosynthesis and accumulation by regulating acetylation levels of histones H3 and H4. Therefore, alterations in histone modification can significantly regulate the expression of genes involved in anthocyanin biosynthesis and affect grape ripening.
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Affiliation(s)
- Haifeng Jia
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
- NJAU (Suqian) Academy of Protected Horticultures, Suqian, China
| | - Qianqian Zuo
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - Ehsan Sadeghnezhad
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - Ting Zheng
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - Xueqin Chen
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - Tianyu Dong
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - JinggGui Fang
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
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12
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Mhetre VB, Patel V, Singh S, Mishra GP, Verma M, Kumar C, Dahuja A, Kumar S, Singh R, Wasim Siddiqui M. Unraveling the pathways influencing the berry color and firmness of grapevine cv. Flame Seedless treated with bioregulators using biochemical and RNA-Seq analysis under semi-arid subtropics. FOOD CHEMISTRY: MOLECULAR SCIENCES 2022; 5:100116. [PMID: 35818381 PMCID: PMC9270244 DOI: 10.1016/j.fochms.2022.100116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/11/2022] [Accepted: 06/18/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Vishal B. Mhetre
- Division of Fruits and Horticultural Technology, ICAR- Indian Agricultural Research Institute, New Delhi 110012, India
| | - V.B. Patel
- Division of Fruits and Horticultural Technology, ICAR- Indian Agricultural Research Institute, New Delhi 110012, India
- Corresponding author.
| | - S.K. Singh
- Division of Fruits and Horticultural Technology, ICAR- Indian Agricultural Research Institute, New Delhi 110012, India
| | - Gyan P. Mishra
- Division of Genetics, ICAR- Indian Agricultural Research Institute, New Delhi 110012, India
| | - M.K. Verma
- Division of Fruits and Horticultural Technology, ICAR- Indian Agricultural Research Institute, New Delhi 110012, India
| | - Chavlesh Kumar
- Division of Fruits and Horticultural Technology, ICAR- Indian Agricultural Research Institute, New Delhi 110012, India
| | - Anil Dahuja
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Sanjeev Kumar
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Rakesh Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
| | - M. Wasim Siddiqui
- Department of Food Science and Postharvest Technology, Bihar Agricultural University, Sabour 813210, Bhagalpur, Bihar, India
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13
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Morreale G, Possamai T, Panighel A, De Rosso M, Lovat L, Flamini R, Migliaro D. First investigation on polyphenols and glycosidic aroma precursors in a spontaneous colour mutant of 'Glera', the principal grape variety of Prosecco sparkling wine. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:6623-6631. [PMID: 35608915 DOI: 10.1002/jsfa.12029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/18/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Somatic mutations in Vitis spp. are relatively frequent and can generate new agronomically interesting phenotypes. We report the discovery, genetic and chemical characterization of 'Glera rosa', a mutant for the berry skin colour of 'Glera', the main white cultivar used to produce Prosecco wine. RESULTS We ascertained the relationship between the skin colour of 'Glera rosa' and the polymorphisms in the Myb-gene transcription factors involved in polyphenol biosynthesis. We established that VvMybA1 was homozygous (VvMybA1a/VvMybA1a) in 'Glera' but heterozygous (VvmybA1a/VvmybA1b) in the 'Glera rosa' mutant. We verified that the VvMybA1a non-functional allele contained Grapevine Retrotransposon 1 (Gret1), while in the VvmybA1b allele Gret1 was missing, and the gene function was partially restored. The effects of mutation on 'Glera rosa' grape metabolites were studied by high-resolution mass spectrometry and gas chromatography/mass spectrometry analysis. Fifteen anthocyanins and five unique flavonols were found in the 'Glera rosa' mutant. The mutation also increased the contents of trans-resveratrol and its derivatives (i.e., piceatannol, E-ε-viniferin, cis- and trans-piceid) and of some flavonols in grape. Finally, the mutation did not significantly affect the typical aroma precursors of Glera grape such as glycosidic monoterpenes, norisoprenoids and benzenoids. CONCLUSION 'Glera rosa' could be an interesting genetic source for the wine industry to produce Prosecco DOC rosé typology (made by adding up to 15% of 'Pinot Noir'), which was introduced to the market in 2020 with a worldwide massive success. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Giacomo Morreale
- CREA - Research Centre for Viticulture and Enology, Conegliano, Italy
| | - Tyrone Possamai
- CREA - Research Centre for Viticulture and Enology, Conegliano, Italy
| | - Annarita Panighel
- CREA - Research Centre for Viticulture and Enology, Conegliano, Italy
| | - Mirko De Rosso
- CREA - Research Centre for Viticulture and Enology, Conegliano, Italy
| | - Lorenzo Lovat
- CREA - Research Centre for Viticulture and Enology, Conegliano, Italy
| | - Riccardo Flamini
- CREA - Research Centre for Viticulture and Enology, Conegliano, Italy
| | - Daniele Migliaro
- CREA - Research Centre for Viticulture and Enology, Conegliano, Italy
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14
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Ismail A, Gajjar P, Park M, Mahboob A, Tsolova V, Subramanian J, Darwish AG, El-Sharkawy I. A recessive mutation in muscadine grapes causes berry color-loss without influencing anthocyanin pathway. Commun Biol 2022; 5:1012. [PMID: 36153380 PMCID: PMC9509324 DOI: 10.1038/s42003-022-04001-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 09/13/2022] [Indexed: 11/10/2022] Open
Abstract
Anthocyanins, a major class of flavonoids, are important pigments of grape berries. Despite the recent discovery of the genetic cause underlying the loss of color, the metabolomic and molecular responses are unknown. Anthocyanin quantification among diverse berry color muscadines suggests that all genotypes could produce adequate anthocyanin quantities, irrespective of berry color. Transcriptome profiling of contrasting color muscadine genotypes proposes a potential deficiency that occurs within the anthocyanin transport and/or degradation mechanisms and might cause unpigmented berries. Genome-wide association studies highlighted a region on chromosome-4, comprising several genes encoding glutathione S-transferases involved in anthocyanin transport. Sequence comparison among genotypes reveals the presence of two GST4b alleles that differ by substituting the conserved amino acid residue Pro171-to-Leu. Molecular dynamics simulations demonstrate that GST4b2–Leu171 encodes an inactive protein due to modifications within the H-binding site. Population genotyping suggests the recessive inheritance of the unpigmented trait with a GST4b2/2 homozygous. A model defining colorless muscadines’ response to the mutation stimulus, avoiding the impact of trapped anthocyanins within the cytoplasm is established. Transcriptome profiling and mutational analysis suggest a potential deficiency in anthocyanin transport by glutathione S-transferases and/or degradation mechanisms that might cause unpigmented berries.
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15
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Yoder JB, Dang A, MacGregor C, Plaza M. Plant‐associate interactions and diversification across trophic levels. Evol Lett 2022; 6:375-389. [PMID: 36254257 PMCID: PMC9554764 DOI: 10.1002/evl3.296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 08/27/2022] [Indexed: 11/11/2022] Open
Abstract
Interactions between species are widely understood to have promoted the diversification of life on Earth, but how interactions spur the formation of new species remains unclear. Interacting species often become locally adapted to each other, but they may also be subject to shared dispersal limitations and environmental conditions. Moreover, theory predicts that different kinds of interactions have different effects on diversification. To better understand how species interactions promote diversification, we compiled population genetic studies of host plants and intimately associated herbivores, parasites, and mutualists. We used Bayesian multiple regressions and the BEDASSLE modeling framework to test whether host and associate population structures were correlated over and above the potentially confounding effects of geography and shared environmental variation. We found that associates' population structure often paralleled their hosts' population structure, and that this effect is robust to accounting for geographic distance and climate. Associate genetic structure was significantly explained by plant genetic structure somewhat more often in antagonistic interactions than in mutualistic ones. This aligns with a key prediction of coevolutionary theory that antagonistic interactions promote diversity through local adaptation of antagonists to hosts, while mutualistic interactions more often promote diversity via the effect of hosts' geographic distribution on mutualists' dispersal.
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Affiliation(s)
- Jeremy B. Yoder
- Department of Biology California State University Northridge Northridge CA 91330 USA
| | - Albert Dang
- Department of Biology California State University Northridge Northridge CA 91330 USA
| | - Caitlin MacGregor
- Department of Biology California State University Northridge Northridge CA 91330 USA
| | - Mikhail Plaza
- Program in Plant Biology and Conservation Northwestern University Evanston IL 60208 USA
- Negaunee Institute for Plant Conservation Science and Action Chicago Botanic Garden Glencoe IL 60035 USA
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16
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Yang Y, Ke J, Han X, Wuddineh WA, Song GQ, Zhong GY. Removal of a 10-kb Gret1 transposon from VvMybA1 of Vitis vinifera cv. Chardonnay. HORTICULTURE RESEARCH 2022; 9:uhac201. [PMID: 36406285 PMCID: PMC9669667 DOI: 10.1093/hr/uhac201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/31/2022] [Indexed: 06/10/2023]
Abstract
Many white grape cultivars have a nonfunctional VvMybA1 gene due to the presence of a 10-kb Gret1 transposon in its promoter. In this study, we successfully demonstrated removal of the 10-kb Gret1 transposon and functional restoration of a VvMybA1 allele in Vitis vinifera cv. Chardonnay through transgenic expression of Cas9 and two gRNAs simultaneously targeting two junction sequences between Gret1 LTRs and VvMybA1. We generated 67 and 24 Cas9-positive vines via Agrobacterium-mediated and biolistic bombardment transformation, respectively. While the editing efficiencies were as high as 17% for the 5' target site and 65% for the 3' target site, simultaneous editing of both 5' and 3' target sites resulting in the removal of Gret1 transposon from the VvMybA1 promoter was 0.5% or less in most transgenic calli, suggesting that these calli had very limited numbers of cells with the Gret1 removed. Nevertheless, two bombardment-transformed vines, which shared the same unique editing features and were likely derived from a singly edited event, were found to have the Gret1 successfully edited out from one of their two VvMybA1 alleles. The edited allele was functionally restored based on the detection of its expression and a positive coloring assay result in leaves. Precise removal of more than a 10-kb DNA fragment from a gene locus in grape broadens the possibilities of using gene editing technologies to modify various trait genes in grapes and other plants.
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Affiliation(s)
- Yingzhen Yang
- USDA-Agricultural Research Service Grape Genetics Research Unit, Geneva, NY 14456, USA
| | - John Ke
- USDA-Agricultural Research Service Grape Genetics Research Unit, Geneva, NY 14456, USA
| | - Xiaoyan Han
- Department of Horticulture, Michigan State University, East Lansing, MI 48823, USA
| | - Wegi A Wuddineh
- USDA-Agricultural Research Service Grape Genetics Research Unit, Geneva, NY 14456, USA
| | - Guo-qing Song
- Department of Horticulture, Michigan State University, East Lansing, MI 48823, USA
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17
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Azuma A, Kobayashi S. Demethylation of the 3' LTR region of retrotransposon in VvMYBA1 BEN allele enhances anthocyanin biosynthesis in berry skin and flesh in 'Brazil' grape. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 322:111341. [PMID: 35667250 DOI: 10.1016/j.plantsci.2022.111341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 05/10/2023]
Abstract
Black-skinned and red-fleshed grape 'Brazil' is a bud sport of rosy-skinned 'Benitaka'. 'Brazil' has a much higher anthocyanin content in the skin than that of 'Benitaka' and is characterized by the accumulation of anthocyanins in the flesh. Our genomic analysis of the VvMYBA loci, which regulate anthocyanin biosynthesis, suggested that the difference in skin and flesh color between 'Brazil' and 'Benitaka' cannot be explained by genomic alteration at the loci. Expression levels of VvMYBA1 and anthocyanin biosynthesis-related genes in skin and flesh were significantly higher in 'Brazil' than in 'Benitaka' throughout berry development. DNA methylation levels in the 3' long terminal repeat (LTR) of a retrotransposon in the upstream region of VvMYBA1BEN allele were clearly higher in the skin and flesh of 'Benitaka' than in those of 'Brazil' throughout berry development. These findings suggest that a dramatic decrease in DNA methylation level in the 3' LTR of the retrotransposon in the VvMYBA1BEN allele in 'Brazil' increases the expression levels of VvMYBA1 and anthocyanin accumulation in skin and flesh. Our findings also suggest that skin and flesh colors are inherited together and vary depending on the presence or absence of the VvMYBA1BEN allele.
