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Aversano R, Iovene M, Esposito S, L'Abbate A, Villano C, Di Serio E, Cardone MF, Bergamini C, Cigliano RA, D'Amelia V, Frusciante L, Carputo D. Distinct structural variants and repeat landscape shape the genomes of the ancient grapes Aglianico and Falanghina. BMC PLANT BIOLOGY 2024; 24:88. [PMID: 38317087 PMCID: PMC10845522 DOI: 10.1186/s12870-024-04778-2] [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: 08/10/2023] [Accepted: 01/29/2024] [Indexed: 02/07/2024]
Abstract
Mounting evidence recognizes structural variations (SVs) and repetitive DNA sequences as crucial players in shaping the existing grape phenotypic diversity at intra- and inter-species levels. To deepen our understanding on the abundance, diversity, and distribution of SVs and repetitive DNAs, including transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), we re-sequenced the genomes of the ancient grapes Aglianico and Falanghina. The analysis of large copy number variants (CNVs) detected candidate polymorphic genes that are involved in the enological features of these varieties. In a comparative analysis of Aglianico and Falanghina sequences with 21 publicly available genomes of cultivated grapes, we provided a genome-wide annotation of grape TEs at the lineage level. We disclosed that at least two main clusters of grape cultivars could be identified based on the TEs content. Multiple TEs families appeared either significantly enriched or depleted. In addition, in silico and cytological analyses provided evidence for a diverse chromosomal distribution of several satellite repeats between Aglianico, Falanghina, and other grapes. Overall, our data further improved our understanding of the intricate grape diversity held by two Italian traditional varieties, unveiling a pool of unique candidate genes never so far exploited in breeding for improved fruit quality.
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Affiliation(s)
- Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.
| | - Marina Iovene
- Institute of Biosciences and Bioresources, National Research Council of Italy (CNR-IBBR), Portici, Italy.
| | - Salvatore Esposito
- Institute of Biosciences and Bioresources, National Research Council of Italy (CNR-IBBR), Portici, Italy
- Research Centre for Cereal and Industrial Crops, Council for Agricultural Research and Economics (CREA-CI), Foggia, Italy
| | - Alberto L'Abbate
- Institute of Biomembranes, Bioenergetics, and Molecular Biotechnologies, National Research Council (IBIOM-CNR), Bari, Italy
| | - Clizia Villano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Ermanno Di Serio
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Maria Francesca Cardone
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Turi, Italy
| | - Carlo Bergamini
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Turi, Italy
| | | | - Vincenzo D'Amelia
- Institute of Biosciences and Bioresources, National Research Council of Italy (CNR-IBBR), Portici, Italy
| | - Luigi Frusciante
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Domenico Carputo
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
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2
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Wang X, Tu M, Wang Y, Zhang Y, Yin W, Fang J, Gao M, Li Z, Zhan W, Fang Y, Song J, Xi Z, Wang X. Telomere-to-telomere and gap-free genome assembly of a susceptible grapevine species (Thompson Seedless) to facilitate grape functional genomics. HORTICULTURE RESEARCH 2024; 11:uhad260. [PMID: 38288254 PMCID: PMC10822838 DOI: 10.1093/hr/uhad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 11/26/2023] [Indexed: 01/31/2024]
Abstract
Grapes are globally recognized as economically significant fruit trees. Among grape varieties, Thompson Seedless holds paramount influence for fresh consumption and for extensive applications in winemaking, drying, and juicing. This variety is one of the most efficient genotypes for grape genetic modification. However, the lack of a high-quality genome has impeded effective breeding efforts. Here, we present the high-quality reference genome of Thompson Seedless with all 19 chromosomes represented as 19 contiguous sequences (N50 = 27.1 Mb) with zero gaps and prediction of all telomeres and centromeres. Compared with the previous assembly (TSv1 version), the new assembly incorporates an additional 31.5 Mb of high-quality sequenced data with annotation of a total of 30 397 protein-coding genes. We also performed a meticulous analysis to identify nucleotide-binding leucine-rich repeat genes (NLRs) in Thompson Seedless and two wild grape varieties renowned for their disease resistance. Our analysis revealed a significant reduction in the number of two types of NLRs, TIR-NB-LRR (TNL) and CC-NB-LRR (CNL), in Thompson Seedless, which may have led to its sensitivity to many fungal diseases, such as powdery mildew, and an increase in the number of a third type, RPW8 (resistance to powdery mildew 8)-NB-LRR (RNL). Subsequently, transcriptome analysis showed significant enrichment of NLRs during powdery mildew infection, emphasizing the pivotal role of these elements in grapevine's defense against powdery mildew. The successful assembly of a high-quality Thompson Seedless reference genome significantly contributes to grape genomics research, providing insight into the importance of seedlessness, disease resistance, and color traits, and these data can be used to facilitate grape molecular breeding efforts.
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Affiliation(s)
- Xianhang Wang
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingxing Tu
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ya Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yali Zhang
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wuchen Yin
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jinghao Fang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Min Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhi Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wei Zhan
- Xi'an Haorui Genomics Technology Co., Ltd, Xi'an 710116, China
| | - Yulin Fang
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junyang Song
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhumei Xi
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiping Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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3
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Sichel V, Sarah G, Girollet N, Laucou V, Roux C, Roques M, Mournet P, Cunff LL, Bert P, This P, Lacombe T. Chimeras in Merlot grapevine revealed by phased assembly. BMC Genomics 2023; 24:396. [PMID: 37452318 PMCID: PMC10347889 DOI: 10.1186/s12864-023-09453-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 06/09/2023] [Indexed: 07/18/2023] Open
Abstract
Chimerism is the phenomenon when several genotypes coexist in a single individual. Used to understand plant ontogenesis they also have been valorised through new cultivar breeding. Viticulture has been taking economic advantage out of chimeras when the variant induced an important modification of wine type such as berry skin colour. Crucial agronomic characters may also be impacted by chimeras that aren't identified yet. Periclinal chimera where the variant has entirely colonised a cell layer is the most stable and can be propagated through cuttings. In grapevine, leaves are derived from both meristem layers, L1 and L2. However, lateral roots are formed from the L2 cell layer only. Thus, comparing DNA sequences of roots and leaves allows chimera detection. In this study we used new generation Hifi long reads sequencing, recent bioinformatics tools and trio-binning with parental sequences to detect periclinal chimeras on 'Merlot' grapevine cultivar. Sequencing of cv. 'Magdeleine Noire des Charentes' and 'Cabernet Franc', the parents of cv. 'Merlot', allowed haplotype resolved assembly. Pseudomolecules were built with a total of 33 to 47 contigs and in few occasions a unique contig for one chromosome. This high resolution allowed haplotype comparison. Annotation was transferred from PN40024 VCost.v3 to all pseudomolecules. After strong selection of variants, 51 and 53 'Merlot' specific periclinal chimeras were found on the Merlot-haplotype-CF and Merlot-haplotype-MG respectively, 9 and 7 been located in a coding region. A subset of positions was analysed using Molecular Inversion Probes (MIPseq) and 69% were unambiguously validated, 25% are doubtful because of technological noise or weak depth and 6% invalidated. These results open new perspectives on chimera detection as an important resource to improve cultivars through clonal selection or breeding.
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Affiliation(s)
- V. Sichel
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398 France
| | - G. Sarah
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398 France
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier, F-34398 France
| | - N. Girollet
- EGFV, Université de Bordeaux, Bordeaux-Sciences Agro, INRAe, ISVV, 210 Chemin de Leysotte, F-33882 Villenave d’Ornon, France
| | - V. Laucou
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398 France
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier, F-34398 France
| | - C. Roux
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398 France
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier, F-34398 France
| | - M. Roques
- Institut Français de la Vigne et du Vin, Montpellier, F-34398 France
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier, F-34398 France
| | - P. Mournet
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398 France
- UMR AGAP Institut, CIRAD, Montpellier, F-34398 France
| | - L. Le Cunff
- Institut Français de la Vigne et du Vin, Montpellier, F-34398 France
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier, F-34398 France
| | - P.F. Bert
- EGFV, Université de Bordeaux, Bordeaux-Sciences Agro, INRAe, ISVV, 210 Chemin de Leysotte, F-33882 Villenave d’Ornon, France
| | - P. 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
| | - T. Lacombe
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398 France
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier, F-34398 France
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4
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Cheng G, Wu D, Guo R, Li H, Wei R, Zhang J, Wei Z, Meng X, Yu H, Xie L, Lin L, Yao N, Zhou S. Chromosome-scale genomics, metabolomics, and transcriptomics provide insight into the synthesis and regulation of phenols in Vitis adenoclada grapes. FRONTIERS IN PLANT SCIENCE 2023; 14:1124046. [PMID: 36760645 PMCID: PMC9907855 DOI: 10.3389/fpls.2023.1124046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Vitis adenoclada is a wild grape unique to China. It exhibits well resistance to heat, humidity, fungal disease, drought, and soil infertility. Here, we report the high-quality, chromosome-level genome assembly of GH6 (V. adenoclada). The 498.27 Mb genome contained 221.78 Mb of transposable elements, 28,660 protein-coding genes, and 481.44 Mb of sequences associated with 19 chromosomes. GH6 shares a common ancestor with PN40024 (Vitis vinifera) from approximately 4.26-9.01 million years ago, whose divergence occurred later than Vitis rotundifolia and Vitis riparia. Widely-targeted metabolome and transcriptome analysis revealed that the profiles and metabolism of phenolic compounds in V. adenoclada varieties significantly were differed from other grape varieties. Specifically, V. adenoclada varieties were rich in phenolic acids and flavonols, whereas the flavan-3-ol and anthocyanin content was lower compared with other varieties that have V. vinifera consanguinity in this study. In addition, ferulic acid and stilbenes content were associated with higher expressions of COMT and STSs in V. adenoclada varieties. Furthermore, MYB2, MYB73-1, and MYB73-2 were presumably responsible for the high expression level of COMT in V. adenoclada berries. MYB12 (MYBF1) was positively correlated with PAL, CHS, FLS and UFGT.Meanwhile, MYB4 and MYBC2-L1 may inhibit the synthesis of flavan-3-ols and anthocyanins in two V. adenoclada varieties (YN2 and GH6). The publication of the V. adenoclada grape genome provides a molecular foundation for further revealing its flavor and quality characteristics, is also important for identifying favorable genes of the East Asian species for future breeding.
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Affiliation(s)
- Guo Cheng
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Daidong Wu
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Rongrong Guo
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Hongyan Li
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Rongfu Wei
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Jin Zhang
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Zhiyong Wei
- Bureau of Agriculture and Rural Affairs of Luocheng Mulao Autonomous County, Hechi, China
| | - Xian Meng
- Bureau of Agriculture and Rural Affairs of Luocheng Mulao Autonomous County, Hechi, China
| | - Huan Yu
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Linjun Xie
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Ling Lin
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Ning Yao
- Guangxi Luocheng Maoputao Experimental Station, Hechi, China
| | - Sihong Zhou
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
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5
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Minio A, Cochetel N, Vondras AM, Massonnet M, Cantu D. Assembly of complete diploid-phased chromosomes from draft genome sequences. G3 GENES|GENOMES|GENETICS 2022; 12:6605224. [PMID: 35686922 PMCID: PMC9339290 DOI: 10.1093/g3journal/jkac143] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/30/2022] [Indexed: 01/27/2023]
Abstract
De novo genome assembly is essential for genomic research. High-quality genomes assembled into phased pseudomolecules are challenging to produce and often contain assembly errors because of repeats, heterozygosity, or the chosen assembly strategy. Although algorithms that produce partially phased assemblies exist, haploid draft assemblies that may lack biological information remain favored because they are easier to generate and use. We developed HaploSync, a suite of tools that produces fully phased, chromosome-scale diploid genome assemblies, and performs extensive quality control to limit assembly artifacts. HaploSync scaffolds sequences from a draft diploid assembly into phased pseudomolecules guided by a genetic map and/or the genome of a closely related species. HaploSync generates a report that visualizes the relationships between current and legacy sequences, for both haplotypes, and displays their gene and marker content. This quality control helps the user identify misassemblies and guides Haplosync’s correction of scaffolding errors. Finally, HaploSync fills assembly gaps with unplaced sequences and resolves collapsed homozygous regions. In a series of plant, fungal, and animal kingdom case studies, we demonstrate that HaploSync efficiently increases the assembly contiguity of phased chromosomes, improves completeness by filling gaps, corrects scaffolding, and correctly phases highly heterozygous, complex regions.
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Affiliation(s)
- Andrea Minio
- Department of Viticulture and Enology, University of California Davis , Davis, CA 95616, USA
| | - Noé Cochetel
- Department of Viticulture and Enology, University of California Davis , Davis, CA 95616, USA
| | - Amanda M Vondras
- Department of Viticulture and Enology, University of California Davis , Davis, CA 95616, USA
| | - Mélanie Massonnet
- 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
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Amato A, Cardone MF, Ocarez N, Alagna F, Ruperti B, Fattorini C, Velasco R, Mejía N, Zenoni S, Bergamini C. VviAGL11 self-regulates and targets hormone- and secondary metabolism-related genes during seed development. HORTICULTURE RESEARCH 2022; 9:uhac133. [PMID: 36061618 PMCID: PMC9433981 DOI: 10.1093/hr/uhac133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/04/2022] [Indexed: 06/15/2023]
Abstract
VviAGL11, the Arabidopsis SEEDSTICK homolog, has been proposed to have a causative role in grapevine stenospermocarpy. An association between a mutation in the coding sequence (CDS) and the seedless phenotype was reported, however, no working mechanisms have been demonstrated yet. We performed a deep investigation of the full VviAGL11 gene sequence in a collection of grapevine varieties belonging to several seedlessness classes that revealed three different promoter-CDS combinations. By investigating the expression of the three VviAGL11 alleles, and by evaluating their ability to activate the promoter region, we observed that VviAGL11 self-activates in a specific promoter-CDS combination manner. Furthermore, by transcriptomic analyses on ovule and developing seeds in seeded and seedless varieties and co-expression approaches, candidate VviAGL11 targets were identified and further validated through luciferase assay and in situ hybridization. We demonstrated that VviAGL11 Wild Type CDS activates Methyl jasmonate esterase and Indole-3-acetate beta-glucosyltransferase, both involved in hormone signaling and Isoflavone reductase, involved in secondary metabolism. The dominant-negative effect of the mutated CDS was also functionally ectopically validated in target induction. VviAGL11 was shown to co-localize with its targets in the outer seed coat integument, supporting its direct involvement in seed development, possibly by orchestrating the crosstalk among MeJA, auxin, and isoflavonoids synthesis. In conclusion, the VviAGL11 expression level depends on the promoter-CDS allelic combination, and this will likely affect its ability to activate important triggers of the seed coat development. The dominant-negative effect of the mutated VviAGL11 CDS on the target genes activation was molecularly validated. A new regulatory mechanism correlating VviAGL11 haplotype assortment and seedlessness class in grapevine is proposed.
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Affiliation(s)
- Alessandra Amato
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Maria Francesca Cardone
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA), 70010 Turi, Italy
| | - Nallatt Ocarez
- Instituto de Investigaciones Agropecuarias (INIA), Centro Regional de Investigación La Platina, Santiago RM 8831314, Chile
| | - Fiammetta Alagna
- Trisaia Research Centre, National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), 75026 Rotondella, Italy
| | - Benedetto Ruperti
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, 35020 Padova, Italy
| | - Chiara Fattorini
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Riccardo Velasco
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA), 70010 Turi, Italy
| | - Nilo Mejía
- Instituto de Investigaciones Agropecuarias (INIA), Centro Regional de Investigación La Platina, Santiago RM 8831314, Chile
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7
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Olivares F, Loyola R, Olmedo B, Miccono MDLÁ, Aguirre C, Vergara R, Riquelme D, Madrid G, Plantat P, Mora R, Espinoza D, Prieto H. CRISPR/Cas9 Targeted Editing of Genes Associated With Fungal Susceptibility in Vitis vinifera L. cv. Thompson Seedless Using Geminivirus-Derived Replicons. FRONTIERS IN PLANT SCIENCE 2021; 12:791030. [PMID: 35003180 PMCID: PMC8733719 DOI: 10.3389/fpls.2021.791030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/29/2021] [Indexed: 05/14/2023]
Abstract
The woody nature of grapevine (Vitis vinifera L.) has hindered the development of efficient gene editing strategies to improve this species. The lack of highly efficient gene transfer techniques, which, furthermore, are applied in multicellular explants such as somatic embryos, are additional technical handicaps to gene editing in the vine. The inclusion of geminivirus-based replicons in regular T-DNA vectors can enhance the expression of clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) elements, thus enabling the use of these multicellular explants as starting materials. In this study, we used Bean yellow dwarf virus (BeYDV)-derived replicon vectors to express the key components of CRISPR/Cas9 system in vivo and evaluate their editing capability in individuals derived from Agrobacterium-mediated gene transfer experiments of 'Thompson Seedless' somatic embryos. Preliminary assays using a BeYDV-derived vector for green fluorescent protein reporter gene expression demonstrated marker visualization in embryos for up to 33 days post-infiltration. A universal BeYDV-based vector (pGMV-U) was assembled to produce all CRISPR/Cas9 components with up to four independent guide RNA (gRNA) expression cassettes. With a focus on fungal tolerance, we used gRNA pairs to address considerably large deletions of putative grape susceptibility genes, including AUXIN INDUCED IN ROOT CULTURE 12 (VviAIR12), SUGARS WILL EVENTUALLY BE EXPORTED TRANSPORTER 4 (VviSWEET4), LESION INITIATION 2 (VviLIN2), and DIMERIZATION PARTNER-E2F-LIKE 1 (VviDEL1). The editing functionality of gRNA pairs in pGMV-U was evaluated by grapevine leaf agroinfiltration assays, thus enabling longer-term embryo transformations. These experiments allowed for the establishment of greenhouse individuals exhibiting a double-cut edited status for all targeted genes under different allele-editing conditions. After approximately 18 months, the edited grapevine plants were preliminary evaluated regarding its resistance to Erysiphe necator and Botrytis cinerea. Assays have shown that a transgene-free VviDEL1 double-cut edited line exhibits over 90% reduction in symptoms triggered by powdery mildew infection. These results point to the use of geminivirus-based replicons for gene editing in grapevine and other relevant fruit species.
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Affiliation(s)
- Felipe Olivares
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Rodrigo Loyola
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Blanca Olmedo
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - María de los Ángeles Miccono
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Carlos Aguirre
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Ricardo Vergara
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Danae Riquelme
- Phytopathology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Gabriela Madrid
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Philippe Plantat
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Roxana Mora
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Daniel Espinoza
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Humberto Prieto
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
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8
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Freitas S, Gazda MA, Rebelo MÂ, Muñoz-Pajares AJ, Vila-Viçosa C, Muñoz-Mérida A, Gonçalves LM, Azevedo-Silva D, Afonso S, Castro I, Castro PH, Sottomayor M, Beja-Pereira A, Tereso J, Ferrand N, Gonçalves E, Martins A, Carneiro M, Azevedo H. Pervasive hybridization with local wild relatives in Western European grapevine varieties. SCIENCE ADVANCES 2021; 7:eabi8584. [PMID: 34797710 PMCID: PMC8604406 DOI: 10.1126/sciadv.abi8584] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Grapevine (Vitis vinifera L.) diversity richness results from a complex domestication history over multiple historical periods. Here, we used whole-genome resequencing to elucidate different aspects of its recent evolutionary history. Our results support a model in which a central domestication event in grapevine was followed by postdomestication hybridization with local wild genotypes, leading to the presence of an introgression signature in modern wine varieties across Western Europe. The strongest signal was associated with a subset of Iberian grapevine varieties showing large introgression tracts. We targeted this study group for further analysis, demonstrating how regions under selection in wild populations from the Iberian Peninsula were preferentially passed on to the cultivated varieties by gene flow. Examination of underlying genes suggests that environmental adaptation played a fundamental role in both the evolution of wild genotypes and the outcome of hybridization with cultivated varieties, supporting a case of adaptive introgression in grapevine.
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Affiliation(s)
- Sara Freitas
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Małgorzata A. Gazda
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
| | - Miguel Â. Rebelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Antonio J. Muñoz-Pajares
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Campus Fuentenueva, 18071 Granada, Spain
| | - Carlos Vila-Viçosa
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- MHNC-UP, Museum of Natural History and Science of the University of Porto–PO Herbarium, University of Porto, Praça Gomes Teixeira, 4099-002 Porto, Portugal
| | - Antonio Muñoz-Mérida
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Luís M. Gonçalves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - David Azevedo-Silva
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Isaura Castro
- CITAB, Centre for the Research and Technology of Agro-Environmental and Biological Sciences, Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801 Vila Real, Portugal
| | - Pedro H. Castro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Mariana Sottomayor
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Albano Beja-Pereira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- DGAOT, Faculty of Sciences, Universidade do Porto, Rua Campo Alegre 687, 4169-007 Porto, Portugal
- Sustainable Agrifood Production Research Centre (GreenUPorto), Universidade do Porto, Rua da Agrária 747, 4485-646 Vairão, Portugal
| | - João Tereso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- MHNC-UP, Museum of Natural History and Science of the University of Porto–PO Herbarium, University of Porto, Praça Gomes Teixeira, 4099-002 Porto, Portugal
- Centre for Archaeology, UNIARQ, School of Arts and Humanities, University of Lisbon, 1600-214 Lisbon, Portugal
| | - Nuno Ferrand
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, 2006 Johannesburg, South Africa
| | - Elsa Gonçalves
- LEAF, Linking Landscape, Environment, Agriculture, and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
- Portuguese Association for Grapevine Diversity-PORVID, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Antero Martins
- LEAF, Linking Landscape, Environment, Agriculture, and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
- Portuguese Association for Grapevine Diversity-PORVID, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Herlander Azevedo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Corresponding author.
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9
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Li S, Geng X, Chen S, Liu K, Yu S, Wang X, Zhang C, Zhang J, Wen Y, Luo Q, Xu Y, Wang Y. The co-expression of genes involved in seed coat and endosperm development promotes seed abortion in grapevine. PLANTA 2021; 254:87. [PMID: 34585280 DOI: 10.1007/s00425-021-03728-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
The seed coat gene VviAGL11 coordinates with endosperm development genes FIS2, PHERESE1 and IKU2 and functions as the key regulator in seed development and abortion processes in grapevine. Seed development is essential for the reproduction of flowering plants. Seed abortion is a specific characteristic that produces seedless berries and is often observed in cultivated grapevines. Although seedlessness is an important trait for table and dried grapevine production, the mechanism of seed abortion remains poorly understood. This research aimed to analyze the co-expression of the seed coat development gene VviAGL11 and the endosperm development genes FERTILIZATION INDEPENDENT SEED2 (FIS2), PHERESE1 and HAIKU2 (IKU2) that regulate seedless fruit development in grapevine. The transcript levels of VviAGL11, FIS2, PHERESE1 and IKU2 all decreased during seed abortion in the seedless grape 'Thompson Seedless' plants, compared to those of the seeded grape 'Pinot Noir'. The transcript levels of the salicylic acid (SA)-dependent defense response genes EDS1, NPR1, NDR1 and SID2 were higher in 'Thompson Seedless' than 'Pinot Noir' during seed development. Also, WRKY3, WRKY6 and WRKY52, which participate in the SA pathway, were higher expressed in 'Thompson Seedless' than in 'Pinot Noir', indicating that SA-dependent defense responses may regulate seed abortion. The genes related to synthesis and metabolism of gibberellic acid (GA) and abscisic acid (ABA) also showed differential expression between 'Thompson Seedless' and 'Pinot Noir'. Exogenous applications of plant growth regulators (PGRs) to inflorescences of three stenospermocarpy grapevines before flowering showed that GA3 was critical prominently in seed development. Therefore, the co-expression of seed coat and endosperm development-related genes, SA pathway genes, and genes for the synthesis and metabolism of GA3 together enhance seed abortion in seedless grapes.
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Affiliation(s)
- Shasha Li
- College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Xiangyu Geng
- College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shuo Chen
- College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Keke Liu
- College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Saisai Yu
- College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Xiping Wang
- College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Chaohong Zhang
- College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Jianxia Zhang
- College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Yingqiang Wen
- College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Qiangwei Luo
- Research Institute of Xinjiang Grape, Melon and Fruit, Shanshan, 838200, Xinjiang, People's Republic of China
| | - Yan Xu
- College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China.
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China.
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China.
| | - Yuejin Wang
- College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China.
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China.
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China.