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Affiliation(s)
- Akifumi Azuma
- Division of Grape and Persimmon Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Higashihiroshima, Hiroshima 739-2494, Japan.
| | - Shozo Kobayashi
- Division of Grape and Persimmon Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Higashihiroshima, Hiroshima 739-2494, Japan
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18
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Chang Y, Ahlawat YK, Gu T, Sarkhosh A, Liu T. Transcriptional profiling of two muscadine grape cultivars "Carlos" and "Noble" to reveal new genes, gene regulatory networks, and pathways that involved in grape berry ripening. FRONTIERS IN PLANT SCIENCE 2022; 13:949383. [PMID: 36061784 PMCID: PMC9435441 DOI: 10.3389/fpls.2022.949383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
In commercial fruit production, synchronized ripening and stable shelf life are important properties. The loosely clustered or non-bunching muscadine grape has unrealized potential as a disease-resistant cash crop, but requires repeated hand harvesting due to its unsynchronized or long or heterogeneous maturation period. Genomic research can be used to identify the developmental and environmental factors that control fruit ripening and postharvest quality. This study coupled the morphological, biochemical, and genetic variations between "Carlos" and "Noble" muscadine grape cultivars with RNA-sequencing analysis during berry maturation. The levels of antioxidants, anthocyanins, and titratable acids varied between the two cultivars during the ripening process. We also identified new genes, pathways, and regulatory networks that modulated berry ripening in muscadine grape. These findings may help develop a large-scale database of the genetic factors of muscadine grape ripening and postharvest profiles and allow the discovery of the factors underlying the ripeness heterogeneity at harvest. These genetic resources may allow us to combine applied and basic research methods in breeding to improve table and wine grape ripening uniformity, quality, stress tolerance, and postharvest handling and storage.
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Affiliation(s)
- Yuru Chang
- Department of Horticultural Science, University of Florida, Gainesville, FL, United States
| | - Yogesh Kumar Ahlawat
- Department of Horticultural Science, University of Florida, Gainesville, FL, United States
| | - Tongjun Gu
- Bioinformatics, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
- Department of Biostatistics, University of Florida, Gainesville, FL, United States
| | - Ali Sarkhosh
- Department of Horticultural Science, University of Florida, Gainesville, FL, United States
| | - Tie Liu
- Department of Horticultural Science, University of Florida, Gainesville, FL, United States
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19
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Flutre T, Le Cunff L, Fodor A, Launay A, Romieu C, Berger G, Bertrand Y, Terrier N, Beccavin I, Bouckenooghe V, Roques M, Pinasseau L, Verbaere A, Sommerer N, Cheynier V, Bacilieri R, Boursiquot JM, Lacombe T, Laucou V, This P, Péros JP, Doligez A. A genome-wide association and prediction study in grapevine deciphers the genetic architecture of multiple traits and identifies genes under many new QTLs. G3 (BETHESDA, MD.) 2022; 12:6575896. [PMID: 35485948 PMCID: PMC9258538 DOI: 10.1093/g3journal/jkac103] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/21/2022] [Indexed: 12/11/2022]
Abstract
To cope with the challenges facing agriculture, speeding-up breeding programs is a worthy endeavor, especially for perennial species such as grapevine, but requires understanding the genetic architecture of target traits. To go beyond the mapping of quantitative trait loci in bi-parental crosses, we exploited a diversity panel of 279 Vitis vinifera L. cultivars planted in 5 blocks in the vineyard. This panel was phenotyped over several years for 127 traits including yield components, organic acids, aroma precursors, polyphenols, and a water stress indicator. The panel was genotyped for 63k single nucleotide polymorphisms by combining an 18K microarray and genotyping-by-sequencing. The experimental design allowed to reliably assess the genotypic values for most traits. Marker densification via genotyping-by-sequencing markedly increased the proportion of genetic variance explained by single nucleotide polymorphisms, and 2 multi-single nucleotide polymorphism models identified quantitative trait loci not found by a single nucleotide polymorphism-by-single nucleotide polymorphism model. Overall, 489 reliable quantitative trait loci were detected for 41% more response variables than by a single nucleotide polymorphism-by-single nucleotide polymorphism model with microarray-only single nucleotide polymorphisms, many new ones compared with the results from bi-parental crosses. A prediction accuracy higher than 0.42 was obtained for 50% of the response variables. Our overall approach as well as quantitative trait locus and prediction results provide insights into the genetic architecture of target traits. New candidate genes and the application into breeding are discussed.
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Affiliation(s)
- Timothée Flutre
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France.,Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190 Gif-sur-Yvette, France
| | - Loïc Le Cunff
- UMT Géno-Vigne, 34398 Montpellier, France.,IFV, 30240 Le Grau-du-Roi, France
| | - Agota Fodor
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Amandine Launay
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Charles Romieu
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Gilles Berger
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Yves Bertrand
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Nancy Terrier
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France
| | | | | | - Maryline Roques
- UMT Géno-Vigne, 34398 Montpellier, France.,IFV, 30240 Le Grau-du-Roi, France
| | - Lucie Pinasseau
- SPO, Univ Montpellier, INRAE, Institut Agro, 34060 Montpellier, France
| | - Arnaud Verbaere
- SPO, Univ Montpellier, INRAE, Institut Agro, 34060 Montpellier, France
| | - Nicolas Sommerer
- SPO, Univ Montpellier, INRAE, Institut Agro, 34060 Montpellier, France
| | | | - Roberto Bacilieri
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Jean-Michel Boursiquot
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Thierry Lacombe
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Valérie Laucou
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Patrice This
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Jean-Pierre Péros
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Agnès Doligez
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
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20
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Faralli M, Bontempo L, Bianchedi PL, Moser C, Bertamini M, Lawson T, Camin F, Stefanini M, Varotto C. Natural variation in stomatal dynamics drives divergence in heat stress tolerance and contributes to seasonal intrinsic water-use efficiency in Vitis vinifera (subsp. sativa and sylvestris). JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3238-3250. [PMID: 34929033 DOI: 10.1093/jxb/erab552] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/20/2021] [Indexed: 05/20/2023]
Abstract
Stomata control CO2 uptake for photosynthesis and water loss through transpiration, thus playing a key role in leaf thermoregulation, water-use efficiency (iWUE), and plant productivity. In this work, we investigated the relationship between several leaf traits and hypothesized that stomatal behavior to fast (i.e. minutes) environmental changes co-determines, along with steady-state traits, the physiological response of grapevine to the surrounding fluctuating environment over the growing season. No relationship between iWUE, heat stress tolerance, and stomatal traits was observed in field-grown grapevine, suggesting that other physiological mechanisms are involved in determining leaf evaporative cooling capacity and the seasonal ratio of CO2 uptake (A) to stomatal conductance (gs). Indeed, cultivars that in the field had an unexpected combination of high iWUE but low sensitivity to thermal stress displayed a quick stomatal closure to light, but a sluggish closure to increased vapor pressure deficit (VPD) levels. This strategy, aiming both at conserving water under a high to low light transition and in prioritizing evaporative cooling under a low to high VPD transition, was mainly observed in the cultivars Regina and Syrah. Moreover, cultivars with different known responses to soil moisture deficit or high air VPD (isohydric versus anisohydric) had opposite behavior under fluctuating environments, with the isohydric cultivar showing slow stomatal closure to reduced light intensity but quick temporal responses to VPD manipulation. We propose that stomatal behavior to fast environmental fluctuations can play a critical role in leaf thermoregulation and water conservation under natural field conditions in grapevine.
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Affiliation(s)
- Michele Faralli
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, 38098 San Michele all'Adige (TN), Italy
- Center Agriculture Food Environment (C3A), University of Trento, Via Mach 1, 38098 San Michele all'Adige (TN), Italy
| | - Luana Bontempo
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, 38098 San Michele all'Adige (TN), Italy
| | - Pier Luigi Bianchedi
- Technology Transfer Centre, Fondazione Edmund Mach, via Mach 1, 38098 San Michele all'Adige (TN), Italy
| | - Claudio Moser
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, 38098 San Michele all'Adige (TN), Italy
| | - Massimo Bertamini
- Center Agriculture Food Environment (C3A), University of Trento, Via Mach 1, 38098 San Michele all'Adige (TN), Italy
- Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, 38098 San Michele all'Adige (TN), Italy
| | - Tracy Lawson
- School of Life Sciences, University of Essex, Colchester, UK
| | - Federica Camin
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, 38098 San Michele all'Adige (TN), Italy
- Center Agriculture Food Environment (C3A), University of Trento, Via Mach 1, 38098 San Michele all'Adige (TN), Italy
- International Atomic Energy Agency, Vienna International Centre, PO Box 100, A-1400 Vienna, Austria
| | - Marco Stefanini
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, 38098 San Michele all'Adige (TN), Italy
| | - Claudio Varotto
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, 38098 San Michele all'Adige (TN), Italy
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21
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Varanasi A, Worthington M, Nelson L, Brown A, Chizk TM, Threlfall R, Howard L, Conner P, Figueroa-Balderas R, Massonnet M, Cantu D, Clark JR. Glutathione S-transferase: a candidate gene for berry color in muscadine grapes (Vitis rotundifolia). G3 (BETHESDA, MD.) 2022; 12:6550507. [PMID: 35302606 PMCID: PMC9073687 DOI: 10.1093/g3journal/jkac060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/09/2022] [Indexed: 01/27/2023]
Abstract
Muscadine grapes (Vitis rotundifolia Michx.) are a specialty crop cultivated in the southern United States. Muscadines (2n = 40) belong to the Muscadinia subgenus of Vitis, while other cultivated grape species belong to the subgenus Euvitis (2n = 38). The muscadine berry color locus was mapped to a 0.8 Mbp region syntenic with chromosome 4 of Vitis vinifera. In this study, we identified glutathione S-transferase4 as a likely candidate gene for anthocyanin transport within the berry color locus. PCR and Kompetitive allele-specific PCR genotyping identified a single intragenic SNP (C/T) marker corresponding to a proline to leucine mutation within the muscadine glutathione S-transferase4 (VrGST4) that differentiated black (CC and CT) from bronze (TT) muscadines in 126 breeding selections, 76 cultivars, and 359 progeny from 3 mapping populations. Anthocyanin profiling on a subset of the progeny indicated a dominant VrGST4 action. VrGST4 was expressed in skins of both black and bronze muscadines at similar levels. While nonsynonymous polymorphisms between black and bronze muscadines were discovered in VrGSTF12, another Type I GST-coding gene in the muscadine color locus, this gene was ruled out as a possible candidate for berry color because RNA sequencing indicated it is not expressed in berry skins at véraison from black or bronze genotypes. These results suggest that the bronze phenotype in muscadines is regulated by a mechanism distinct from the MybA gene cluster responsible for berry color variation in Vitis vinifera.