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10
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Seeing the Forest through the (Phylogenetic) Trees: Functional Characterisation of Grapevine Terpene Synthase ( VviTPS) Paralogues and Orthologues. PLANTS 2021; 10:plants10081520. [PMID: 34451565 PMCID: PMC8401418 DOI: 10.3390/plants10081520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/09/2021] [Accepted: 07/10/2021] [Indexed: 11/17/2022]
Abstract
Gene families involved in specialised metabolism play a key role in a myriad of ecophysiological and biochemical functions. The Vitis vinifera sesquiterpene synthases represent the largest subfamily of grapevine terpene synthase (VviTPS) genes and are important volatile metabolites for wine flavour and aroma, as well as ecophysiological interactions. The functional characterisation of VviTPS genes is complicated by a reliance on a single reference genome that greatly underrepresents this large gene family, exacerbated by extensive duplications and paralogy. The recent release of multiple phased diploid grapevine genomes, as well as extensive whole-genome resequencing efforts, provide a wealth of new sequence information that can be utilised to overcome the limitations of the reference genome. A large cluster of sesquiterpene synthases, localised to chromosome 18, was explored by means of comparative sequence analyses using the publicly available grapevine reference genome, three PacBio phased diploid genomes and whole-genome resequencing data from multiple genotypes. Two genes, VviTPS04 and -10, were identified as putative paralogues and/or allelic variants. Subsequent gene isolation from multiple grapevine genotypes and characterisation by means of a heterologous in planta expression and volatile analysis resulted in the identification of genotype-specific structural variations and polymorphisms that impact the gene function. These results present novel insight into how grapevine domestication likely shaped the VviTPS landscape to result in genotype-specific functions.
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11
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Whole genome resequencing and custom genotyping unveil clonal lineages in 'Malbec' grapevines (Vitis vinifera L.). Sci Rep 2021; 11:7775. [PMID: 33833358 PMCID: PMC8032709 DOI: 10.1038/s41598-021-87445-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/30/2021] [Indexed: 01/23/2023] Open
Abstract
Grapevine cultivars are clonally propagated to preserve their varietal attributes. However, genetic variations accumulate due to the occurrence of somatic mutations. This process is anthropically influenced through plant transportation, clonal propagation and selection. Malbec is a cultivar that is well-appreciated for the elaboration of red wine. It originated in Southwestern France and was introduced in Argentina during the 1850s. In order to study the clonal genetic diversity of Malbec grapevines, we generated whole-genome resequencing data for four accessions with different clonal propagation records. A stringent variant calling procedure was established to identify reliable polymorphisms among the analyzed accessions. The latter procedure retrieved 941 single nucleotide variants (SNVs). A reduced set of the detected SNVs was corroborated through Sanger sequencing, and employed to custom-design a genotyping experiment. We successfully genotyped 214 Malbec accessions using 41 SNVs, and identified 14 genotypes that clustered in two genetically divergent clonal lineages. These lineages were associated with the time span of clonal propagation of the analyzed accessions in Argentina and Europe. Our results show the usefulness of this approach for the study of the scarce intra-cultivar genetic diversity in grapevines. We also provide evidence on how human actions might have driven the accumulation of different somatic mutations, ultimately shaping the Malbec genetic diversity pattern.
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12
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Naegele RP, Londo JP, Zou C, Cousins P. Identification of SNPs associated with magnesium and sodium uptake and the effect of their accumulation on micro and macro nutrient levels in Vitis vinifera. PeerJ 2021; 9:e10773. [PMID: 33614279 PMCID: PMC7877238 DOI: 10.7717/peerj.10773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 12/22/2020] [Indexed: 11/20/2022] Open
Abstract
Macro and micro nutrient accumulation affects all stages of plant growth and development. When nutrient deficiencies or excesses occur, normal plant growth is altered resulting in symptoms such as leaf chlorosis, plant stunting or death. In grapes, few genomic regions associated with nutrient accumulation or deficiencies have been identified. Our study evaluated micro and macro nutrient concentrations in Vitis vinifera L. to identify associated SNPs using an association approach with genotype by sequencing data. Nutrient concentrations and foliar symptoms (leaf chlorosis and stunting) were compared among 249 F1Vitis vinifera individuals in 2015 and 2016. Foliar symptoms were consistent (≥90%) between years and correlated with changes in nutrient concentrations of magnesium (r = 0.65 and r = 0.38 in 2015 and 2016, respectively), aluminum (r = 0.24 and r = 0.49), iron (r = 0.21 and r = 0.49), and sodium (r = 0.32 and r = 0.21). Single nucleotide polymorphisms associated with symptoms, sodium, and magnesium were detected on each chromosome with the exception of 5, 7 and 17 depending on the trait and genome used for analyses explaining up to 40% of the observed variation. Symptoms and magnesium concentration were primarily associated with SNPs on chromosome 3, while SNPs associated with increased sodium content were primarily found on chromosomes 11 and 18. Mean concentrations for each nutrient varied between years in the population between symptomatic and asymptomatic plants, but relative relationships were mostly consistent. These data suggest a complex relationship among foliar symptoms and micro and macro nutrients accumulating in grapevines.
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Affiliation(s)
- Rachel P Naegele
- San Joaquin Valley Agricultural Sciences Center, USDA ARS, Parlier, CA, United States of America
| | - Jason P Londo
- Grape Genetics Unit, USDA ARS, Geneva, NY, United States of America
| | - Cheng Zou
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, United States of America
| | - Peter Cousins
- E&J Gallo Winery, Modesto, CA, United States of America
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13
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Rahman MA, Balasubramani SP, Basha SM. Molecular Characterization and Phylogenetic Analysis of MADS-Box Gene VroAGL11 Associated with Stenospermocarpic Seedlessness in Muscadine Grapes. Genes (Basel) 2021; 12:genes12020232. [PMID: 33562620 PMCID: PMC7915462 DOI: 10.3390/genes12020232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/06/2021] [Accepted: 02/02/2021] [Indexed: 01/02/2023] Open
Abstract
Reduced expression of MADS-box gene AGAMOUS-LIKE11 (VviAGL11) is responsible for stenospermocarpic seedlessness in bunch grapes. This study is aimed to characterize the VviAGL11 orthologous gene (VroAGL11) in native muscadine grapes (Vitis rotundifolia) at the molecular level and analyze its divergence from other plants. The VroAGL11 transcripts were found in all muscadine cultivars tested and highly expressed in berries while barely detectable in leaves. RT-PCR and sequencing of predicted ORFs from diverse grape species showed that AGL11 transcripts were conservatively spliced. The encoded VroAGL11 protein contains highly conserved MADS-MEF2-like domain, MADS domain, K box, putative phosphorylation site and two sumoylation motifs. The muscadine VroAGL11 proteins are almost identical (99%) to that of seeded bunch cultivar, Chardonnay, except in one amino acid (A79G), but differs from mutant protein of seedless bunch grape, Sultanina, in two amino acids, R197L and T210A. Phylogenetic analysis showed that AGL11 gene of muscadine and other Vitis species formed a separate clade than that of other eudicots and monocots. Muscadine grape cultivar "Jane Bell" containing the highest percentage of seed content in berry (7.2% of berry weight) had the highest VroAGL11 expression, but almost none to nominal expression in seedless cultivars Fry Seedless (muscadine) and Reliance Seedless (bunch). These findings suggest that VroAGL11 gene controls the seed morphogenesis in muscadine grapes like in bunch grape and can be manipulated to induce stenospermocarpic seedlessness using gene editing technology.
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14
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di Rienzo V, Imanifard Z, Mascio I, Gasser CS, Skinner DJ, Pierri CL, Marini M, Fanelli V, Sabetta W, Montemurro C, Bellin D. Functional conservation of the grapevine candidate gene INNER NO OUTER for ovule development and seed formation. HORTICULTURE RESEARCH 2021; 8:29. [PMID: 33518713 PMCID: PMC7848007 DOI: 10.1038/s41438-021-00467-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 12/19/2020] [Accepted: 12/22/2020] [Indexed: 05/06/2023]
Abstract
Seedlessness represents a highly appreciated trait in table grapes. Based on an interesting case of seedless fruit production described in the crop species Annona squamosa, we focused on the Vitis vinifera INNER NO OUTER (INO) gene as a candidate. This gene encodes a transcription factor belonging to the YABBY family involved in the determination of abaxial identity in several organs. In Arabidopsis thaliana, this gene was shown to be essential for the formation and asymmetric growth of the ovule outer integument and its mutation leads to a phenotypic defect of ovules and failure in seed formation. In this study, we identified in silico the V. vinifera orthologue and investigated its phylogenetic relationship to INO genes from other species and its expression in different organs in seeded and seedless varieties. Applying cross-species complementation, we have tested its functionality in the Arabidopsis ino-1 mutant. We show that the V. vinifera INO successfully rescues the ovule outer integument growth and seeds set and also partially complements the outer integument asymmetric growth in the Arabidopsis mutant, differently from orthologues from other species. These data demonstrate that VviINO retains similar activity and protein targets in grapevine as in Arabidopsis. Potential implications for grapevine breeding are discussed.
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Affiliation(s)
- Valentina di Rienzo
- Department of Soil, Plant and Food Sciences, Section of Genetics and Breeding, University of Bari Aldo Moro, via Amendola 165/A, 70125, Bari, Italy
- Spin off Sinagri s.r.l., University of Bari Aldo Moro, via Amendola 165/A, 70125, Bari, Italy
| | - Zahra Imanifard
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
| | - Isabella Mascio
- Department of Soil, Plant and Food Sciences, Section of Genetics and Breeding, University of Bari Aldo Moro, via Amendola 165/A, 70125, Bari, Italy
| | - Charles S Gasser
- Department of Molecular and Cellular Biology, University of California, Davis, 1 Shields Ave., Davis, CA, 95616, USA
| | - Debra J Skinner
- Department of Molecular and Cellular Biology, University of California, Davis, 1 Shields Ave., Davis, CA, 95616, USA
| | - Ciro Leonardo Pierri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry Molecular and Structural Biology, University of Bari Aldo Moro, Via E. Orabona 4, 70126 Bari, Italy
- Spin off BROWSer S.r.l. (https://browser-bioinf.com/) c/o Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona 4, 70126, Bari, Italy
| | - Martina Marini
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
| | - Valentina Fanelli
- Department of Soil, Plant and Food Sciences, Section of Genetics and Breeding, University of Bari Aldo Moro, via Amendola 165/A, 70125, Bari, Italy
| | - Wilma Sabetta
- Institute of Biosciences and Bioresources of the National Research Council (IBBR-CNR), Via Amendola 165/A, 70125, Bari, Italy
| | - Cinzia Montemurro
- Department of Soil, Plant and Food Sciences, Section of Genetics and Breeding, University of Bari Aldo Moro, via Amendola 165/A, 70125, Bari, Italy.
- Spin off Sinagri s.r.l., University of Bari Aldo Moro, via Amendola 165/A, 70125, Bari, Italy.
- Institute for Sustainable Plant Protection-Support Unit Bari, National Research Council of Italy (CNR), Via Amendola 165/A, 70125 Bari, Italy.
| | - Diana Bellin
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134, Verona, Italy.
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15
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Richter R, Rossmann S, Gabriel D, Töpfer R, Theres K, Zyprian E. Differential expression of transcription factor- and further growth-related genes correlates with contrasting cluster architecture in Vitis vinifera 'Pinot Noir' and Vitis spp. genotypes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3249-3272. [PMID: 32812062 PMCID: PMC7567691 DOI: 10.1007/s00122-020-03667-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 08/03/2020] [Indexed: 05/18/2023]
Abstract
Grapevine (Vitis vinifera L.) is an economically important crop that needs to comply with high quality standards for fruit, juice and wine production. Intense plant protection is required to avoid fungal damage. Grapevine cultivars with loose cluster architecture enable reducing protective treatments due to their enhanced resilience against fungal infections, such as Botrytis cinerea-induced gray mold. A recent study identified transcription factor gene VvGRF4 as determinant of pedicel length, an important component of cluster architecture, in samples of two loose and two compact quasi-isogenic 'Pinot Noir' clones. Here, we extended the analysis to 12 differently clustered 'Pinot Noir' clones from five diverse clonal selection programs. Differential gene expression of these clones was studied in three different locations over three seasons. Two phenotypically opposite clones were grown at all three locations and served for standardization. Data were correlated with the phenotypic variation of cluster architecture sub-traits. A set of 14 genes with consistent expression differences between loosely and compactly clustered clones-independent from season and location-was newly identified. These genes have annotations related to cellular growth, cell division and auxin metabolism and include two more transcription factor genes, PRE6 and SEP1-like. The differential expression of VvGRF4 in relation to loose clusters was exclusively found in 'Pinot Noir' clones. Gene expression studies were further broadened to phenotypically contrasting F1 individuals of an interspecific cross and OIV reference varieties of loose cluster architecture. This investigation confirmed PRE6 and six growth-related genes to show differential expression related to cluster architecture over genetically divergent backgrounds.