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Affiliation(s)
- Aruna Varanasi
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
| | | | - Lacy Nelson
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Autumn Brown
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Thomas Mason Chizk
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Renee Threlfall
- Department of Food Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - Luke Howard
- Department of Food Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - Patrick Conner
- Department of Horticulture, University of Georgia, Tifton, GA 31793, USA
| | - Rosa Figueroa-Balderas
- Department of Viticulture & Enology, University of California, Davis, Davis, CA 95616, USA
| | - Mélanie Massonnet
- Department of Viticulture & Enology, University of California, Davis, Davis, CA 95616, USA
| | - Dario Cantu
- Department of Viticulture & Enology, University of California, Davis, Davis, CA 95616, USA
| | - John R Clark
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
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22
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A 69 kbp Deletion at the Berry Color Locus Is Responsible for Berry Color Recovery in Vitis vinifera L. Cultivar 'Riesling Rot'. Int J Mol Sci 2022; 23:ijms23073708. [PMID: 35409066 PMCID: PMC8998622 DOI: 10.3390/ijms23073708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 11/18/2022] Open
Abstract
‘Riesling Weiss’ is a white grapevine variety famous worldwide for fruity wines with higher acidity. Hardly known is ‘Riesling Rot’, a red-berried variant of ‘Riesling Weiss’ that disappeared from commercial cultivation but has increased in awareness in the last decades. The question arises of which variant, white or red, is the original and, consequently, which cultivar is the true ancestor. Sequencing the berry color locus of ‘Riesling Rot’ revealed a new VvmybA gene variant in one of the two haplophases called VvmybA3/1RR. The allele displays homologous recombination of VvmybA3 and VvmybA1 with a deletion of about 69 kbp between both genes that restores VvmybA1 transcripts. Furthermore, analysis of ‘Riesling Weiss’, ‘Riesling Rot’, and the ancestor ‘Heunisch Weiss’ along chromosome 2 using SSR (simple sequence repeat) markers elucidated that the haplophase of ‘Riesling Weiss’ was inherited from the white-berried parent variety ‘Heunisch Weiss’. Since no color mutants of ‘Heunisch Weiss’ are described that could have served as allele donors, we concluded that, in contrast to the public opinion, ‘Riesling Rot’ resulted from a mutational event in ‘Riesling Weiss’ and not vice versa.
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23
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Berry Anthocyanin, Acid, and Volatile Trait Analyses in a Grapevine-Interspecific F2 Population Using an Integrated GBS and rhAmpSeq Genetic Map. PLANTS 2022; 11:plants11050696. [PMID: 35270166 PMCID: PMC8912348 DOI: 10.3390/plants11050696] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 11/29/2022]
Abstract
Increased map density and transferability of markers are essential for the genetic analysis of fruit quality and stress tolerance in interspecific grapevine populations. We used 1449 GBS and 2000 rhAmpSeq markers to develop a dense map for an interspecific F2 population (VRS-F2) that was derived by selfing a single F1 from a Vitis riparia x ‘Seyval blanc’ cross. The resultant map contained 2519 markers spanning 1131.3 cM and was highly collinear with the Vitis vinifera ‘PN40024’ genome. Quantitative trait loci (QTL) for berry skin color and flower type were used to validate the map. Four rhAmpSeq transferable markers were identified that can be used in pairs (one pistillate and one hermaphroditic) to predict pistillate and hermaphrodite flower type with ≥99.7% accuracy. Total and individual anthocyanin diglucoside QTL mapped to chromosome 9 near a 5-O-GLUCOSYLTRANSFERASE candidate gene. Malic acid QTL were observed on chromosome 1 and 6 with two MALATE DEHYRDROGENASE CYTOPLASMIC 1 and ALUMINUM-ACTIVATED MALATE TRANSPORTER 2-LIKE (ALMT) candidate genes, respectively. Modeling malic acid identified a potential QTL on chromosome 8 with peak position in proximity of another ALMT. A first-ever reported QTL for the grassy smelling volatile (E)-2-hexenal was found on chromosome 2 with a PHOSPHOLIPID HYDROPEROXIDE GLUTATHIONE PEROXIDASE candidate gene near peak markers.
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24
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Karn A, Diaz-Garcia L, Reshef N, Zou C, Manns DC, Cadle-Davidson L, Mansfield AK, Reisch BI, Sacks GL. The Genetic Basis of Anthocyanin Acylation in North American Grapes ( Vitis spp.). Genes (Basel) 2021; 12:1962. [PMID: 34946911 PMCID: PMC8701791 DOI: 10.3390/genes12121962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 11/16/2022] Open
Abstract
Hydroxycinnamylated anthocyanins (or simply 'acylated anthocyanins') increase color stability in grape products, such as wine. Several genes that are relevant for anthocyanin acylation in grapes have been previously described; however, control of the degree of acylation in grapes is complicated by the lack of genetic markers quantitatively associated with this trait. To characterize the genetic basis of anthocyanin acylation in grapevine, we analyzed the acylation ratio in two closely related biparental families, Vitis rupestris B38 × 'Horizon' and 'Horizon' × Illinois 547-1, for 2 and 3 years, respectively. The acylation ratio followed a bimodal and skewed distribution in both families, with repeatability estimates larger than 0.84. Quantitative trait locus (QTL) mapping with amplicon-based markers (rhAmpSeq) identified a strong QTL from 'Horizon' on chromosome 3, near 15.85 Mb in both families and across years, explaining up to 85.2% of the phenotypic variance. Multiple candidate genes were identified in the 14.85-17.95 Mb interval, in particular, three copies of a gene encoding an acetyl-CoA-benzylalcohol acetyltransferase-like protein within the two most strongly associated markers. Additional population-specific QTLs were found in chromosomes 9, 10, 15, and 16; however, no candidate genes were described. The rhAmpSeq markers reported here, which were previously shown to be highly transferable among the Vitis genus, could be immediately implemented in current grapevine breeding efforts to control the degree of anthocyanin acylation and improve the quality of grapes and their products.
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Affiliation(s)
- Avinash Karn
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA; (A.K.); (L.C.-D.); (B.I.R.)
| | - Luis Diaz-Garcia
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Campo Experimental Pabellón, Aguascalientes 20676, Mexico
| | - Noam Reshef
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA;
| | - Cheng Zou
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA;
| | - David C. Manns
- Department of Food Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA; (D.C.M.); (A.K.M.)
| | - Lance Cadle-Davidson
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA; (A.K.); (L.C.-D.); (B.I.R.)
- USDA-Agricultural Research Service, Grape Genetics Research Unit, Geneva, NY 14456, USA
| | - Anna Katharine Mansfield
- Department of Food Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA; (D.C.M.); (A.K.M.)
| | - Bruce I. Reisch
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA; (A.K.); (L.C.-D.); (B.I.R.)
| | - Gavin L. Sacks
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA;
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25
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Brault C, Doligez A, Cunff L, Coupel-Ledru A, Simonneau T, Chiquet J, This P, Flutre T. Harnessing multivariate, penalized regression methods for genomic prediction and QTL detection of drought-related traits in grapevine. G3-GENES GENOMES GENETICS 2021; 11:6325507. [PMID: 34544146 PMCID: PMC8496232 DOI: 10.1093/g3journal/jkab248] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 07/02/2021] [Indexed: 11/13/2022]
Abstract
Viticulture has to cope with climate change and to decrease pesticide inputs, while maintaining yield and wine quality. Breeding is a key lever to meet this challenge, and genomic prediction a promising tool to accelerate breeding programs. Multivariate methods are potentially more accurate than univariate ones. Moreover, some prediction methods also provide marker selection, thus allowing quantitative trait loci (QTLs) detection and the identification of positional candidate genes. To study both genomic prediction and QTL detection for drought-related traits in grapevine, we applied several methods, interval mapping (IM) as well as univariate and multivariate penalized regression, in a bi-parental progeny. With a dense genetic map, we simulated two traits under four QTL configurations. The penalized regression method Elastic Net (EN) for genomic prediction, and controlling the marginal False Discovery Rate on EN selected markers to prioritize the QTLs. Indeed, penalized methods were more powerful than IM for QTL detection across various genetic architectures. Multivariate prediction did not perform better than its univariate counterpart, despite strong genetic correlation between traits. Using 14 traits measured in semi-controlled conditions under different watering conditions, penalized regression methods proved very efficient for intra-population prediction whatever the genetic architecture of the trait, with predictive abilities reaching 0.68. Compared to a previous study on the same traits, these methods applied on a denser map found new QTLs controlling traits linked to drought tolerance and provided relevant candidate genes. Overall, these findings provide a strong evidence base for implementing genomic prediction in grapevine breeding.
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Affiliation(s)
- Charlotte Brault
- Institut Français de la Vigne et du Vin, Montpellier F-34398, France.,UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier F-34398, France.,UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier F-34398, France
| | - Agnès Doligez
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier F-34398, France.,UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier F-34398, France
| | - Le Cunff
- Institut Français de la Vigne et du Vin, Montpellier F-34398, France.,UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier F-34398, France.,UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier F-34398, France
| | - Aude Coupel-Ledru
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier 34000, France
| | - Thierry Simonneau
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier 34000, France
| | | | - Patrice This
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier F-34398, France.,UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier F-34398, France
| | - Timothée Flutre
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
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26
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Jiu S, Guan L, Leng X, Zhang K, Haider MS, Yu X, Zhu X, Zheng T, Ge M, Wang C, Jia H, Shangguan L, Zhang C, Tang X, Abdullah M, Javed HU, Han J, Dong Z, Fang J. 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 BIOTECHNOLOGY JOURNAL 2021; 19:1216-1239. [PMID: 33440072 PMCID: PMC8196647 DOI: 10.1111/pbi.13543] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 08/05/2020] [Accepted: 09/01/2020] [Indexed: 05/23/2023]
Abstract
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, R44 L substitution abolished the interaction of VvMYBA2w with VvMYCA1. Meanwhile, both R44 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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Affiliation(s)
- Songtao Jiu
- Key Laboratory of Genetics and Fruit developmentCollege of HorticultureNanjing Agricultural UniversityNanjingJiangsu ProvinceChina
- Department of Plant ScienceSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Le Guan
- Key Laboratory of Genetics and Fruit developmentCollege of HorticultureNanjing Agricultural UniversityNanjingJiangsu ProvinceChina
| | - Xiangpeng Leng
- College of HorticultureQingdao Agricultural UniversityQingdaoShandong ProvinceChina
| | - Kekun Zhang
- Key Laboratory of Genetics and Fruit developmentCollege of HorticultureNanjing Agricultural UniversityNanjingJiangsu ProvinceChina
| | - Muhammad Salman Haider
- Key Laboratory of Genetics and Fruit developmentCollege of HorticultureNanjing Agricultural UniversityNanjingJiangsu ProvinceChina
| | - Xiang Yu
- School of MedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Xudong Zhu
- Key Laboratory of Genetics and Fruit developmentCollege of HorticultureNanjing Agricultural UniversityNanjingJiangsu ProvinceChina
| | - Ting Zheng
- Key Laboratory of Genetics and Fruit developmentCollege of HorticultureNanjing Agricultural UniversityNanjingJiangsu ProvinceChina
| | - Mengqing Ge
- Key Laboratory of Genetics and Fruit developmentCollege of HorticultureNanjing Agricultural UniversityNanjingJiangsu ProvinceChina
| | - Chen Wang
- Key Laboratory of Genetics and Fruit developmentCollege of HorticultureNanjing Agricultural UniversityNanjingJiangsu ProvinceChina
| | - Haifeng Jia
- Key Laboratory of Genetics and Fruit developmentCollege of HorticultureNanjing Agricultural UniversityNanjingJiangsu ProvinceChina
| | - Lingfei Shangguan
- Key Laboratory of Genetics and Fruit developmentCollege of HorticultureNanjing Agricultural UniversityNanjingJiangsu ProvinceChina
| | - Caixi Zhang
- Department of Plant ScienceSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Xiaoping Tang
- Shanxi Academy of Agricultural Sciences Pomology InstituteTaiguShanxi ProvinceChina
| | - Muhammad Abdullah
- Department of Plant ScienceSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Hafiz Umer Javed
- Department of Plant ScienceSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Jian Han
- Key Laboratory of Genetics and Fruit developmentCollege of HorticultureNanjing Agricultural UniversityNanjingJiangsu ProvinceChina
| | - Zhigang Dong
- Shanxi Academy of Agricultural Sciences Pomology InstituteTaiguShanxi ProvinceChina
| | - Jinggui Fang
- Key Laboratory of Genetics and Fruit developmentCollege of HorticultureNanjing Agricultural UniversityNanjingJiangsu ProvinceChina
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27
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Kong J, Wu J, Guan L, Hilbert G, Delrot S, Fan P, Liang Z, Wu B, Matus JT, Gomès E, Dai Z. Metabolite analysis reveals distinct spatio-temporal accumulation of anthocyanins in two teinturier variants of cv. 'Gamay' grapevines (Vitis vinifera L.). PLANTA 2021; 253:84. [PMID: 33788027 DOI: 10.1007/s00425-021-03613-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/24/2021] [Indexed: 06/12/2023]
Abstract
White-fleshed grape cv. 'Gamay' and its two teinturier variants presented distinct spatial-temporal accumulation of anthocyanins, with uncoupled accumulation of sugars and anthocyanins in 'Gamay Fréaux'. In most red grape cultivars, anthocyanins accumulate exclusively in the berry skin, while 'teinturier' cultivars also accumulate anthocyanins in the pulp. Here, we investigated the teinturier cvs. 'Gamay de Bouze' and 'Gamay Fréaux' (two somatic variants of the white-fleshed cv. 'Gamay') through metabolic and transcript analysis to clarify whether these two somatic variants have the same anthocyanin accumulation pattern in the skin and pulp, and whether primary metabolites are also affected. The skin of the three cultivars and the pulp of 'Gamay de Bouze' begun to accumulate anthocyanins at the onset of berry ripening. However, the pulp of 'Gamay Fréaux' exhibited a distinct anthocyanin accumulation pattern, starting as early as fruit set with very low level of sugars. The highest level of anthocyanins was found in 'Gamay Fréaux' skin, followed by 'Gamay de Bouze' and 'Gamay'. Consistently, the transcript abundance of genes involved in anthocyanin biosynthesis were in line with the anthocyanin levels in the three cultivars. Despite no evident differences in pulp sugar content, the concentration of glucose and fructose in the skin of 'Gamay Fréaux' was only half of those in the skin of 'Gamay' and 'Gamay de Bouze' throughout all berry ripening, suggesting an uncoupled accumulation of sugars and anthocyanins in 'Gamay Fréaux'. The study provides a comprehensive view of metabolic consequences in grape somatic variants and the three almost isogenic genotypes can serve as ideal reagents to further uncover the mechanisms underlying the linkage between sugar and anthocyanin accumulation.
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Affiliation(s)
- Junhua Kong
- Beijing Key Laboratory of Grape Science and Enology, Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jing Wu
- EGFV, Univ. Bordeaux, Bordeaux Science Agro, INRAE, ISVV, 33882, Villenave-d'Ornon, France
| | - Le Guan
- College of Life Science, Northeast Forestry University/ Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Harbin, 150040, China
| | - Ghislaine Hilbert
- EGFV, Univ. Bordeaux, Bordeaux Science Agro, INRAE, ISVV, 33882, Villenave-d'Ornon, France
| | - Serge Delrot
- EGFV, Univ. Bordeaux, Bordeaux Science Agro, INRAE, ISVV, 33882, Villenave-d'Ornon, France
| | - Peige Fan
- Beijing Key Laboratory of Grape Science and Enology, Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Science and Enology, Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Benhong Wu
- Beijing Key Laboratory of Grape Science and Enology, Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Eric Gomès
- EGFV, Univ. Bordeaux, Bordeaux Science Agro, INRAE, ISVV, 33882, Villenave-d'Ornon, France
| | - Zhanwu Dai
- Beijing Key Laboratory of Grape Science and Enology, Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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28
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Gomès É, Maillot P, Duchêne É. Molecular Tools for Adapting Viticulture to Climate Change. FRONTIERS IN PLANT SCIENCE 2021; 12:633846. [PMID: 33643361 PMCID: PMC7902699 DOI: 10.3389/fpls.2021.633846] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/19/2021] [Indexed: 05/04/2023]
Abstract
Adaptation of viticulture to climate change includes exploration of new geographical areas, new training systems, new management practices, or new varieties, both for rootstocks and scions. Molecular tools can be defined as molecular approaches used to study DNAs, RNAs, and proteins in all living organisms. We present here the current knowledge about molecular tools and their potential usefulness in three aspects of grapevine adaptation to the ongoing climate change. (i) Molecular tools for understanding grapevine response to environmental stresses. A fine description of the regulation of gene expression is a powerful tool to understand the physiological mechanisms set up by the grapevine to respond to abiotic stress such as high temperatures or drought. The current knowledge on gene expression is continuously evolving with increasing evidence of the role of alternative splicing, small RNAs, long non-coding RNAs, DNA methylation, or chromatin activity. (ii) Genetics and genomics of grapevine stress tolerance. The description of the grapevine genome is more and more precise. The genetic variations among genotypes are now revealed with new technologies with the sequencing of very long DNA molecules. High throughput technologies for DNA sequencing also allow now the genetic characterization at the same time of hundreds of genotypes for thousands of points in the genome, which provides unprecedented datasets for genotype-phenotype associations studies. We review the current knowledge on the genetic determinism of traits for the adaptation to climate change. We focus on quantitative trait loci and molecular markers available for developmental stages, tolerance to water stress/water use efficiency, sugar content, acidity, and secondary metabolism of the berries. (iii) Controlling the genome and its expression to allow breeding of better-adapted genotypes. High-density DNA genotyping can be used to select genotypes with specific interesting alleles but genomic selection is also a powerful method able to take into account the genetic information along the whole genome to predict a phenotype. Modern technologies are also able to generate mutations that are possibly interesting for generating new phenotypes but the most promising one is the direct editing of the genome at a precise location.
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Affiliation(s)
- Éric Gomès
- EGFV, University of Bordeaux – Bordeaux Sciences-Agro – INRAE, Villenave d’Ornon, France
| | - Pascale Maillot
- SVQV, INRAE – University of Strasbourg, Colmar, France
- University of Haute Alsace, Mulhouse, France
| | - Éric Duchêne
- SVQV, INRAE – University of Strasbourg, Colmar, France
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29
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Color Intensity of the Red-Fleshed Berry Phenotype of Vitis vinifera Teinturier Grapes Varies Due to a 408 bp Duplication in the Promoter of VvmybA1. Genes (Basel) 2020; 11:genes11080891. [PMID: 32764272 PMCID: PMC7464560 DOI: 10.3390/genes11080891] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/28/2020] [Accepted: 07/31/2020] [Indexed: 11/18/2022] Open
Abstract
Grapevine (Vitis vinifera) teinturier cultivars are characterized by their typical reddish leaves and red-fleshed berries due to ectopic anthocyanin formation. Wines of these varieties have economic importance as they can be used for blending to enhance the color of red wines. The unique and heritable mutation has been known for a long time but the underlying genetic mechanism still is not yet understood. Here we describe the association of the red-fleshed berry phenotype with a 408 bp repetitive DNA element in the promoter of the VvmybA1 gene (grapevine color enhancer, GCE). Three different clones of ‘Teinturier’ were discovered with two, three and five allelic GCE repeats (MybA1t2, MybA1t3 and MybA1t5). All three clones are periclinal chimeras; these clones share the same L1 layer, but have distinct L2 layers with different quantities of GCE repeats. Quantitative real time PCR and HPLC analysis of leaf and berry samples showed that the GCE repeat number strongly correlates with an increase of the expression of VvmybA1 itself and the VvUFGT gene regulated by it and the anthocyanin content. A model is proposed based on autoregulation of VvmybA1t to explain the red phenotype which is similar to that of red-fleshed apples. This study presents results about the generation and modes of action of three MybA1t alleles responsible for the red-fleshed berry phenotype of teinturier grapevines.
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30
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Sun L, Li S, Jiang J, Tang X, Fan X, Zhang Y, Liu J, Liu C. New quantitative trait locus (QTLs) and candidate genes associated with the grape berry color trait identified based on a high-density genetic map. BMC PLANT BIOLOGY 2020; 20:302. [PMID: 32605636 PMCID: PMC7325011 DOI: 10.1186/s12870-020-02517-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/23/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Berry color is an important trait in grapes and is mainly determined by the anthocyanin content and composition. To further explore the coloring mechanism of grape berries, the F1 population of Vitis vinifera 'Red Globe' × 'Muscat Hamburg' was used to map the color locus, and transcriptome analysis was performed to assist in screening candidate genes. RESULTS A total of 438,407 high-quality single-nucleotide polymorphisms (SNPs) were obtained from whole-genome resequencing (WGS) of the population, and 27,454 SNPs were selected to construct a high-density genetic map. The selected SNPs were clustered into 19 linkage groups (LGs) spanning a genetic distance of 1442.638 cM. Berry color was evaluated by color grade, chromatic aberration, total anthocyanin content and anthocyanin composition. The Pearson correlation coefficients of these phenotypes in 2017 and 2018 were significant at the 0.01 level. The major color locus of MYBA1 and MYBA2 on LG2 was identified, explaining between 26 and 63.6% of all phenotypic variance. Furthermore, 9 additional QTLs with smaller effects were detected on Chr2, Chr4, Chr6, Chr11 and Chr17. Combined with the gene annotation and RNA-seq data, multiple new candidate genes were selected from the above QTLs. CONCLUSION These results indicated that grape berry color is a quantitative trait controlled by a major color locus and multiple minor loci. Though the major color locus was consistent with previous studies, several minor QTLs and candidate genes associated with grape berry color and anthocyanin accumulation were identified in this study. And the specific regulatory mechanism still needs to be further explored.
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Affiliation(s)
- Lei Sun
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Shenchang Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Jianfu Jiang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaoping Tang
- Pomology Institute, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Xiucai Fan
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Ying Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Jihong Liu
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China.
| | - Chonghuai Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China.