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Affiliation(s)
- Robert Richter
- Federal Research Centre for Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, Julius Kühn Institute, 76833, Siebeldingen, Germany
| | - Susanne Rossmann
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Doreen Gabriel
- Federal Research Centre for Cultivated Plants, Institute for Crop and Soil Science, Julius Kühn Institute, Bundesallee 58, 38116, Brunswick, Germany
| | - Reinhard Töpfer
- Federal Research Centre for Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, Julius Kühn Institute, 76833, Siebeldingen, Germany
| | - Klaus Theres
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Eva Zyprian
- Federal Research Centre for Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, Julius Kühn Institute, 76833, Siebeldingen, Germany.
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Tanaka K, Hamaguchi Y, Suzuki S, Enoki S. Genomic Characterization of the Japanese Indigenous Wine Grape Vitis sp. cv. Koshu. FRONTIERS IN PLANT SCIENCE 2020; 11:532211. [PMID: 33329619 PMCID: PMC7720679 DOI: 10.3389/fpls.2020.532211] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 10/01/2020] [Indexed: 06/12/2023]
Abstract
Vitis sp. cv. Koshu is indigenous to Japan and used as a table and processing grape. It also constitutes an important grape cultivar in Japanese white wine making and is phylogenetically distinct from European grapes. To understand its genomic information, we compared its small and structural variations with those of the table grape cultivar "Thompson seedless" and European wine grape cultivar "Tannat" via a short-read-based resequencing approach. The Koshu genome exhibited high heterozygosity compared to these cultivars, with this characteristic being particularly prominent on chromosome 7. Furthermore, Koshu structural variation encompassed the most and largest extent of duplications and the fewest and smallest extent of deletions with regard to copy number variation and the fewest absence variations among the compared grape cultivars. Plant disease resistance related to cell death associated with hypersensitive response and environmental stress response, such as water deprivation, oxidative stress, and cell wall organization, was inferred through enrichment analysis of small and structural variations. Variant accumulation levels in Koshu indicated that phenylpropanoid, flavonoid, glutathione, and α-linolenic acid pathways were related to polyphenol and flavor components. Together, this Koshu genomic information provides a foundation for improving the quality of Koshu wine and may facilitate the use of Koshu as a genetic resource.
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Affiliation(s)
- Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Yu Hamaguchi
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Shunji Suzuki
- Laboratory of Fruit Genetic Engineering, The Institute of Enology and Viticulture, University of Yamanashi, Kofu, Japan
| | - Shinichi Enoki
- Laboratory of Fruit Genetic Engineering, The Institute of Enology and Viticulture, University of Yamanashi, Kofu, Japan
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Genome Resequencing, Improvement of Variant Calling, and Population Genomic Analyses Provide Insights into the Seedlessness in the Genus Vitis. G3-GENES GENOMES GENETICS 2020; 10:3365-3377. [PMID: 32699042 PMCID: PMC7467000 DOI: 10.1534/g3.120.401521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The seedlessness of grape derived from stenospermocarpy is one of the most prized traits of table or raisin grapes. It is controlled by a complex genetic system containing one dominant gene and multiple recessive genes. Here, we collected dense variation data from high-depth resequencing data of seeded, seedless, and wild relative grape genomes sequenced to > 37x mean depth. Variant calls were made using a modified variant calling pipeline that was suitable for highly diverse interspecific grape accessions. The modified pipeline enabled us to call several million more variants than the commonly recommended pipeline. The quality was validated by Sanger sequencing data and subsequently supported by the genetic population structure and the phylogenetic tree constructed using the obtained variation data, results of which were generally consistent with known pedigree and taxonomic classifications. Variation data enabled us to confirm a dominant gene and identify recessive loci for seedlessness. Incidentally, we found that grape cultivar Rizamat contains an ancestral chromosomal region of the dominant gene in Sultanina, a predominant seedlessness donor cultivar. Furthermore, we predicted new candidate causal genes including Vitvi01g00455, Vitvi08g01528, and Vitvi18g01237 associated with the recessive seedless-regulating loci, which showed high homology with genes that regulate seed development in Arabidopsis. This study provides fundamental insights relevant to variant calling from genome resequencing data of diverse interspecific hybrid germplasms such as grape and will accelerate future efforts aimed at crop improvement.
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Muñoz-Espinoza C, Di Genova A, Sánchez A, Correa J, Espinoza A, Meneses C, Maass A, Orellana A, Hinrichsen P. Identification of SNPs and InDels associated with berry size in table grapes integrating genetic and transcriptomic approaches. BMC PLANT BIOLOGY 2020; 20:365. [PMID: 32746778 PMCID: PMC7397606 DOI: 10.1186/s12870-020-02564-4] [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: 03/18/2020] [Accepted: 07/21/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Berry size is considered as one of the main selection criteria in table grapes breeding programs, due to the consumer preferences. However, berry size is a complex quantitive trait under polygenic control, and its genetic determination of berry weight is not yet fully understood. The aim of this work was to perform marker discovery using a transcriptomic approach, in order to identify and characterize SNP and InDel markers associated with berry size in table grapes. We used an integrative analysis based on RNA-Seq, SNP/InDel search and validation on table grape segregants and varieties with different genetic backgrounds. RESULTS Thirty SNPs and eight InDels were identified using a transcriptomic approach (RNA-Seq). These markers were selected from SNP/InDel found among segregants from a Ruby x Sultanina population with contrasting phenotypes for berry size. The set of 38 SNP and InDel markers was distributed in eight chromosomes. Genotype-phenotype association analyses were performed using a set of 13 RxS segregants and 41 table grapes varieties with different genetic backgrounds during three seasons. The results showed several degrees of association of these markers with berry size (10.2 to 30.7%) as other berry-related traits such as length and width. The co-localization of SNP and /or InDel markers and previously reported QTLs and candidate genes associated with berry size were analysed. CONCLUSIONS We identified a set of informative and transferable SNP and InDel markers associated with berry size. Our results suggest the suitability of SNPs and InDels as candidate markers for berry weight in seedless table grape breeding. The identification of genomic regions associated with berry weight in chromosomes 8, 15 and 17 was achieved with supporting evidence derived from a transcriptome experiment focused on SNP/InDel search, as well as from a QTL-linkage mapping approach. New regions possibly associated with berry weight in chromosomes 3, 6, 9 and 14 were identified.
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Affiliation(s)
- Claudia Muñoz-Espinoza
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, Santiago, Chile
- Centro de Biotecnología Vegetal, Universidad Andrés Bello, Av. República 330, 3rd floor, Santiago, Chile
| | - Alex Di Genova
- Center for Mathematical Modeling (UMI2807-CNRS) and Department of Mathematical Engineering, Faculty of Mathematical and Physical Sciences, Universidad de Chile, Av. Blanco Encalada 2120, 7th floor, Santiago, Chile
| | - Alicia Sánchez
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, Santiago, Chile
| | - José Correa
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, Santiago, Chile
| | - Alonso Espinoza
- Centro de Biotecnología Vegetal, Universidad Andrés Bello, Av. República 330, 3rd floor, Santiago, Chile
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Universidad Andrés Bello, Av. República 330, 3rd floor, Santiago, Chile
- Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile
| | - Alejandro Maass
- Center for Mathematical Modeling (UMI2807-CNRS) and Department of Mathematical Engineering, Faculty of Mathematical and Physical Sciences, Universidad de Chile, Av. Blanco Encalada 2120, 7th floor, Santiago, Chile
- Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile
| | - Ariel Orellana
- Centro de Biotecnología Vegetal, Universidad Andrés Bello, Av. República 330, 3rd floor, Santiago, Chile
- Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile
| | - Patricio Hinrichsen
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, Santiago, Chile
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Patel S, Robben M, Fennell A, Londo JP, Alahakoon D, Villegas-Diaz R, Swaminathan P. Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. 'Manitoba 37'. HORTICULTURE RESEARCH 2020; 7:92. [PMID: 32528704 PMCID: PMC7261805 DOI: 10.1038/s41438-020-0316-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/31/2020] [Accepted: 03/31/2020] [Indexed: 05/31/2023]
Abstract
Vitis riparia, a critically important Native American grapevine species, is used globally in rootstock and scion breeding and contributed to the recovery of the French wine industry during the mid-19th century phylloxera epidemic. This species has abiotic and biotic stress tolerance and the largest natural geographic distribution of the North American grapevine species. Here we report an Illumina short-read 369X coverage, draft de novo heterozygous genome sequence of V. riparia Michx. 'Manitoba 37' with the size of ~495 Mb for 69,616 scaffolds and a N50 length of 518,740 bp. Using RNAseq data, 40,019 coding sequences were predicted and annotated. Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models found 96% of the complete BUSCOs in this assembly. The assembly continuity and completeness were further validated using V. riparia ESTs, BACs, and three de novo transcriptome assemblies of three different V. riparia genotypes resulting in >98% of respective sequences/transcripts mapping with this assembly. Alignment of the V. riparia assembly and predicted CDS with the latest V. vinifera 'PN40024' CDS and genome assembly showed 99% CDS alignment and a high degree of synteny. An analysis of plant transcription factors indicates a high degree of homology with the V. vinifera transcription factors. QTL mapping to V. riparia 'Manitoba 37' and V. vinifera PN40024 has identified genetic relationships to phenotypic variation between species. This assembly provides reference sequences, gene models for marker development and understanding V. riparia's genetic contributions in grape breeding and research.
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Affiliation(s)
- Sagar Patel
- Agronomy, Horticulture and Plant Science Department and BioSNTR, South Dakota State University, Brookings, SD 57006 USA
| | - Michael Robben
- Agronomy, Horticulture and Plant Science Department and BioSNTR, South Dakota State University, Brookings, SD 57006 USA
| | - Anne Fennell
- Agronomy, Horticulture and Plant Science Department and BioSNTR, South Dakota State University, Brookings, SD 57006 USA
| | - Jason P. Londo
- Grape Genetics Research Unit, USDA ARS, Geneva, NY 14456 USA
| | - Dilmini Alahakoon
- Agronomy, Horticulture and Plant Science Department and BioSNTR, South Dakota State University, Brookings, SD 57006 USA
| | - Roberto Villegas-Diaz
- Agronomy, Horticulture and Plant Science Department and BioSNTR, South Dakota State University, Brookings, SD 57006 USA
| | - Padmapriya Swaminathan
- Agronomy, Horticulture and Plant Science Department and BioSNTR, South Dakota State University, Brookings, SD 57006 USA
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20
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Yang Y, Cuenca J, Wang N, Liang Z, Sun H, Gutierrez B, Xi X, Arro J, Wang Y, Fan P, Londo J, Cousins P, Li S, Fei Z, Zhong GY. A key 'foxy' aroma gene is regulated by homology-induced promoter indels in the iconic juice grape 'Concord'. HORTICULTURE RESEARCH 2020; 7:67. [PMID: 32337050 PMCID: PMC7166211 DOI: 10.1038/s41438-020-0304-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/19/2020] [Accepted: 03/30/2020] [Indexed: 05/25/2023]
Abstract
'Concord', the most well-known juice grape with a parentage of the North American grape species Vitis labrusca L., possesses a special 'foxy' aroma predominantly resulted from the accumulation of methyl anthranilate (MA) in berries. This aroma, however, is often perceived as an undesirable attribute by wine consumers and rarely noticeable in the common table and wine grape species V. vinifera. Here we discovered homology-induced promoter indels as a major genetic mechanism for species-specific regulation of a key 'foxy' aroma gene, anthraniloyl-CoA:methanol acyltransferase (AMAT), that is responsible for MA biosynthesis. We found the absence of a 426-bp and/or a 42-bp sequence in AMAT promoters highly associated with high levels of AMAT expression and MA accumulation in 'Concord' and other V. labrusca-derived grapes. These promoter variants, all with direct and inverted repeats, were further confirmed in more than 1,300 Vitis germplasm. Moreover, functional impact of these indels was validated in transgenic Arabidopsis. Superimposed on the promoter regulation, large structural changes including exonic insertion of a retrotransposon were present at the AMAT locus in some V. vinifera grapes. Elucidation of the AMAT genetic regulation advances our understanding of the 'foxy' aroma trait and makes it genetically trackable and amenable in grapevine breeding.