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31
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Xie S, Lei Y, Chen H, Li J, Chen H, Zhang Z. R2R3-MYB Transcription Factors Regulate Anthocyanin Biosynthesis in Grapevine Vegetative Tissues. FRONTIERS IN PLANT SCIENCE 2020; 11:527. [PMID: 32457776 PMCID: PMC7221203 DOI: 10.3389/fpls.2020.00527] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/07/2020] [Indexed: 06/02/2023]
Abstract
Anthocyanins with important physiological functions mainly accumulate in grape berry, but teinturier grape cultivars can accumulate anthocyanins in both reproductive and vegetative tissues. The molecular regulatory mechanisms of anthocyanin biosynthesis in grapevine reproductive and vegetative tissues are different. Therefore, teinturier grapevine cultivar provides opportunities to investigate transcriptional regulation of vegetative anthocyanins, and to compare with mechanisms that regulate grape berry anthocyanins. Yan73 is a teinturier Vitis vinifera variety with vegetative tissues able to accumulate anthocyanins, but the anthocyanin pattern and the molecular mechanism regulating anthocyanin biosynthesis in these tissues remain uncharacterized. We analyzed the anthocyanin metabolic and transcriptome profiles of the vegetative tissues of Yan73 and its male parent with HPLC-ESI-MS/MS and RNA-sequencing technologies. Yan73 vegetative tissues had relatively high 3'-OH, acylated, and methoxylated anthocyanins. Furthermore, peonidin-3-O-(trans-6-coumaryl)-glucoside is the most abundant anthocyanin in Yan73 grapevine vegetative tissues. A total of 30,17 and 10 anthocyanin biosynthesis genes showed up-regulated expression in Yan73 leaf, stem and tendril, respectively, indicating anthocyanin biosynthesis in Yan73 vegetative tissues is regulated by transcription factors. The up-regulated expression of VvMYBA1 on chromosome 2 and VvMYBA5, VvMYBA6, and VvMYBA7 on chromosome 14 are responsible for the anthocyanin patterns of Yan73 vegetative tissues. The expression of a set of R2R3-MYB C2 repressor genes is activated and may negatively regulate anthocyanin biosynthesis in Yan73 vegetative tissues. These findings enhance our understanding of anthocyanin biosynthesis in grapevine.
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Affiliation(s)
- Sha Xie
- College of Enology, Northwest A&F University, Xianyang, China
| | - Yujuan Lei
- College of Food Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao, China
| | - Huawei Chen
- College of Enology, Northwest A&F University, Xianyang, China
| | - Junnan Li
- College of Enology, Northwest A&F University, Xianyang, China
| | - Huangzhao Chen
- College of Enology, Northwest A&F University, Xianyang, China
- College of Food and Biological Engineering, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Zhenwen Zhang
- College of Enology, Northwest A&F University, Xianyang, China
- Shaanxi Engineering Research Center for Viti-Viniculture, Xianyang, China
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32
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Yu M, Chen JC, Qu JZ, Liu F, Zhou M, Ma YM, Xiang SY, Pan XX, Zhang HB, Yang MZ. Exposure to endophytic fungi quantitatively and compositionally alters anthocyanins in grape cells. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 149:144-152. [PMID: 32066082 DOI: 10.1016/j.plaphy.2020.02.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 02/03/2020] [Accepted: 02/08/2020] [Indexed: 05/25/2023]
Abstract
Anthocyanins contribute greatly to the organoleptic and biochemical properties of grapes and wines. Although there are broadly documented factors involved in grape anthocyanin synthesis, the present work focused on fungal endophytes and their possible role in grape coloration. Our results showed that exposure to endophytic fungi within a dual culture system differentially affected total anthocyanin concentrations and PAL activities in grape cells. Grape cells dual cultured with fungal strains XH-2, R2-21 and B2-17 showed significant differences of their anthocyanin concentrations were subjected to further analysis of their anthocyanidin compositions. Compared to the no-fungus controls, grape cells exposed to fungal strains XH-2 and R2-21 exhibited quantitative promotion of their total anthocyanidin concentrations by 74% and 28%, respectively, whereas treatment with the fungus B2-17 reduced the anthocyanidin content by 19%. A total of 14 species of anthocyanidins were detected from the grape cells in these experiments. Most interestingly, exposure to any of these fungal strains differentially modified the compositional patterns of grape cellular anthocyanidins. The obvious upregulation of the transcription of VvMYB in grape cells treated with fungal strains XH-2 and R2-21 implies that the increased anthocyanin levels in these grape cells may be due to the activated transcriptional factors. In addition, the exposure of grape cells to extracts of these fungi initiated similar responses of anthocyanin contents and PAL activities to exposure to the living fungi and appeared obvious dosage effects. The influence of fungal endophytes on the coloration of grape berries was also examined in this study.
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Affiliation(s)
- Man Yu
- School of Life Science, Yunnan University, Kunming, 650504, China.
| | - Jing-Chao Chen
- School of Life Science, Yunnan University, Kunming, 650504, China.
| | - Jin-Zhuo Qu
- School of Life Science, Yunnan University, Kunming, 650504, China.
| | - Fang Liu
- School of Life Science, Yunnan University, Kunming, 650504, China.
| | - Ming Zhou
- School of Life Science, Yunnan University, Kunming, 650504, China.
| | - Yin-Min Ma
- School of Life Science, Yunnan University, Kunming, 650504, China.
| | - Si-Yu Xiang
- School of Life Science, Yunnan University, Kunming, 650504, China.
| | - Xiao-Xia Pan
- School of Agronomy, Yunnan University, Kunming, 650504, China.
| | - Han-Bo Zhang
- School of Life Science, Yunnan University, Kunming, 650504, China.
| | - Ming-Zhi Yang
- School of Life Science, Yunnan University, Kunming, 650504, China.
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33
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Sun L, Li S, Tang X, Fan X, Zhang Y, Jiang J, Liu J, Liu C. Transcriptome analysis reveal the putative genes involved in light-induced anthocyanin accumulation in grape ‘Red Globe’ (V. vinifera L.). Gene 2020; 728:144284. [DOI: 10.1016/j.gene.2019.144284] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/05/2019] [Accepted: 12/05/2019] [Indexed: 12/18/2022]
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34
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Underhill AN, Hirsch CD, Clark MD. Evaluating and Mapping Grape Color Using Image-Based Phenotyping. PLANT PHENOMICS (WASHINGTON, D.C.) 2020; 2020:8086309. [PMID: 33313563 PMCID: PMC7706331 DOI: 10.34133/2020/8086309] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/05/2020] [Indexed: 05/19/2023]
Abstract
Grape berry color is an economically important trait that is controlled by two major genes influencing anthocyanin synthesis in the skin. Color is often described qualitatively using six major categories; however, this is a subjective rating that often fails to describe variation within these six classes. To investigate minor genes influencing berry color, image analysis was used to quantify berry color using different color spaces. An image analysis pipeline was developed and utilized to quantify color in a segregating hybrid wine grape population across two years. Images were collected from grape clusters immediately after harvest and segmented by color to determine the red, green, and blue (RGB); hue, saturation, and intensity (HSI); and lightness, red-green, and blue-yellow values (L∗a∗b∗) of berries. QTL analysis identified known major QTL for color on chromosome 2 along with several previously unreported smaller-effect QTL on chromosomes 1, 5, 6, 7, 10, 15, 18, and 19. This study demonstrated the ability of an image analysis phenotyping system to characterize berry color and to more effectively capture variability within a population and identify genetic regions of interest.
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Affiliation(s)
- A. N. Underhill
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, USA
| | - C. D. Hirsch
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - M. D. Clark
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, USA
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35
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Xie S, Qiao X, Chen H, Nan H, Zhang Z. Coordinated Regulation of Grape Berry Flesh Color by Transcriptional Activators and Repressors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:11815-11824. [PMID: 31550160 DOI: 10.1021/acs.jafc.9b05234] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Yan73 is a teinturier Vitis vinifera variety with red berry flesh, but the molecular mechanisms underlying its flesh coloration remain unclear. We analyzed the flavonoid metabolic and transcriptome profiles of Yan73 berry red and white flesh using HPLC-ESI-MS/MS and RNA-sequencing technologies. Anthocyanins are the main flavonoids responsible for Yan73 berry flesh color, and the coloration is coordinately regulated by the VvMYBA1 transcriptional activator and VvMYBC2-L1 transcriptional repressor. Furthermore, yeast one- and two-hybrid, dual luciferase, and bimolecular fluorescence complementation assays suggested that VvMYBA1 positively regulates Yan73 berry flesh color via interactions with VvWDR1 and the activation of the VvCHI3, VvOMT, and VvGST4 promoters, whereas VvMYBC2-L1 negatively regulates Yan73 berry flesh color, possibly by competing with the R2R3-MYB transcriptional activators for bHLH partners or by repressing VvOMT and VvGST4 expression. Our findings provide new insights into the molecular mechanisms regulating grape flesh color.
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Affiliation(s)
- Sha Xie
- College of Enology , Northwest A&F University , No. 22 Xinong Road , Yangling , Shaanxi 712100 , China
| | - Xinlong Qiao
- Laboratory of Interdisciplinary Research Institute of Biophysics , Chinese Academy of Sciences , Beijing 100101 , China
- University of the Chinese Academy of Sciences , Beijing 100049 , China
| | - Huawei Chen
- College of Enology , Northwest A&F University , No. 22 Xinong Road , Yangling , Shaanxi 712100 , China
| | - Hao Nan
- College of Life Sciences , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Zhenwen Zhang
- College of Enology , Northwest A&F University , No. 22 Xinong Road , Yangling , Shaanxi 712100 , China
- Shaanxi Engineering Research Center for Viti-Viniculture , Yangling , Shaanxi 712100 , China
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36
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Zhou Y, Minio A, Massonnet M, Solares E, Lv Y, Beridze T, Cantu D, Gaut BS. The population genetics of structural variants in grapevine domestication. NATURE PLANTS 2019; 5:965-979. [PMID: 31506640 DOI: 10.1038/s41477-019-0507-8] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/26/2019] [Indexed: 05/20/2023]
Abstract
Structural variants (SVs) are a largely unexplored feature of plant genomes. Little is known about the type and size of SVs, their distribution among individuals and, especially, their population dynamics. Understanding these dynamics is critical for understanding both the contributions of SVs to phenotypes and the likelihood of identifying them as causal genetic variants in genome-wide associations. Here, we identify SVs and study their evolutionary genomics in clonally propagated grapevine cultivars and their outcrossing wild progenitors. To catalogue SVs, we assembled the highly heterozygous Chardonnay genome, for which one in seven genes is hemizygous based on SVs. Using an integrative comparison between Chardonnay and Cabernet Sauvignon genomes by whole-genome, long-read and short-read alignment, we extended SV detection to population samples. We found that strong purifying selection acts against SVs but particularly against inversion and translocation events. SVs nonetheless accrue as recessive heterozygotes in clonally propagated lineages. They also define outlier regions of genomic divergence between wild and cultivated grapevines, suggesting roles in domestication. Outlier regions include the sex-determination region and the berry colour locus, where independent large, complex inversions have driven convergent phenotypic evolution.
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Affiliation(s)
- Yongfeng Zhou
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA
| | - Andrea Minio
- Department of Viticulture and Enology, UC Davis, Davis, CA, USA
| | | | - Edwin Solares
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA
| | - Yuanda Lv
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA
| | - Tengiz Beridze
- Institute of Molecular Genetics, Agricultural University of Georgia, Tbilisi, Georgia
| | - Dario Cantu
- Department of Viticulture and Enology, UC Davis, Davis, CA, USA.
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA.