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Affiliation(s)
- Yingzhen Yang
- US Department of Agriculture-Agricultural Research Service, Grape Genetics Research Unit, Geneva, NY USA
| | - José Cuenca
- US Department of Agriculture-Agricultural Research Service, Grape Genetics Research Unit, Geneva, NY USA
- Present Address: Centro de Citricultura y Producción Vegetal. Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
| | - Nian Wang
- US Department of Agriculture-Agricultural Research Service, Grape Genetics Research Unit, Geneva, NY USA
- Present Address: College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, Hubei China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Honghe Sun
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY USA
| | - Benjamin Gutierrez
- US Department of Agriculture-Agricultural Research Service, Plant Genetic Resources Unit, Geneva, NY USA
| | - Xiaojun Xi
- US Department of Agriculture-Agricultural Research Service, Plant Genetic Resources Unit, Geneva, NY USA
- Forestry and Pomology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jie Arro
- US Department of Agriculture-Agricultural Research Service, Plant Genetic Resources Unit, Geneva, NY USA
| | - Yi Wang
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peige Fan
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jason Londo
- US Department of Agriculture-Agricultural Research Service, Grape Genetics Research Unit, Geneva, NY USA
| | | | - Shaohua Li
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY USA
- US Department of Agriculture–Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY USA
| | - Gan-Yuan Zhong
- US Department of Agriculture-Agricultural Research Service, Grape Genetics Research Unit, Geneva, NY USA
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21
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Holtgräwe D, Rosleff Soerensen T, Hausmann L, Pucker B, Viehöver P, Töpfer R, Weisshaar B. A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock 'Börner' ( Vitis riparia × Vitis cinerea) and Its Exploitation for Marker Development and Targeted Mapping. FRONTIERS IN PLANT SCIENCE 2020; 11:156. [PMID: 32194587 PMCID: PMC7064618 DOI: 10.3389/fpls.2020.00156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/31/2020] [Indexed: 06/10/2023]
Abstract
Grapevine breeding has become highly relevant due to upcoming challenges like climate change, a decrease in the number of available fungicides, increasing public concern about plant protection, and the demand for a sustainable production. Downy mildew caused by Plasmopara viticola is one of the most devastating diseases worldwide of cultivated Vitis vinifera. In modern breeding programs, therefore, genetic marker technologies and genomic data are used to develop new cultivars with defined and stacked resistance loci. Potential sources of resistance are wild species of American or Asian origin. The interspecific hybrid of Vitis riparia Gm 183 x Vitis cinerea Arnold, available as the rootstock cultivar 'Börner,' carries several relevant resistance loci. We applied next-generation sequencing to enable the reliable identification of simple sequence repeats (SSR), and we also generated a draft genome sequence assembly of 'Börner' to access genome-wide sequence variations in a comprehensive and highly reliable way. These data were used to cover the 'Börner' genome with genetic marker positions. A subset of these marker positions was used for targeted mapping of the P. viticola resistance locus, Rpv14, to validate the marker position list. Based on the reference genome sequence PN40024, the position of this resistance locus can be narrowed down to less than 0.5 Mbp on chromosome 5.
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Affiliation(s)
- Daniela Holtgräwe
- Faculty of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | | | - Ludger Hausmann
- Institute for Grapevine Breeding Geilweilerhof, Julius Kuehn-Institute, Federal Research Centre for Cultivated Plants, Siebeldingen, Germany
| | - Boas Pucker
- Faculty of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Prisca Viehöver
- Faculty of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Reinhard Töpfer
- Institute for Grapevine Breeding Geilweilerhof, Julius Kuehn-Institute, Federal Research Centre for Cultivated Plants, Siebeldingen, Germany
| | - Bernd Weisshaar
- Faculty of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
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22
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Barbalho SM, Bueno Ottoboni AMM, Fiorini AMR, Guiguer ÉL, Nicolau CCT, Goulart RDA, Flato UAP. Grape juice or wine: which is the best option? Crit Rev Food Sci Nutr 2020; 60:3876-3889. [PMID: 31920107 DOI: 10.1080/10408398.2019.1710692] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Grapes used in the wine or juice production are mainly Vitis vinifera and Vitis labrusca and possess high amounts of polyphenolic compounds. These compounds are associated with the reduction of the inflammatory processes, oxidative stress, and protection against cardiovascular diseases. The industrial processes used for juice and wine production may interfere with the antioxidant composition of these products and the effects on human health. The aim of this review is to compare the effects of the consumption of wine or grape juice on cardiovascular risk factors. We used PRISMA guidelines and Medline/PUBMED and EMBASE to perform our search. The main effects of red wine and grape juice in humans were a reduction of body mass index, waist circumference, glycemia, plasma lipid peroxidation, total cholesterol, LDL-c, triglycerides, blood pressure, and homocysteine levels. Both wine and grape juice possess numerous bioactive compounds that are potentially responsible for many beneficial effects on human health. Nevertheless, there is a need for more double-blind, randomized controlled studies comparing the effects of juice and wine consumption without the biases that occur when comparisons are made with different populations, ages, doses, and different types of wine or juice.
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Affiliation(s)
- Sandra Maria Barbalho
- Medical School of Marília, UNIMAR, Marília, São Paulo, Brazils.,Food Technology School, Marília, São Paulo, Brazil
| | | | | | - Élen Landgraf Guiguer
- Medical School of Marília, UNIMAR, Marília, São Paulo, Brazils.,Food Technology School, Marília, São Paulo, Brazil
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23
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Kui L, Tang M, Duan S, Wang S, Dong X. Identification of Selective Sweeps in the Domesticated Table and Wine Grape ( Vitis vinifera L.). FRONTIERS IN PLANT SCIENCE 2020; 11:572. [PMID: 32477387 PMCID: PMC7240110 DOI: 10.3389/fpls.2020.00572] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 04/17/2020] [Indexed: 05/05/2023]
Abstract
Grapevine (Vitis vinifera) is one of the most important fruit species in the Classical Mediterranean world. It is thought to have been domesticated 6,000-8,000 years ago in the Near East. However, the domestication of its wild relative into wine grapes or table grapes remains largely unknown. In this study, we analyzed 30 table grapes, 30 wine grapes, 30 dual-purpose grape accessions, as well as 30 wild relatives (Vitis vinifera ssp. sylvestris). The phenotypic comparison showed striking differences in berry weight, acidity and the content of aroma. Based on a total of 7,522,958 single-nucleotide polymorphisms, we identified several significant selective sweep regions for table and wine grapes. Besides the well-known sex-determination locus on chromosome 2, the other four highest signals shared by table and wine grapes could not be linked to the known QTLs. The identification of these genomic regions under selection sweep may reveal agronomically important traits that have been selected during grape domestication. This information not only sheds light on the mechanisms of adaptions and diversification, but also guide the genetic improvement in breeding programs.
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Affiliation(s)
- Ling Kui
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, United States
| | - Min Tang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Shengchang Duan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Nowbio Biotechnology Company, Kunming, China
| | | | - Xiao Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Nowbio Biotechnology Company, Kunming, China
- *Correspondence: Xiao Dong,
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24
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Andolfo G, Villano C, Errico A, Frusciante L, Carputo D, Aversano R, Ercolano MR. Inferring RPW8-NLRs's evolution patterns in seed plants: case study in Vitis vinifera. PLANTA 2019; 251:32. [PMID: 31823009 DOI: 10.1007/s00425-019-03324-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/03/2019] [Indexed: 05/20/2023]
Abstract
Genomic and transcriptomic studies in plants and, more in deep, in grapevine reveal that the disease-resistance RNL gene family is highly variable. RNLs (RPW8-NLRs) are a phylogenetically distinct class of nucleotide oligomerization domain (NOD)-like receptors (NLRs) identified in plants. Two RNLs, namely, the NRG1 (N Requirement Gene 1) and the ADR1 (Activated Disease Resistance 1), have been characterized; however, little is known about the RNL evolutionary history in higher plants. To trace the diversification of RNL gene subfamily, we scanned the NLR proteins of 73 plant genomes belonging to 29 taxa, revealing a noticeable diversification across species and within the same genus or botanic family together with a conspicuous expansion in important crop species. To explore the RNL variability in Vitis vinifera and gain information with respect to their structure, evolutionary diversification of five grape genomes ('Aglianico', 'Falanghina', 'Sultanina', 'Tannat', and 'Nebbiolo') has been compared to the reference genome ('Pinot Noir'). The number of RNLs ranged from 6 ('Sultanina') to 14 ('Nebbiolo'), in contrast to the 10 'Pinot Noir' RNLs. The phylogenetic study on grapevine RNLs revealed that all collapsed into NRG1-clade, rather than four. To investigate more in depth the means of intraspecific variability of grape RNL copies, a transcriptomic profiling in response to powdery mildew (PM) infection was carried out through qRT-PCRs and public databases interrogation. The RNL expression variability identified in transcriptome data sets supports the hypothesis of a functional expansion/contraction in grapevine varieties. Although no direct correlations between grapevine PM-resistance and RNL expression was identified, our work can provide good candidates for functional studies able to elucidate the putative "helper" role of RNLs in grape immune signalling.
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Affiliation(s)
- Giuseppe Andolfo
- Department of Agriculture Sciences, University of Naples Federico II, via Università 100, 80055, Portici, NA, Italy
| | - Clizia Villano
- Department of Agriculture Sciences, University of Naples Federico II, via Università 100, 80055, Portici, NA, Italy
| | - Angela Errico
- Department of Agriculture Sciences, University of Naples Federico II, via Università 100, 80055, Portici, NA, Italy
| | - Luigi Frusciante
- Department of Agriculture Sciences, University of Naples Federico II, via Università 100, 80055, Portici, NA, Italy
| | - Domenico Carputo
- Department of Agriculture Sciences, University of Naples Federico II, via Università 100, 80055, Portici, NA, Italy
| | - Riccardo Aversano
- Department of Agriculture Sciences, University of Naples Federico II, via Università 100, 80055, Portici, NA, Italy.
| | - Maria R Ercolano
- Department of Agriculture Sciences, University of Naples Federico II, via Università 100, 80055, Portici, NA, Italy.
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Abstract
Grapevine is one of the most important fruit species in the world. In order to better understand genetic basis of traits variation and facilitate the breeding of new genotypes, we sequenced, assembled, and annotated the genome of the American native Vitis riparia, one of the main species used worldwide for rootstock and scion breeding. A total of 164 Gb raw DNA reads were obtained from Vitis riparia resulting in a 225X depth of coverage. We generated a genome assembly of the V. riparia grape de novo using the PacBio long-reads that was phased with the 10x Genomics Chromium linked-reads. At the chromosome level, a 500 Mb genome was generated with a scaffold N50 size of 1 Mb. More than 34% of the whole genome were identified as repeat sequences, and 37,207 protein-coding genes were predicted. This genome assembly sets the stage for comparative genomic analysis of the diversification and adaptation of grapevine and will provide a solid resource for further genetic analysis and breeding of this economically important species. Design Type(s) | sequence assembly objective • genetic mapping and linkage analysis objective • sequence annotation objective | Measurement Type(s) | whole genome sequencing assay | Technology Type(s) | DNA sequencing | Factor Type(s) | | Sample Characteristic(s) | Vitis riparia • leaf |
Machine-accessible metadata file describing the reported data (ISA-Tab format)
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26
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Foflonker F, Mollegard D, Ong M, Yoon HS, Bhattacharya D. Genomic Analysis of Picochlorum Species Reveals How Microalgae May Adapt to Variable Environments. Mol Biol Evol 2019; 35:2702-2711. [PMID: 30184126 DOI: 10.1093/molbev/msy167] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Understanding how microalgae adapt to rapidly changing environments is not only important to science but can help clarify the potential impact of climate change on the biology of primary producers. We sequenced and analyzed the nuclear genome of multiple Picochlorum isolates (Chlorophyta) to elucidate strategies of environmental adaptation. It was previously found that coordinated gene regulation is involved in adaptation to salinity stress, and here we show that gene gain and loss also play key roles in adaptation. We determined the extent of horizontal gene transfer (HGT) from prokaryotes and their role in the origin of novel functions in the Picochlorum clade. HGT is an ongoing and dynamic process in this algal clade with adaptation being driven by transfer, divergence, and loss. One HGT candidate that is differentially expressed under salinity stress is indolepyruvate decarboxylase that is involved in the production of a plant auxin that mediates bacteria-diatom symbiotic interactions. Large differences in levels of heterozygosity were found in diploid haplotypes among Picochlorum isolates. Biallelic divergence was pronounced in P. oklahomensis (salt plains environment) when compared with its closely related sister taxon Picochlorum SENEW3 (brackish water environment), suggesting a role of diverged alleles in response to environmental stress. Our results elucidate how microbial eukaryotes with limited gene inventories expand habitat range from mesophilic to halophilic through allelic diversity, and with minor but important contributions made by HGT. We also explore how the nature and quality of genome data may impact inference of nuclear ploidy.