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Lewter J, Worthington ML, Clark JR, Varanasi AV, Nelson L, Owens CL, Conner P, Gunawan G. High-density linkage maps and loci for berry color and flower sex in muscadine grape (Vitis rotundifolia). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1571-1585. [PMID: 30756127 DOI: 10.1007/s00122-019-03302-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/02/2019] [Indexed: 06/09/2023]
Abstract
Linkage maps of muscadine grape generated using genotyping-by-sequencing (GBS) provide insight into genome collinearity between Muscadinia and Euvitis subgenera and genetic control of flower sex and berry color. The muscadine grape, Vitis rotundifolia, is a specialty crop native to the southeastern USA. Muscadine vines can be male, female, or perfect-flowered, and berry color ranges from bronze to black. Genetic linkage maps were constructed using genotyping-by-sequencing in two F1 populations segregating for flower sex and berry color. The linkage maps consisted of 1244 and 2069 markers assigned to 20 linkage groups (LG) for the 'Black Beauty' × 'Nesbitt' and 'Supreme' × 'Nesbitt' populations, respectively. Data from both populations were used to generate a consensus map with 2346 markers across 20 LGs. A high degree of collinearity was observed between the genetic maps and the Vitis vinifera physical map. The higher chromosome number in muscadine (2n = 40) compared to V. vinifera (2n = 38) was accounted for by the behavior of V. vinifera chromosome 7 as two independently segregating LGs in muscadine. The muscadine sex locus mapped to an interval that aligned to 4.64-5.09 Mb on V. vinifera chromosome 2, a region which includes the previously described V. vinifera subsp. sylvestris sex locus. While the MYB transcription factor genes controlling fruit color in V. vinifera are located on chromosome 2, the muscadine berry color locus mapped to an interval aligning to 11.09-11.88 Mb on V. vinifera chromosome 4, suggesting that a mutation in a different gene in the anthocyanin biosynthesis pathway determines berry color in muscadine. These linkage maps lay the groundwork for marker-assisted breeding in muscadine and provide insight into the evolution of Vitis species.
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Affiliation(s)
- Jennifer Lewter
- Department of Horticulture, University of Arkansas, 316 Plant Sciences Bldg., Fayetteville, AR, 72701, USA
| | - Margaret L Worthington
- Department of Horticulture, University of Arkansas, 316 Plant Sciences Bldg., Fayetteville, AR, 72701, USA.
| | - John R Clark
- Department of Horticulture, University of Arkansas, 316 Plant Sciences Bldg., Fayetteville, AR, 72701, USA
| | - Aruna V Varanasi
- Department of Horticulture, University of Arkansas, 316 Plant Sciences Bldg., Fayetteville, AR, 72701, USA
| | - Lacy Nelson
- Department of Horticulture, University of Arkansas, 316 Plant Sciences Bldg., Fayetteville, AR, 72701, USA
| | - Christopher L Owens
- USDA-ARS Grape Genetics Research Unit, Cornell University, 630 W. North St., Geneva, NY, 14456, USA
- IFG, 8224 Espresso Dr. Suite 200, Bakersfield, CA, 93312, USA
| | - Patrick Conner
- Department of Horticulture, University of Georgia, 4604 Research Way, Tifton, GA, 31793, USA
| | - Gunawati Gunawan
- Department of Horticulture, University of Georgia, 4604 Research Way, Tifton, GA, 31793, USA
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Vezzulli S, Malacarne G, Masuero D, Vecchione A, Dolzani C, Goremykin V, Mehari ZH, Banchi E, Velasco R, Stefanini M, Vrhovsek U, Zulini L, Franceschi P, Moser C. The Rpv3-3 Haplotype and Stilbenoid Induction Mediate Downy Mildew Resistance in a Grapevine Interspecific Population. FRONTIERS IN PLANT SCIENCE 2019; 10:234. [PMID: 30894868 PMCID: PMC6414455 DOI: 10.3389/fpls.2019.00234] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 02/12/2019] [Indexed: 05/04/2023]
Abstract
The development of new resistant varieties to the oomycete Plasmopara viticola (Berk.& Curt) is a promising way to combat downy mildew (DM), one of the major diseases threatening the cultivated grapevine (Vitis vinifera L.). Taking advantage of a segregating population derived from "Merzling" (a mid-resistant hybrid) and "Teroldego" (a susceptible landrace), 136 F1 individuals were characterized by combining genetic, phenotypic, and gene expression data to elucidate the genetic basis of DM resistance and polyphenol biosynthesis upon P. viticola infection. An improved consensus linkage map was obtained by scoring 192 microsatellite markers. The progeny were screened for DM resistance and production of 42 polyphenols. QTL mapping showed that DM resistance is associated with the herein named Rpv3-3 specific haplotype and it identified 46 novel metabolic QTLs linked to 30 phenolics-related parameters. A list of the 95 most relevant candidate genes was generated by specifically exploring the stilbenoid-associated QTLs. Expression analysis of 11 genes in Rpv3-3 +/- genotypes displaying disparity in DM resistance level and stilbenoid accumulation revealed significant new candidates for the genetic control of stilbenoid biosynthesis and oligomerization. These overall findings emphasized that DM resistance is likely mediated by the major Rpv3-3 haplotype and stilbenoid induction.
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Affiliation(s)
- Silvia Vezzulli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Giulia Malacarne
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Domenico Masuero
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Antonella Vecchione
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Chiara Dolzani
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Vadim Goremykin
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Zeraye Haile Mehari
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
- Ethiopian Institute of Agricultural Research, Addis Ababa, Ethiopia
| | - Elisa Banchi
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Riccardo Velasco
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
- CREA Research Centre for Viticulture and Enology, Conegliano, Italy
| | - Marco Stefanini
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Urska Vrhovsek
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Luca Zulini
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Pietro Franceschi
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Claudio Moser
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
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Fang J, Jogaiah S, Guan L, Sun X, Abdelrahman M. Coloring biology in grape skin: a prospective strategy for molecular farming. PHYSIOLOGIA PLANTARUM 2018; 164:429-441. [PMID: 30144090 DOI: 10.1111/ppl.12822] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 08/14/2018] [Accepted: 08/20/2018] [Indexed: 06/08/2023]
Abstract
Grapevine is one of the earliest domesticated fruit crops that has been widely prized and cultivated for its fruit and wine. Grapes exhibit a wide range of colors, ranging from the green/yellow to the dark blue tones according to the amount and composition of anthocyanin. During the last decades, many studies regarding the genetic control of the grape color in European, American and Asian cultivars have been well documented. DNA binding genes for several transcription factors, such as MYBA1 and MYBA2 haplotype compositions at the color locus are the key determinant of anthocyanin diversity and grape skin color development. Retrotransposon in the MYBA1 promoter region and mutation in MYBA2 coding sequence resulted in a white-skinned grape. The MYB haplotypes affect the ratio of tri/di-hydroxylated anthocyanins and methylated/non-methylated anthocyanins through the regulation of several structural genes involved in the anthocyanin biosynthesis, resulting in diverse colored tones. The present review provides an overview of the current state of the molecular mechanisms underlying the genetic regulations of the anthocyanin accumulation and diversification in grapes. The hypothesized models described in this review is a step forward to potentially predict the color diversification in different grape cultivars, which translate the advances in fundamental plant biology toward the application of grape molecular breeding.
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Affiliation(s)
- Jinggui Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, Puerto Rico, China
| | - Sudisha Jogaiah
- Plant Healthcare and Diagnostic Center, PG Department of Studies in Biotechnology and Microbiology, Karnatak University, Dharwad, Karnataka 580003, India
| | - Le Guan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, Puerto Rico, China
| | - Xin Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, Puerto Rico, China
| | - Mostafa Abdelrahman
- Botany Department, Faculty of Science, Aswan University, Aswan 81528, Egypt
- Arid Land Reseach Center, Tottori University, Tottori 680-0001, Japan
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40
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Molecular characterization of a diverse Iranian table grapevine germplasm using REMAP markers: population structure, linkage disequilibrium and association mapping of berry yield and quality traits. Biologia (Bratisl) 2018. [DOI: 10.2478/s11756-018-0158-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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41
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Ferreira V, Pinto-Carnide O, Arroyo-García R, Castro I. Berry color variation in grapevine as a source of diversity. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 132:696-707. [PMID: 30146416 DOI: 10.1016/j.plaphy.2018.08.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/17/2018] [Accepted: 08/18/2018] [Indexed: 06/08/2023]
Abstract
Even though it is one of the oldest perennial domesticated fruit crops in the world, grapevine (Vitis vinifera L.) cultivation today is the result of both conventional breeding practices (i.e. hybridizations adopted during the last century) and vegetative propagation. Human-assisted asexual propagation has allowed the maintenance of desired traits but has largely impacted the frequency of spontaneous somatic mutations observed in the field. Consequently, many grapevine fruit attributes to date have been artificially selected, including: fruit yield, compactness, size and composition, the latter being greatly diversified in the pursuit of altering berry skin coloration. The present review provides an overview of various aspects related to grapevine diversity, with a special emphasis on grape berry skin color variation and will discuss the current knowledge of how grape skin color variation is affected by the synthesis of phenolic compounds, particularly anthocyanins and their underlying genetic factors. We hope this knowledge will be useful in supporting the importance of the berry color trait diversity in cultivated grapevines, which is used as basis for selection during breeding programs because of its application for vine growers, winemakers and consumers.
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Affiliation(s)
- Vanessa Ferreira
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Centre for Plant Biotechnology and Genomics (UPM-INIA, CBGP), Campus de Montegancedo, Autovía M40 km38, 28223 Pozuelo de Alarcón, Madrid, Spain.
| | - Olinda Pinto-Carnide
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
| | - Rosa Arroyo-García
- Centre for Plant Biotechnology and Genomics (UPM-INIA, CBGP), Campus de Montegancedo, Autovía M40 km38, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Isaura Castro
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
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42
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Zhang Y, Hu W, Peng X, Sun B, Wang X, Tang H. Characterization of anthocyanin and proanthocyanidin biosynthesis in two strawberry genotypes during fruit development in response to different light qualities. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2018; 186:225-231. [PMID: 30092558 DOI: 10.1016/j.jphotobiol.2018.07.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 07/17/2018] [Accepted: 07/24/2018] [Indexed: 12/14/2022]
Abstract
LED-based light sources that can provide narrowly-centered spectrum have been frequently applied to manipulate the plant growth, development and metabolism in recent years. This study aimed to find out the effect of different light qualities on the production of anthocyanins and proanthocyanidins. The results showed RL (red light), BL (blue light), RBL (red light: blue light = 1:1) induced the strawberry fruit coloration earlier by increasing the content of total anthocyanins as a result of high expression of related genes, which was also concluded from a⁎, C⁎, h° values in 'Tokun' at 28 DAF, and RBL significantly promoted anthocyanin and proanthocyanidin biosynthesis in these two strawberry genotypes during fruit development. Simultaneously, the contents of anthocyanins and proanthocyanidins in 'Toyonaka' were also remarkably upregulated by BL and RL, respectively, indicating different strawberry genotypes to some extent probably had a distinct response to light quality. Hence, genotype factor should be taken into consideration when supplement of light quality was used as practical application in strawberry cultivation. Taken together, this study provided an insight into a further understanding of roles of light quality in the color formation for strawberry and a potential means to increase the health-related values of strawberry through altering the anthocyanin and proanthocyanidin contents of the fruit.
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Affiliation(s)
- Yunting Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Wenjie Hu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaorui Peng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Bo Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China.
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Foster TM, Aranzana MJ. Attention sports fans! The far-reaching contributions of bud sport mutants to horticulture and plant biology. HORTICULTURE RESEARCH 2018; 5:44. [PMID: 30038785 PMCID: PMC6046048 DOI: 10.1038/s41438-018-0062-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 06/06/2018] [Indexed: 05/08/2023]
Abstract
A bud sport is a lateral shoot, inflorescence or single flower/fruit with a visibly different phenotype from the rest of the plant. The new phenotype is often caused by a stable somatic mutation in a single cell that is passed on to its clonal descendants and eventually populates part or all of a meristem. In many cases, a bud sport can be vegetatively propagated, thereby preserving the novel phenotype without sexual reproduction. Bud sports provide new characteristics while retaining the desirable qualities of the parent plant, which is why many bud sports have been developed into popular cultivars. We present an overview of the history of bud sports, the causes and methods of detecting somaclonal variation, and the types of mutant phenotypes that have arisen spontaneously. We focus on examples where the molecular or cytological changes causing the phenotype have been identified. Analysis of these sports has provided valuable insight into developmental processes, gene function and regulation, and in some cases has revealed new information about layer-specific roles of some genes. Examination of the molecular changes causing a phenotype and in some cases reversion back to the original state has contributed to our understanding of the mechanisms that drive genomic evolution.