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Affiliation(s)
- Fatima Foflonker
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ
| | - Devin Mollegard
- Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, New Brunswick, NJ
| | - Meichin Ong
- Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, New Brunswick, NJ
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ
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27
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Ramos-Madrigal J, Runge AKW, Bouby L, Lacombe T, Samaniego Castruita JA, Adam-Blondon AF, Figueiral I, Hallavant C, Martínez-Zapater JM, Schaal C, Töpfer R, Petersen B, Sicheritz-Pontén T, This P, Bacilieri R, Gilbert MTP, Wales N. Palaeogenomic insights into the origins of French grapevine diversity. NATURE PLANTS 2019; 5:595-603. [PMID: 31182840 DOI: 10.1038/s41477-019-0437-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 04/30/2019] [Indexed: 05/20/2023]
Abstract
The Eurasian grapevine (Vitis vinifera) has long been important for wine production as well as being a food source. Despite being clonally propagated, modern cultivars exhibit great morphological and genetic diversity, with thousands of varieties described in historic and contemporaneous records. Through historical accounts, some varieties can be traced to the Middle Ages, but the genetic relationships between ancient and modern vines remain unknown. We present target-enriched genome-wide sequencing data from 28 archaeological grape seeds dating to the Iron Age, Roman era and medieval period. When compared with domesticated and wild accessions, we found that the archaeological samples were closely related to western European cultivars used for winemaking today. We identified seeds with identical genetic signatures present at different Roman sites, as well as seeds sharing parent-offspring relationships with varieties grown today. Furthermore, we discovered that one seed dated to ~1100 CE was a genetic match to 'Savagnin Blanc', providing evidence for 900 years of uninterrupted vegetative propagation.
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Affiliation(s)
| | - Anne Kathrine Wiborg Runge
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Laurent Bouby
- ISEM-UMR 5554, CNRS-IRD-EPHE-Université Montpellier, Montpellier, France
| | - Thierry Lacombe
- UMR AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | | | | | - Isabel Figueiral
- Inrap, Méditerranée and ISEM-UMR 5554, CNRS-IRD-EPHE-Université Montpellier, Montpellier, France
| | - Charlotte Hallavant
- Bureau d'études Hadès, laboratoire TRACES-UMR 5608 (pôle Terrae)-UT2J, Toulouse, France
| | | | - Caroline Schaal
- GéoArchEon Sarl, Laboratoire Chrono-Environnement-UMR 6249, Université de Franche Comté, Besançon, France
| | - Reinhard Töpfer
- Julius Kühn-Institut Bundesforschungsinstitut für Kulturpflanzen, Institut für Rebenzüchtung Geilweilerhof, Siebeldingen, Germany
| | - Bent Petersen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Thomas Sicheritz-Pontén
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Patrice This
- UMR AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Roberto Bacilieri
- UMR AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - M Thomas P Gilbert
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
- NTNU University Museum, Trondheim, Norway.
| | - Nathan Wales
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
- BioArCh, Department of Archaeology, University of York, York, UK.
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université Paul Sabatier, Toulouse, France.
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28
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Richter R, Gabriel D, Rist F, Töpfer R, Zyprian E. Identification of co-located QTLs and genomic regions affecting grapevine cluster architecture. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1159-1177. [PMID: 30569367 DOI: 10.1007/s00122-018-3269-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 12/12/2018] [Indexed: 05/18/2023]
Abstract
Loose cluster architecture is an important aim in grapevine breeding since it has high impact on the phytosanitary status of grapes. This investigation analyzed the contributions of individual cluster sub-traits to the overall trait of cluster architecture. Six sub-traits showed large impact on cluster architecture as major determinants. They explained 57% of the OIV204 descriptor for cluster compactness rating in a highly diverse cross-population of 149 genotypes. Genetic analysis revealed several genomic regions involved in the expression of this trait. Based on the linkage of phenotypic features to molecular markers, QTL calculations shed new light on the genetic determinants of cluster architecture. Eight QTL clusters harbor overlapping confidence intervals of up to four co-located QTLs. A physical projection of the QTL clusters by confidence interval-flanking markers onto the PN40024 reference genome sequence revealed genes enriched in these regions.
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Affiliation(s)
- Robert Richter
- Institute for Grapevine Breeding Geilweilerhof, Julius Kuehn Institute, Federal Research Centre of Cultivated Plants, Geilweilerhof, 76833, Siebeldingen, Germany
| | - Doreen Gabriel
- Institute for Crop and Soil Science, Julius Kuehn Institute, Federal Research Centre of Cultivated Plants, Bundesallee 58, 38116, Brunswick, Germany
| | - Florian Rist
- Institute for Grapevine Breeding Geilweilerhof, Julius Kuehn Institute, Federal Research Centre of Cultivated Plants, Geilweilerhof, 76833, Siebeldingen, Germany
| | - Reinhard Töpfer
- Institute for Grapevine Breeding Geilweilerhof, Julius Kuehn Institute, Federal Research Centre of Cultivated Plants, Geilweilerhof, 76833, Siebeldingen, Germany
| | - Eva Zyprian
- Institute for Grapevine Breeding Geilweilerhof, Julius Kuehn Institute, Federal Research Centre of Cultivated Plants, Geilweilerhof, 76833, Siebeldingen, Germany.
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Minio A, Massonnet M, Figueroa-Balderas R, Vondras AM, Blanco-Ulate B, Cantu D. Iso-Seq Allows Genome-Independent Transcriptome Profiling of Grape Berry Development. G3 (BETHESDA, MD.) 2019; 9:755-767. [PMID: 30642874 PMCID: PMC6404599 DOI: 10.1534/g3.118.201008] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/09/2019] [Indexed: 01/13/2023]
Abstract
Transcriptomics has been widely applied to study grape berry development. With few exceptions, transcriptomic studies in grape are performed using the available genome sequence, PN40024, as reference. However, differences in gene content among grape accessions, which contribute to phenotypic differences among cultivars, suggest that a single reference genome does not represent the species' entire gene space. Though whole genome assembly and annotation can reveal the relatively unique or "private" gene space of any particular cultivar, transcriptome reconstruction is a more rapid, less costly, and less computationally intensive strategy to accomplish the same goal. In this study, we used single molecule-real time sequencing (SMRT) to sequence full-length cDNA (Iso-Seq) and reconstruct the transcriptome of Cabernet Sauvignon berries during berry ripening. In addition, short reads from ripening berries were used to error-correct low-expression isoforms and to profile isoform expression. By comparing the annotated gene space of Cabernet Sauvignon to other grape cultivars, we demonstrate that the transcriptome reference built with Iso-Seq data represents most of the expressed genes in the grape berries and includes 1,501 cultivar-specific genes. Iso-Seq produced transcriptome profiles similar to those obtained after mapping on a complete genome reference. Together, these results justify the application of Iso-Seq to identify cultivar-specific genes and build a comprehensive reference for transcriptional profiling that circumvents the necessity of a genome reference with its associated costs and computational weight.
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Affiliation(s)
- Andrea Minio
- Department of Viticulture and Enology, University of California Davis, Davis, CA
| | - Mélanie Massonnet
- Department of Viticulture and Enology, University of California Davis, Davis, CA
| | | | - Amanda M Vondras
- Department of Viticulture and Enology, University of California Davis, Davis, CA
| | | | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, CA
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30
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Vignani R, Liò P, Scali M. How to integrate wet lab and bioinformatics procedures for wine DNA admixture analysis and compositional profiling: Case studies and perspectives. PLoS One 2019; 14:e0211962. [PMID: 30753217 PMCID: PMC6376920 DOI: 10.1371/journal.pone.0211962] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/24/2019] [Indexed: 01/03/2023] Open
Abstract
The varietal authentication of wines is fundamental for assessing wine quality, and it is part of its compositional profiling. The availability of historical, cultural and chemical composition information is extremely important for quality evaluation. DNA-based techniques are a powerful tool for proving the varietal composition of a wine. SSR-amplification of genomic residual Vitis vinifera DNA, namely Wine DNA Fingerprinting (WDF) is able to produce strong, analytical evidence concerning the monovarietal nature of a wine, and for blended wines by generating the probability of the presence/absence of a certain variety, all in association with a dedicated bioinformatics elaboration of genotypes associated with possible varietal candidates. Together with WDF we could exploit Bioinformatics techniques, due to the number of grape genomes grown. In this paper, the use of WDF and the development of a bioinformatics tool for allelic data validation, retrieved from the amplification of 7 to 10 SSRs markers in the Vitis vinifera genome, are reported. The wines were chosen based on increasing complexity; from monovarietal, experimental ones, to commercial monovarietals, to blended commercial wines. The results demonstrate that WDF, after calculation of different distance matrices and Neighbor-Joining input data, followed by Principal Component Analysis (PCA) can effectively describe the varietal nature of wines. In the unknown blended wines the WDF profiles were compared to possible varietal candidates (Merlot, Pinot Noir, Cabernet Sauvignon and Zinfandel), and the output graphs show the most probable varieties used in the blend as closeness to the tested wine. This pioneering work should be meant as to favor in perspective the multidisciplinary building-up of on-line databanks and bioinformatics toolkits on wine. The paper concludes with a discussion on an integrated decision support system based on bioinformatics, chemistry and cultural data to assess wine quality.
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Affiliation(s)
- Rita Vignani
- Department of Life Science, University of Siena, Siena,
Italy
- Serge-genomics, Siena, Italy
| | - Pietro Liò
- Computer Laboratory, University of Cambridge, Cambridge, United
Kingdom
| | - Monica Scali
- Department of Life Science, University of Siena, Siena,
Italy
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Zhang S, Wang L, Sun X, Li Y, Yao J, van Nocker S, Wang X. Genome-Wide Analysis of the YABBY Gene Family in Grapevine and Functional Characterization of VvYABBY4. FRONTIERS IN PLANT SCIENCE 2019; 10:1207. [PMID: 31649691 PMCID: PMC6791920 DOI: 10.3389/fpls.2019.01207] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 09/03/2019] [Indexed: 05/22/2023]
Abstract
Genes of the plant-specific YABBY transcription factor family have various roles, including lateral organ development, establishment of dorsoventral polarity, and response to abiotic stress. In this study, we carried out a genomic census of YABBY genes in grapevine (Vitis vinifera) and characterized their expression pattern during ovule development. We identified seven YABBY genes and classified them into five subfamilies, based on peptide sequence, similarity of exon-intron structure and composition of peptide sequence motifs. Analysis of YABBY gene expression in various grapevine structures and organs suggested that these genes function in diverse aspects of development and physiology. Analysis of expression during ovule development in four cultivars showed that one gene, VvYABBY4, was preferentially expressed during the period of ovule abortion in seedless cultivars. Transgenic expression of VvYABBY4 in tomato conferred reduced plant stature, dark green leaves, elongated pistil, and reduced size of fruit and seeds. Reduced seed size was associated with smaller endosperm cells. Expression of VvYABBY4 also affected expression of numerous tomato genes with presumed roles in seed development. These data suggest the potential for VvYABBY4 to influence seed development in grapevine, which may impact seedless grape breeding.
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Affiliation(s)
- Songlin Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Li Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
- College of Horticulture, Agricultural University of Hebei, Baoding, China
| | - Xiaomeng Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Yunduan Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Jin Yao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Steve van Nocker
- Department of Horticulture, Michigan State University, East Lansing, MI, United States
| | - Xiping Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, China
- *Correspondence: Xiping Wang,
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32
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Liu G, Fu J. Squalene synthase cloning and functional identification in wintersweet plant (Chimonanthus zhejiangensis). BOTANICAL STUDIES 2018; 59:30. [PMID: 30539325 PMCID: PMC6289936 DOI: 10.1186/s40529-018-0246-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 12/05/2018] [Indexed: 05/27/2023]
Abstract
BACKGROUND Three species of wintersweets: Chimonanthus salicifolius S. Y. Hu, Chimonanthus zhejiangensis M. C. Liu and Chimonanthus grammalus M. C. Liu are widely distributed in China. The three wintersweets belonging to the genus of Chimonanthus that can synthesize abundant terpenoids that are beneficial to human health. Their buds and leaves are traditional Chinese herb applied by the 'She' ethnic minority in southeast of China. Squalene is a multi-functional and ubiquitous triterpene in plants, which is biosynthesized by squalene synthase (SQS) using farnesyl diphosphate (FPP) as the substrate. The synthesis of squalene in wintersweet was not clearly. This work would provide us much help to further understand the terpene metabolism in wintersweet and its health function to people at phytochemistry and molecular levels. RESULTS In this study, we identified squalene component in the extractions of leaves of three wintersweets and isolated SQS genes from leaf transcriptomes. The three SQSs were highly conservative, so CzSQS from C. zhejiangensis was just determined the enzymatic activity. The in vitro expressed CzSQS that deleted two transmembrane domains could catalyze FPP to generate squalene with the presence of NADPH and Mg2+. CONCLUSIONS The squalene was one of wintersweet leaves phytochemicals. The squalene synthases of three wintersweet plants were highly conserved. The CzSQS was capable to catalyze two FPP molecules to squalene.