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Affiliation(s)
- Toshi M. Foster
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North, 4474 New Zealand
| | - Maria José Aranzana
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
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44
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Laucou V, Launay A, Bacilieri R, Lacombe T, Adam-Blondon AF, Bérard A, Chauveau A, de Andrés MT, Hausmann L, Ibáñez J, Le Paslier MC, Maghradze D, Martinez-Zapater JM, Maul E, Ponnaiah M, Töpfer R, Péros JP, Boursiquot JM. Extended diversity analysis of cultivated grapevine Vitis vinifera with 10K genome-wide SNPs. PLoS One 2018; 13:e0192540. [PMID: 29420602 PMCID: PMC5805323 DOI: 10.1371/journal.pone.0192540] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 01/25/2018] [Indexed: 12/18/2022] Open
Abstract
Grapevine is a very important crop species that is mainly cultivated worldwide for fruits, wine and juice. Identification of the genetic bases of performance traits through association mapping studies requires a precise knowledge of the available diversity and how this diversity is structured and varies across the whole genome. An 18k SNP genotyping array was evaluated on a panel of Vitis vinifera cultivars and we obtained a data set with no missing values for a total of 10207 SNPs and 783 different genotypes. The average inter-SNP spacing was ~47 kbp, the mean minor allele frequency (MAF) was 0.23 and the genetic diversity in the sample was high (He = 0.32). Fourteen SNPs, chosen from those with the highest MAF values, were sufficient to identify each genotype in the sample. Parentage analysis revealed 118 full parentages and 490 parent-offspring duos, thus confirming the close pedigree relationships within the cultivated grapevine. Structure analyses also confirmed the main divisions due to an eastern-western gradient and human usage (table vs. wine). Using a multivariate approach, we refined the structure and identified a total of eight clusters. Both the genetic diversity (He, 0.26-0.32) and linkage disequilibrium (LD, 28.8-58.2 kbp) varied between clusters. Despite the short span LD, we also identified some non-recombining haplotype blocks that may complicate association mapping. Finally, we performed a genome-wide association study that confirmed previous works and also identified new regions for important performance traits such as acidity. Taken together, all the results contribute to a better knowledge of the genetics of the cultivated grapevine.
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Affiliation(s)
- Valérie Laucou
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Amandine Launay
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Roberto Bacilieri
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Thierry Lacombe
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.,INRA Unité Expérimentale de Vassal, Centre de Ressources Biologiques de la Vigne, Marseillan-plage, France
| | | | - Aurélie Bérard
- EPGV, Univ Paris-Saclay, CEA, IG-CNG, INRA, Evry, France
| | | | | | - Ludger Hausmann
- JKI, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Javier Ibáñez
- ICVV, CSIC, Universidad de La Rioja, Gobierno de la Rioja, Logroño, Spain
| | | | | | | | - Erika Maul
- JKI, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Maharajah Ponnaiah
- EPGV, Univ Paris-Saclay, CEA, IG-CNG, INRA, Evry, France.,LBD, Univ UPMC, CNRS, INSERM, Paris, France
| | - Reinhard Töpfer
- JKI, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Jean-Pierre Péros
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Jean-Michel Boursiquot
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.,INRA Unité Expérimentale de Vassal, Centre de Ressources Biologiques de la Vigne, Marseillan-plage, France
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45
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Caramanico L, Rustioni L, De Lorenzis G. Iron deficiency stimulates anthocyanin accumulation in grapevine apical leaves. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 119:286-293. [PMID: 28926799 DOI: 10.1016/j.plaphy.2017.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/07/2017] [Accepted: 09/07/2017] [Indexed: 06/07/2023]
Abstract
Iron chlorosis is a diffuse disorder affecting Mediterranean vineyards. Beside the commonly described symptom of chlorophyll decrease, an apex reddening was recently observed. Secondary metabolites, such as anthocyanins, are often synthetized to cope with stresses in plants. The present work aimed to evaluate grapevine responses to iron deficiency, in terms of anthocyanin metabolism (reflectance spectrum, total anthocyanin content, HPLC profile and gene expression) in apical leaves of Cabernet sauvignon and Sangiovese grown in hydroponic conditions. Iron supply interruption produced after one month an increasing of anthocyanin content associated to a more stable profile in both cultivars. In Cabernet sauvignon, the higher red pigment accumulation was associated to a lower intensity of chlorotic symptoms, while in Sangiovese, despite the activation of the metabolism, the lower anthocyanin accumulation was associated to a stronger decrease in chlorophyll concentration. Gene expression data showed a significant increase of anthocyanin biosynthesis. The effects on the expression of structural and transcription factor genes of phenylpropanoid pathway were cultivar dependent. F3H, F3'H, F3'5'H and LDOX genes, in Cabernet sauvignon, and AOMT1 and AOMT genes, in Sangiovese, were positively affected by the treatment in response to iron deficiency. All data support the hypothesis of an anthocyanin biosynthesis stimulation rather than a decreased degradation of them due to iron chlorosis.
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Affiliation(s)
- Leila Caramanico
- DISAA - Dipartimento di Scienze Agrarie e Ambientali, Università Degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
| | - Laura Rustioni
- DISAA - Dipartimento di Scienze Agrarie e Ambientali, Università Degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy.
| | - Gabriella De Lorenzis
- DISAA - Dipartimento di Scienze Agrarie e Ambientali, Università Degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
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Matus JT, Cavallini E, Loyola R, Höll J, Finezzo L, Dal Santo S, Vialet S, Commisso M, Roman F, Schubert A, Alcalde JA, Bogs J, Ageorges A, Tornielli GB, Arce-Johnson P. A group of grapevine MYBA transcription factors located in chromosome 14 control anthocyanin synthesis in vegetative organs with different specificities compared with the berry color locus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:220-236. [PMID: 28370629 DOI: 10.1111/tpj.13558] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/20/2017] [Accepted: 03/24/2017] [Indexed: 05/19/2023]
Abstract
Grapevine organs accumulate anthocyanins in a cultivar-specific and environmentally induced manner. The MYBA1-A2 genes within the berry color locus in chromosome 2 represent the major genetic determinants of fruit color. The simultaneous occurrence of transposon insertions and point mutations in these genes is responsible for most white-skinned phenotypes; however, the red pigmentation found in vegetative organs suggests the presence of additional regulators. This work describes a genomic region of chromosome 14 containing three closely related R2R3-MYB genes, named MYBA5, MYBA6 and MYBA7. Ectopic expression of the latter two genes in grapevine hairy roots promoted anthocyanin accumulation without affecting other phenylpropanoids. Transcriptomic profiling of hairy roots expressing MYBA1, MYBA6 and MYBA7 showed that these regulators share the activation of late biosynthetic and modification/transport-related genes, but differ in the activation of the FLAVONOID-3'5'-HYDROXYLASE (F3'5'H) family. An alternatively spliced MYBA6 variant was incapable of activating anthocyanin synthesis, however, because of the lack of an MYC1 interaction domain. MYBA1, MYBA6.1 and MYBA7 activated the promoters of UDP-GLUCOSE:FLAVONOID 3-O-GLUCOSYLTRANSFERASE (UFGT) and ANTHOCYANIN 3-O-GLUCOSIDE-6″-O-ACYLTRANSFERASE (3AT), but only MYBA1 induced F3'5'H in concordance with the low proportion of tri-hydroxylated anthocyanins found in MYBA6-A7 hairy roots. This putative new color locus is related to the red/cyanidic pigmentation of vegetative organs in black- and white-skinned cultivars, and forms part of the UV-B radiation response pathway orchestrated by ELONGATED HYPOCOTYL 5 (HY5). These results demonstrate the involvement of additional anthocyanin regulators in grapevine and suggest an evolutionary divergence between the two grape color loci for controlling additional targets of the flavonoid pathway.
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Affiliation(s)
- José Tomás Matus
- Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Erika Cavallini
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Rodrigo Loyola
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Fruticultura y Enología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Janine Höll
- Centre for Organismal Studies Heidelberg (COS Heidelberg), Im Neuenheimer Feld 360, Heidelberg, 69120, Germany
| | - Laura Finezzo
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Silvia Dal Santo
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Sandrine Vialet
- INRA, UMR1083 SPO, 2 place Viala, Montpellier, F-34060, France
| | - Mauro Commisso
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Federica Roman
- Department of Agricultural, Forestry and Food Sciences, University of Turin, Largo Braccini 2, Grugliasco, 10095, Italy
| | - Andrea Schubert
- Department of Agricultural, Forestry and Food Sciences, University of Turin, Largo Braccini 2, Grugliasco, 10095, Italy
| | - José Antonio Alcalde
- Departamento de Fruticultura y Enología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jochen Bogs
- Centre for Organismal Studies Heidelberg (COS Heidelberg), Im Neuenheimer Feld 360, Heidelberg, 69120, Germany
- Dienstleistungszentrum Ländlicher Raum (DLR) Rheinpfalz, Breitenweg 71, Viticulture and Enology group, Neustadt/W, D-67435, Germany
- Fachhochschule Bingen, Berlinstr. 109, Bingen am Rhein, D-55411, Germany
| | - Agnès Ageorges
- INRA, UMR1083 SPO, 2 place Viala, Montpellier, F-34060, France
| | | | - Patricio Arce-Johnson
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
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47
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Aneece IP, Epstein H, Lerdau M. Correlating species and spectral diversities using hyperspectral remote sensing in early-successional fields. Ecol Evol 2017; 7:3475-3488. [PMID: 28515883 PMCID: PMC5433985 DOI: 10.1002/ece3.2876] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 01/29/2017] [Accepted: 02/07/2017] [Indexed: 01/19/2023] Open
Abstract
Advances in remote sensing technology can help estimate biodiversity at large spatial extents. To assess whether we could use hyperspectral visible near‐infrared (VNIR) spectra to estimate species diversity, we examined the correlations between species diversity and spectral diversity in early‐successional abandoned agricultural fields in the Ridge and Valley ecoregion of north‐central Virginia at the Blandy Experimental Farm. We established plant community plots and collected vegetation surveys and ground‐level hyperspectral data from 350 to 1,025 nm wavelengths. We related spectral diversity (standard deviations across spectra) with species diversity (Shannon–Weiner index) and evaluated whether these correlations differed among spectral regions throughout the visible and near‐infrared wavelength regions, and across different spectral transformation techniques. We found positive correlations in the visible regions using band depth data, positive correlations in the near‐infrared region using first derivatives of spectra, and weak to no correlations in the red‐edge region using either of the two spectral transformation techniques. To investigate the role of pigment variability in these correlations, we estimated chlorophyll, carotenoid, and anthocyanin concentrations of five dominant species in the plots using spectral vegetation indices. Although interspecific variability in pigment levels exceeded intraspecific variability, chlorophyll was more varied within species than carotenoids and anthocyanins, contributing to the lack of correlation between species diversity and spectral diversity in the red‐edge region. Interspecific differences in pigment levels, however, made it possible to differentiate these species remotely, contributing to the species‐spectral diversity correlations. VNIR spectra can be used to estimate species diversity, but the relationships depend on the spectral region examined and the spectral transformation technique used.