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Affiliation(s)
- Guanhua Liu
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008, People's Republic of China
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Hangzhou, 310008, People's Republic of China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Jianyu Fu
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008, People's Republic of China.
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Hangzhou, 310008, People's Republic of China.
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Royo C, Torres-Pérez R, Mauri N, Diestro N, Cabezas JA, Marchal C, Lacombe T, Ibáñez J, Tornel M, Carreño J, Martínez-Zapater JM, Carbonell-Bejerano P. The Major Origin of Seedless Grapes Is Associated with a Missense Mutation in the MADS-Box Gene VviAGL11. PLANT PHYSIOLOGY 2018; 177:1234-1253. [PMID: 29853599 PMCID: PMC6053000 DOI: 10.1104/pp.18.00259] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 05/23/2018] [Indexed: 05/22/2023]
Abstract
Seedlessness is greatly prized by consumers of fresh grapes. While stenospermocarpic seed abortion determined by the SEED DEVELOPMENT INHIBITOR (SDI) locus is the usual source of seedlessness in commercial grapevine (Vitis vinifera) cultivars, the underlying sdi mutation remains unknown. Here, we undertook an integrative approach to identify the causal mutation. Quantitative genetics and fine-mapping in two 'Crimson Seedless'-derived F1 mapping populations confirmed the major effect of the SDI locus and delimited the sdi mutation to a 323-kb region on chromosome 18. RNA-sequencing comparing seed traces of seedless and seeds of seeded F1 individuals identified processes triggered during sdi-determined seed abortion, including the activation of salicylic acid-dependent autoimmunity. The RNA-sequencing data set was investigated for candidate genes, and while no evidence for causal cis-acting regulatory mutations was detected, deleterious nucleotide changes in coding sequences of the seedless haplotype were predicted in two genes within the sdi fine-mapping interval. Targeted resequencing of the two genes in a collection of 124 grapevine cultivars showed that only the point variation causing the arginine-197-to-leucine substitution in the seed morphogenesis regulator gene AGAMOUS-LIKE11 (VviAGL11) was fully linked with stenospermocarpy. The concurrent postzygotic variation identified for this missense polymorphism and seedlessness phenotype in seeded somatic variants of the original stenospermocarpic cultivar supports a causal effect. We postulate that seed abortion caused by this amino acid substitution in VviAGL11 is the major cause of seedlessness in cultivated grapevine. This information can be exploited to boost seedless grape breeding.
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Affiliation(s)
- Carolina Royo
- Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, 26007 Logrono, Spain
| | - Rafael Torres-Pérez
- Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, 26007 Logrono, Spain
| | - Nuria Mauri
- Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, 26007 Logrono, Spain
| | - Nieves Diestro
- Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, 26007 Logrono, Spain
| | - José Antonio Cabezas
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Centro de Investigación Forestal, INIA-UPM, 28040 Madrid, Spain
| | - Cécile Marchal
- Institut National de la Recherche Agronomique, Centre de Ressources Biologiques de la Vigne, Domaine de Vassal, 34340 Marseillan-Plage, France
| | - Thierry Lacombe
- AGAP, Universite Montpellier, CIRAD, Institut National de la Recherche Agronomique, Montpellier SupAgro, 34060 Montpellier, France
| | - Javier Ibáñez
- Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, 26007 Logrono, Spain
| | - Manuel Tornel
- Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario, Sociedad Murciana de Investigación y Tecnología de Uva de Mesa, 30150 La Alberca, Spain
| | - Juan Carreño
- Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario, Sociedad Murciana de Investigación y Tecnología de Uva de Mesa, 30150 La Alberca, Spain
| | - José Miguel Martínez-Zapater
- Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, 26007 Logrono, Spain
| | - Pablo Carbonell-Bejerano
- Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, 26007 Logrono, Spain
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Wang X, Tu M, Wang D, Liu J, Li Y, Li Z, Wang Y, Wang X. CRISPR/Cas9-mediated efficient targeted mutagenesis in grape in the first generation. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:844-855. [PMID: 28905515 PMCID: PMC5866948 DOI: 10.1111/pbi.12832] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 08/25/2017] [Accepted: 09/01/2017] [Indexed: 05/19/2023]
Abstract
The clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR/Cas9) system is a powerful tool for editing plant genomes. Efficient genome editing of grape (Vitis vinifera) suspension cells using the type II CRISPR/Cas9 system has been demonstrated; however, it has not been established whether this system can be applied to get biallelic mutations in the first generation of grape. In this current study, we designed four guide RNAs for the VvWRKY52 transcription factor gene for using with the CRISPR/Cas9 system, and obtained transgenic plants via Agrobacterium-mediated transformation, using somatic embryos of the Thompson Seedless cultivar. Analysis of the first-generation transgenic plants verified 22 mutant plants of the 72 T-DNA-inserted plants. Of these, 15 lines carried biallelic mutations and seven were heterozygous. A range of RNA-guided editing events, including large deletions, were found in the mutant plants, while smaller deletions comprised the majority of the detected mutations. Sequencing of potential off-target sites for all four targets revealed no off-target events. In addition, knockout of VvWRKY52 in grape increased the resistance to Botrytis cinerea. We conclude that the CRISPR/Cas9 system allows precise genome editing in the first generation of grape and represents a useful tool for gene functional analysis and grape molecular breeding.
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Affiliation(s)
- Xianhang Wang
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest ChinaMinistry of AgricultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Mingxing Tu
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest ChinaMinistry of AgricultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Dejun Wang
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest ChinaMinistry of AgricultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Jianwei Liu
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest ChinaMinistry of AgricultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Yajuan Li
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest ChinaMinistry of AgricultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Zhi Li
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest ChinaMinistry of AgricultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Yuejin Wang
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest ChinaMinistry of AgricultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Xiping Wang
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest ChinaMinistry of AgricultureNorthwest A&F UniversityYanglingShaanxiChina
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Patel S, Lu Z, Jin X, Swaminathan P, Zeng E, Fennell AY. Comparison of three assembly strategies for a heterozygous seedless grapevine genome assembly. BMC Genomics 2018; 19:57. [PMID: 29343235 PMCID: PMC5773036 DOI: 10.1186/s12864-018-4434-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/04/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND De novo heterozygous assembly is an ongoing challenge requiring improved assembly approaches. In this study, three strategies were used to develop de novo Vitis vinifera 'Sultanina' genome assemblies for comparison with the inbred V. vinifera (PN40024 12X.v2) reference genome and a published Sultanina ALLPATHS-LG assembly (AP). The strategies were: 1) a default PLATANUS assembly (PLAT_d) for direct comparison with AP assembly, 2) an iterative merging strategy using METASSEMBLER to combine PLAT_d and AP assemblies (MERGE) and 3) PLATANUS parameter modifications plus GapCloser (PLAT*_GC). RESULTS The three new assemblies were greater in size than the AP assembly. PLAT*_GC had the greatest number of scaffolds aligning with a minimum of 95% identity and ≥1000 bp alignment length to V. vinifera (PN40024 12X.v2) reference genome. SNP analysis also identified additional high quality SNPs. A greater number of sequence reads mapped back with zero-mismatch to the PLAT_d, MERGE, and PLAT*_GC (>94%) than was found in the AP assembly (87%) indicating a greater fidelity to the original sequence data in the new assemblies than in AP assembly. A de novo gene prediction conducted using seedless RNA-seq data predicted > 30,000 coding sequences for the three new de novo assemblies, with the greatest number (30,544) in PLAT*_GC and only 26,515 for the AP assembly. Transcription factor analysis indicated good family coverage, but some genes found in the VCOST.v3 annotation were not identified in any of the de novo assemblies, particularly some from the MYB and ERF families. CONCLUSIONS The PLAT_d and PLAT*_GC had a greater number of synteny blocks with the V. vinifera (PN40024 12X.v2) reference genome than AP or MERGE. PLAT*_GC provided the most contiguous assembly with only 1.2% scaffold N, in contrast to AP (10.7% N), PLAT_d (6.6% N) and Merge (6.4% N). A PLAT*_GC pseudo-chromosome assembly with chromosome alignment to the reference genome V. vinifera, (PN40024 12X.v2) provides new information for use in seedless grape genetic mapping studies. An annotated de novo gene prediction for the PLAT*_GC assembly, aligned with VitisNet pathways provides new seedless grapevine specific transcriptomic resource that has excellent fidelity with the seedless short read sequence data.
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Affiliation(s)
- Sagar Patel
- Agronomy, Horticulture and Plant Science Department and BioSNTR, 247 McFadden BioStress Laboratory, South Dakota State University, Brookings, SD, 57006, USA
| | - Zhixiu Lu
- Department of Computer Science, University of South Dakota, Vermillion, SD, USA
| | - Xiaozhu Jin
- Agronomy, Horticulture and Plant Science Department and BioSNTR, 247 McFadden BioStress Laboratory, South Dakota State University, Brookings, SD, 57006, USA
| | - Padmapriya Swaminathan
- Agronomy, Horticulture and Plant Science Department and BioSNTR, 247 McFadden BioStress Laboratory, South Dakota State University, Brookings, SD, 57006, USA
| | - Erliang Zeng
- Department of Computer Science, University of South Dakota, Vermillion, SD, USA.,Department of Biology, University of South Dakota, Vermillion, SD, USA
| | - Anne Y Fennell
- Agronomy, Horticulture and Plant Science Department and BioSNTR, 247 McFadden BioStress Laboratory, South Dakota State University, Brookings, SD, 57006, USA.
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Balic I, Vizoso P, Nilo-Poyanco R, Sanhueza D, Olmedo P, Sepúlveda P, Arriagada C, Defilippi BG, Meneses C, Campos-Vargas R. Transcriptome analysis during ripening of table grape berry cv. Thompson Seedless. PLoS One 2018; 13:e0190087. [PMID: 29320527 PMCID: PMC5761854 DOI: 10.1371/journal.pone.0190087] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 12/07/2017] [Indexed: 11/18/2022] Open
Abstract
Ripening is one of the key processes associated with the development of major organoleptic characteristics of the fruit. This process has been extensively characterized in climacteric fruit, in contrast with non-climacteric fruit such as grape, where the process is less understood. With the aim of studying changes in gene expression during ripening of non-climacteric fruit, an Illumina based RNA-Seq transcriptome analysis was performed on four developmental stages, between veraison and harvest, on table grapes berries cv Thompson Seedless. Functional analysis showed a transcriptional increase in genes related with degradation processes of chlorophyll, lipids, macromolecules recycling and nucleosomes organization; accompanied by a decrease in genes related with chloroplasts integrity and amino acid synthesis pathways. It was possible to identify several processes described during leaf senescence, particularly close to harvest. Before this point, the results suggest a high transcriptional activity associated with the regulation of gene expression, cytoskeletal organization and cell wall metabolism, which can be related to growth of berries and firmness loss characteristic to this stage of development. This high metabolic activity could be associated with an increase in the transcription of genes related with glycolysis and respiration, unexpected for a non-climacteric fruit ripening.