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Affiliation(s)
- Itiya P Aneece
- Department of Environmental Sciences University of Virginia Charlottesville VA USA
| | - Howard Epstein
- Department of Environmental Sciences University of Virginia Charlottesville VA USA
| | - Manuel Lerdau
- Department of Environmental Sciences University of Virginia Charlottesville VA USA
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48
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Ferreira V, Fernandes F, Carrasco D, Hernandez MG, Pinto-Carnide O, Arroyo-García R, Andrade P, Valentão P, Falco V, Castro I. Spontaneous variation regarding grape berry skin color: A comprehensive study of berry development by means of biochemical and molecular markers. Food Res Int 2017; 97:149-161. [PMID: 28578035 DOI: 10.1016/j.foodres.2017.03.050] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/27/2017] [Accepted: 03/30/2017] [Indexed: 01/01/2023]
Abstract
Understanding grape berry development and the metabolism of different classes of compounds responsible for traits like berry's color is imperative to control and improve quality aspects of grapes. A colorimetric, biochemical and molecular characterization allowed the comprehensive description of the pigment-related characteristics of nine berry skin color somatic variants, belonging to four different varieties. Although the observed berry skin color variability was not fully explained by MybA locus, the phenolic profiles allowed inferring about specific interferences among the biosynthetic pathways. Data were consistent concerning that grapes showing cyanidin-3-O-glucoside as the major anthocyanin and flavonols with two substituent groups in the lateral B-ring are generally originated by a white ancestor. After retro-mutation, these grapes seem to keep the dysfunction on flavonoid hydroxylases enzymes, which negatively affect the synthesis of both flavonols and anthocyanins with three substituent groups in the lateral B-ring. Overall, the obtained results indicate that the color differences observed between somatic variants are not solely the result of the total amount of compounds synthesized, but rather reflect a different dynamics of the phenolic pathway among the different color variants of the same variety. CHEMICAL COMPOUNDS Gallic acid (PubChem CID: 370); Caftaric acid (PubChem CID: 6,440,397); Catechin (PubChem CID: 73,160); Epigallocatechin gallate (PubChem CID: 65,064); Quercetin-3-O-galactoside (PubChem CID: 5,281,643); Quercetin-3-O-glucoside (PubChem CID: 25,203,368); Malvidin-3-O-glucoside (PubChem CID: 443,652); Peonidin-3-O-p-coumaroylglucoside (PubChem CID: 44,256,849); Malvidin-3-O-p-coumaroylglucoside (PubChem CID: 44,256,988); Resveratrol-3-O-glucoside (PubChem CID: 25,579,167).
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Affiliation(s)
- Vanessa Ferreira
- Centro de Investigação e de Tecnologias Agro-Ambientais e Biológicas (CITAB), Universidade de Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal; Centro de Biotecnología y Genómica de Plantas (CBGP), Campus de Montegancedo, Autovía M40, km38, 28223, Pozuelo de Alarcón, Madrid, Spain.
| | - Fátima Fernandes
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Departamento de Química, Faculdade de Farmácia, Universidade do Porto, R. Jorge Viterbo Ferreira, no 228, 4050-313 Porto, Portugal
| | - David Carrasco
- Centro de Biotecnología y Genómica de Plantas (CBGP), Campus de Montegancedo, Autovía M40, km38, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Marivel Gonzalez Hernandez
- Ciencias Química y Sensorial Enológica, Instituto de Ciencias de la Vid y el Vino, Universidad de La Rioja, Complejo Científico Tecnológico - Madre de Dios 51, 26006 Logroño, Spain
| | - Olinda Pinto-Carnide
- Centro de Investigação e de Tecnologias Agro-Ambientais e Biológicas (CITAB), Universidade de Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal
| | - Rosa Arroyo-García
- Centro de Biotecnología y Genómica de Plantas (CBGP), Campus de Montegancedo, Autovía M40, km38, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Paula Andrade
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Departamento de Química, Faculdade de Farmácia, Universidade do Porto, R. Jorge Viterbo Ferreira, no 228, 4050-313 Porto, Portugal
| | - Patrícia Valentão
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Departamento de Química, Faculdade de Farmácia, Universidade do Porto, R. Jorge Viterbo Ferreira, no 228, 4050-313 Porto, Portugal
| | - Virgílio Falco
- Centro de Química de Vila Real (CQ-VR), Universidade de Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal
| | - Isaura Castro
- Centro de Investigação e de Tecnologias Agro-Ambientais e Biológicas (CITAB), Universidade de Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal
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49
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Pinasseau L, Vallverdú-Queralt A, Verbaere A, Roques M, Meudec E, Le Cunff L, Péros JP, Ageorges A, Sommerer N, Boulet JC, Terrier N, Cheynier V. Cultivar Diversity of Grape Skin Polyphenol Composition and Changes in Response to Drought Investigated by LC-MS Based Metabolomics. FRONTIERS IN PLANT SCIENCE 2017; 8:1826. [PMID: 29163566 PMCID: PMC5663694 DOI: 10.3389/fpls.2017.01826] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 10/10/2017] [Indexed: 05/21/2023]
Abstract
Phenolic compounds represent a large family of plant secondary metabolites, essential for the quality of grape and wine and playing a major role in plant defense against biotic and abiotic stresses. Phenolic composition is genetically driven and greatly affected by environmental factors, including water stress. A major challenge for breeding of grapevine cultivars adapted to climate change and with high potential for wine-making is to dissect the complex plant metabolic response involved in adaptation mechanisms. A targeted metabolomics approach based on ultra high-performance liquid chromatography coupled to triple quadrupole mass spectrometry (UHPLC-QqQ-MS) analysis in the Multiple Reaction Monitoring (MRM) mode has been developed for high throughput profiling of the phenolic composition of grape skins. This method enables rapid, selective, and sensitive quantification of 96 phenolic compounds (anthocyanins, phenolic acids, stilbenoids, flavonols, dihydroflavonols, flavan-3-ol monomers, and oligomers…), and of the constitutive units of proanthocyanidins (i.e., condensed tannins), giving access to detailed polyphenol composition. It was applied on the skins of mature grape berries from a core-collection of 279 Vitis vinifera cultivars grown with or without watering to assess the genetic variation for polyphenol composition and its modulation by irrigation, in two successive vintages (2014-2015). Distribution of berry weights and δ13C values showed that non irrigated vines were subjected to a marked water stress in 2014 and to a very limited one in 2015. Metabolomics analysis of the polyphenol composition and chemometrics analysis of this data demonstrated an influence of water stress on the biosynthesis of different polyphenol classes and cultivar differences in metabolic response to water deficit. Correlation networks gave insight on the relationships between the different polyphenol metabolites and related biosynthetic pathways. They also established patterns of polyphenol response to drought, with different molecular families affected either positively or negatively in the different cultivars, with potential impact on grape and wine quality.
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Affiliation(s)
- Lucie Pinasseau
- Plateforme Polyphénols SPO, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Anna Vallverdú-Queralt
- Plateforme Polyphénols SPO, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Arnaud Verbaere
- Plateforme Polyphénols SPO, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Maryline Roques
- Plateforme Polyphénols SPO, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
- SPO, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
- IFV Pôle national matériel végétal, UMT Génovigne, Montpellier, France
| | - Emmanuelle Meudec
- Plateforme Polyphénols SPO, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Loïc Le Cunff
- IFV Pôle national matériel végétal, UMT Génovigne, Montpellier, France
| | - Jean-Pierre Péros
- AGAP, INRA, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Agnès Ageorges
- SPO, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Nicolas Sommerer
- Plateforme Polyphénols SPO, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Jean-Claude Boulet
- Plateforme Polyphénols SPO, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Nancy Terrier
- SPO, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Véronique Cheynier
- Plateforme Polyphénols SPO, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
- SPO, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
- *Correspondence: Véronique Cheynier
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50
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Migicovsky Z, Sawler J, Gardner KM, Aradhya MK, Prins BH, Schwaninger HR, Bustamante CD, Buckler ES, Zhong GY, Brown PJ, Myles S. Patterns of genomic and phenomic diversity in wine and table grapes. HORTICULTURE RESEARCH 2017; 4:17035. [PMID: 28791127 PMCID: PMC5539807 DOI: 10.1038/hortres.2017.35] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 06/16/2017] [Indexed: 05/18/2023]
Abstract
Grapes are one of the most economically and culturally important crops worldwide, and they have been bred for both winemaking and fresh consumption. Here we evaluate patterns of diversity across 33 phenotypes collected over a 17-year period from 580 table and wine grape accessions that belong to one of the world's largest grape gene banks, the grape germplasm collection of the United States Department of Agriculture. We find that phenological events throughout the growing season are correlated, and quantify the marked difference in size between table and wine grapes. By pairing publicly available historical phenotype data with genome-wide polymorphism data, we identify large effect loci controlling traits that have been targeted during domestication and breeding, including hermaphroditism, lighter skin pigmentation and muscat aroma. Breeding for larger berries in table grapes was traditionally concentrated in geographic regions where Islam predominates and alcohol was prohibited, whereas wine grapes retained the ancestral smaller size that is more desirable for winemaking in predominantly Christian regions. We uncover a novel locus with a suggestive association with berry size that harbors a signature of positive selection for larger berries. Our results suggest that religious rules concerning alcohol consumption have had a marked impact on patterns of phenomic and genomic diversity in grapes.
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Affiliation(s)
- Zoë Migicovsky
- Department of Plant, Food and Environmental
Sciences, Faculty of Agriculture, Dalhousie University, Truro,
NS
B2N 5E3, Canada
| | - Jason Sawler
- Department of Plant, Food and Environmental
Sciences, Faculty of Agriculture, Dalhousie University, Truro,
NS
B2N 5E3, Canada
- Anandia Labs, Vancouver,
BC
V6T 1Z4, Canada
| | - Kyle M Gardner
- Department of Plant, Food and Environmental
Sciences, Faculty of Agriculture, Dalhousie University, Truro,
NS
B2N 5E3, Canada
- Agriculture and Agri-Food Canada, Fredericton
Research and Development Centre, Fredericton, NB,
Canada
E3B 4Z7
| | - Mallikarjuna K Aradhya
- National Clonal Germplasm Repository, United
States Department of Agriculture-Agricultural Research Service, University of
California, Davis, CA
95616, USA
| | - Bernard H Prins
- National Clonal Germplasm Repository, United
States Department of Agriculture-Agricultural Research Service, University of
California, Davis, CA
95616, USA
| | - Heidi R Schwaninger
- United States Department of Agriculture,
Agricultural Research Service, Grape Genetics Research Unit, New York State Agricultural
Experiment Station, Cornell University, Geneva, NY
14456, USA
| | | | - Edward S Buckler
- Department of Plant Breeding and Genetics,
Cornell University, Ithaca, NY
14853, USA
| | - Gan-Yuan Zhong
- United States Department of Agriculture,
Agricultural Research Service, Grape Genetics Research Unit, New York State Agricultural
Experiment Station, Cornell University, Geneva, NY
14456, USA
- United States Department of Agriculture,
Agricultural Research Service, Plant Genetic Resources Unit, New York State Agricultural
Experiment Station, Cornell University, Geneva, NY
14456, USA
| | - Patrick J Brown
- Department of Crop Science, University of
Illinois, Urbana, IL
61801, USA
| | - Sean Myles
- Department of Plant, Food and Environmental
Sciences, Faculty of Agriculture, Dalhousie University, Truro,
NS
B2N 5E3, Canada
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