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Affiliation(s)
- Iván Balic
- Universidad Andrés Bello, Facultad Ciencias Biológicas, Centro de Biotecnología Vegetal, Santiago, Chile
- Universidad de Los Lagos, Departamento de Acuicultura y Recursos Agroalimentarios, Osorno, Chile
| | - Paula Vizoso
- Center of Plant Propagation and Conservation (CEPROVEG), Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | | | - Dayan Sanhueza
- Universidad Andrés Bello, Facultad Ciencias Biológicas, Centro de Biotecnología Vegetal, Santiago, Chile
| | - Patricio Olmedo
- Universidad Andrés Bello, Facultad Ciencias Biológicas, Centro de Biotecnología Vegetal, Santiago, Chile
| | - Pablo Sepúlveda
- Universidad Andrés Bello, Facultad Ciencias Biológicas, Centro de Biotecnología Vegetal, Santiago, Chile
| | - Cesar Arriagada
- Laboratorio Biorremediación, Departamento de Ciencias Forestales, Facultad de Ciencias Agropecuarias y Forestales, Universidad de La Frontera, Temuco, Chile
| | - Bruno G. Defilippi
- Instituto de Investigaciones Agropecuarias, INIA La Platina, Santiago, Chile
| | - Claudio Meneses
- Universidad Andrés Bello, Facultad Ciencias Biológicas, Centro de Biotecnología Vegetal, Santiago, Chile
- FONDAP Center for Genome Regulation, Santiago, Chile
| | - Reinaldo Campos-Vargas
- Universidad Andrés Bello, Facultad Ciencias Biológicas, Centro de Biotecnología Vegetal, Santiago, Chile
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Gambino G, Dal Molin A, Boccacci P, Minio A, Chitarra W, Avanzato CG, Tononi P, Perrone I, Raimondi S, Schneider A, Pezzotti M, Mannini F, Gribaudo I, Delledonne M. Whole-genome sequencing and SNV genotyping of 'Nebbiolo' (Vitis vinifera L.) clones. Sci Rep 2017; 7:17294. [PMID: 29229917 PMCID: PMC5725591 DOI: 10.1038/s41598-017-17405-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 11/23/2017] [Indexed: 01/27/2023] Open
Abstract
‘Nebbiolo’ (Vitis vinifera) is among the most ancient and prestigious wine grape varieties characterised by a wide genetic variability exhibited by a high number of clones (vegetatively propagated lines of selected mother plants). However, limited information is available for this cultivar at the molecular and genomic levels. The whole-genomes of three ‘Nebbiolo’ clones (CVT 71, CVT 185 and CVT 423) were re-sequenced and a de novo transcriptome assembly was produced. Important remarks about the genetic peculiarities of ‘Nebbiolo’ and its intra-varietal variability useful for clonal identification were reported. In particular, several varietal transcripts identified for the first time in ‘Nebbiolo’ were disease resistance genes and single-nucleotide variants (SNVs) identified in ‘Nebbiolo’, but not in other cultivars, were associated with genes involved in the stress response. Ten newly discovered SNVs were successfully employed to identify some periclinal chimeras and to classify 98 ‘Nebbiolo’ clones in seven main genotypes, which resulted to be linked to the geographical origin of accessions. In addition, for the first time it was possible to discriminate some ‘Nebbiolo’ clones from the others.
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Affiliation(s)
- Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Italy.
| | | | - Paolo Boccacci
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Italy
| | - Andrea Minio
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Walter Chitarra
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Italy
| | | | - Paola Tononi
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Irene Perrone
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Italy
| | - Stefano Raimondi
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco (TO), Italy
| | - Anna Schneider
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco (TO), Italy
| | - Mario Pezzotti
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Franco Mannini
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco (TO), Italy
| | - Ivana Gribaudo
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco (TO), Italy
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Abstract
We generated genomic data to estimate the population history of grapes, the most economically important horticultural crop in the world. Domesticated grapes experienced a protracted, 22,000-y population decline prior to domestication; we hypothesize that this decline reflects low-intensity cultivation by humans prior to domestication. Domestication altered the mating system of grapes. The sex determination region is detectable as a region of heightened genetic divergence between wild and cultivated accessions. Based on gene expression analyses, we propose candidate genes that alter sex determination. Finally, grapes contain more deleterious mutations in heterozygous states than do their wild ancestors. The accumulation of deleterious mutations is due in part to clonal propagation, which shelters deleterious recessive mutations. We gathered genomic data from grapes (Vitis vinifera ssp. vinifera), a clonally propagated perennial crop, to address three ongoing mysteries about plant domestication. The first is the duration of domestication; archaeological evidence suggests that domestication occurs over millennia, but genetic evidence indicates that it can occur rapidly. We estimated that our wild and cultivated grape samples diverged ∼22,000 years ago and that the cultivated lineage experienced a steady decline in population size (Ne) thereafter. The long decline may reflect low-intensity management by humans before domestication. The second mystery is the identification of genes that contribute to domestication phenotypes. In cultivated grapes, we identified candidate-selected genes that function in sugar metabolism, flower development, and stress responses. In contrast, candidate-selected genes in the wild sample were limited to abiotic and biotic stress responses. A genomic region of high divergence corresponded to the sex determination region and included a candidate male sterility factor and additional genes with sex-specific expression. The third mystery concerns the cost of domestication. Annual crops accumulate putatively deleterious variants, in part due to strong domestication bottlenecks. The domestication of perennial crops differs from that of annuals in several ways, including the intensity of bottlenecks, and it is not yet clear if they accumulate deleterious variants. We found that grape accessions contained 5.2% more deleterious variants than wild individuals, and these were more often in a heterozygous state. Using forward simulations, we confirm that clonal propagation leads to the accumulation of recessive deleterious mutations but without decreasing fitness.
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Carbonell-Bejerano P, Royo C, Torres-Pérez R, Grimplet J, Fernandez L, Franco-Zorrilla JM, Lijavetzky D, Baroja E, Martínez J, García-Escudero E, Ibáñez J, Martínez-Zapater JM. Catastrophic Unbalanced Genome Rearrangements Cause Somatic Loss of Berry Color in Grapevine. PLANT PHYSIOLOGY 2017; 175:786-801. [PMID: 28811336 PMCID: PMC5619900 DOI: 10.1104/pp.17.00715] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/13/2017] [Indexed: 05/21/2023]
Abstract
Grape (Vitis vinifera) color somatic variants that can be used to develop new grapevine cultivars occasionally appear associated with deletion events of uncertain origin. To understand the mutational mechanisms generating somatic structural variation in grapevine, we compared the Tempranillo Blanco (TB) white berry somatic variant with its black berry ancestor, Tempranillo Tinto. Whole-genome sequencing uncovered a catastrophic genome rearrangement in TB that caused the hemizygous deletion of 313 genes, including the loss of the functional copy for the MYB transcription factors required for anthocyanin pigmentation in the berry skin. Loss of heterozygosity and decreased copy number delimited interspersed monosomic and disomic regions in the right arm of linkage groups 2 and 5. At least 11 validated clustered breakpoints involving intrachromosomal and interchromosomal translocations between three linkage groups flanked the deleted fragments, which, according to segregation analyses, are phased in a single copy of each of the affected chromosomes. These hallmarks, along with the lack of homology between breakpoint joins and the randomness of the order and orientation of the rearranged fragments, are all consistent with a chromothripsis-like pattern generated after chromosome breakage and illegitimate rejoining. This unbalanced genome reshuffling has additional consequences in reproductive development. In TB, lack of sexual transmission of rearranged chromosomes associates with low gamete viability, which compromises fruit set and decreases fruit production. Our findings show that catastrophic genome rearrangements arise spontaneously and stabilize during plant somatic growth. These dramatic rearrangements generate new interesting phenotypes that can be selected for the improvement of vegetatively propagated plant species.
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Affiliation(s)
- Pablo Carbonell-Bejerano
- Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, 26007 Logroño, Spain
| | - Carolina Royo
- Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, 26007 Logroño, Spain
| | - Rafael Torres-Pérez
- Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, 26007 Logroño, Spain
| | - Jérôme Grimplet
- Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, 26007 Logroño, Spain
| | - Lucie Fernandez
- Unité Mixte de Recherche Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, F-33140 Villenave d'Ornon, France
| | | | - Diego Lijavetzky
- Instituto de Biología Agrícola de Mendoza, Consejo Nacional de Investigaciones Científicas y Técnicas-UNCuyo-FCA, M5528AHB Chacras de Coria, Argentina
| | - Elisa Baroja
- Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, 26007 Logroño, Spain
| | - Juana Martínez
- Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, 26007 Logroño, Spain
| | - Enrique García-Escudero
- Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, 26007 Logroño, Spain
| | - Javier Ibáñez
- Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, 26007 Logroño, Spain
| | - José Miguel Martínez-Zapater
- Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, 26007 Logroño, Spain
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Whole genome comparative analysis of four Georgian grape cultivars. Mol Genet Genomics 2017; 292:1377-1389. [PMID: 28785866 DOI: 10.1007/s00438-017-1353-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 07/27/2017] [Indexed: 10/19/2022]
Abstract
Grapevine is the one of the most important fruit species in the world. Comparative genome sequencing of grape cultivars is very important for the interpretation of the grape genome and understanding its evolution. The genomes of four Georgian grape cultivars-Chkhaveri, Saperavi, Meskhetian green, and Rkatsiteli, belonging to different haplogroups, were resequenced. The shotgun genomic libraries of grape cultivars were sequenced on an Illumina HiSeq. Pinot Noir nuclear, mitochondrial, and chloroplast DNA were used as reference. Mitochondrial DNA of Chkhaveri closely matches that of the reference Pinot noir mitochondrial DNA, with the exception of 16 SNPs found in the Chkhaveri mitochondrial DNA. The number of SNPs in mitochondrial DNA from Saperavi, Meskhetian green, and Rkatsiteli was 764, 702, and 822, respectively. Nuclear DNA differs from the reference by 1,800,675 nt in Chkhaveri, 1,063,063 nt in Meskhetian green, 2,174,995 in Saperavi, and 5,011,513 in Rkatsiteli. Unlike mtDNA Pinot noir, chromosomal DNA is closer to the Meskhetian green than to other cultivars. Substantial differences in the number of SNPs in mitochondrial and nuclear DNA of Chkhaveri and Pinot noir cultivars are explained by backcrossing or introgression of their wild predecessors before or during the process of domestication. Annotation of chromosomal DNA of Georgian grape cultivars by MEGANTE, a web-based annotation system, shows 66,745 predicted genes (Chkhaveri-17,409; Saperavi-17,021; Meskhetian green-18,355; and Rkatsiteli-13,960). Among them, 106 predicted genes and 43 pseudogenes of terpene synthase genes were found in chromosomes 12, 18 random (18R), and 19. Four novel TPS genes not present in reference Pinot noir DNA were detected. Two of them-germacrene A synthase (Chromosome 18R) and (-) germacrene D synthase (Chromosome 19) can be identified as putatively full-length proteins. This work performs the first attempt of the comparative whole genome analysis of different haplogroups of Vitis vinifera cultivars. Based on complete nuclear and mitochondrial DNA sequence analysis, hypothetical phylogeny scheme of formation of grape cultivars is presented.
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Yin L, Qu J, Deng S, Liu S, Lu J, Zhang Y. Phytohormone and genome variations in Vitis amurensis resistant to downy mildew. Genome 2017; 60:791-796. [PMID: 28727939 DOI: 10.1139/gen-2017-0008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Downy mildew (DM) resistance is a highly desirable agronomic trait in grape breeding. High variation in Plasmopara viticola resistance was found in Vitis cultivars. Some accessions show high P. viticola resistance even under conditions highly conducive to DM. Here, leaf disc inoculation experiments revealed that Vitis amurensis 'Zuoshaner' exhibited DM resistance with necrotic spots, whereas the V. amurensis × V. vinifera hybrid cultivar 'Zuoyouhong' was susceptible. Changes in plant hormones accumulation profiles differed between the cultivars. To investigate the genetic mechanisms related to DM resistance, we performed genome-wide sequencing of 'Zuoshaner' and 'Zuoyouhong' and identified cultivar-specific single-nucleotide polymorphisms, insertions/deletions (indels), structural variations (SVs), and copy number variations (CNVs), identifying 5399 SVs and 191 CNVs specific for 'Zuoshaner'. Genes affected by these genetic variations were enriched in biological processes, including defense response and response to stress and stimulation, and were associated with sesquiterpenoid and triterpenoid biosynthesis, ABC transporters, and phenylalanine metabolism pathways. Additionally, indels and SVs were detected in six NBS-LRR disease resistance genes, and a CNV was mapped to the Rpv8 locus responsible for downy mildew resistance. These findings further our understanding of the genetic mechanisms underlying grape mildew resistance, and will facilitate genomic marker-assisted breeding for improved V. amurensis cultivars.
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Affiliation(s)
- Ling Yin
- a Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Junjie Qu
- a Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Shuhan Deng
- b College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Shaoli Liu
- b College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jiang Lu
- a Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.,c Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200024, China
| | - Yali Zhang
- b College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
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Boccacci P, Mela A, Pavez Mina C, Chitarra W, Perrone I, Gribaudo I, Gambino G. Cultivar-specific gene modulation in Vitis vinifera: analysis of the promoters regulating the expression of WOX transcription factors. Sci Rep 2017; 7:45670. [PMID: 28358354 PMCID: PMC5372460 DOI: 10.1038/srep45670] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/02/2017] [Indexed: 02/07/2023] Open
Abstract
The family of Wuschel-related Homeobox (WOX) genes is a class of transcription factors involved in the early stages of embryogenesis and organ development in plants. Some of these genes have shown different transcription levels in embryogenic tissues and mature organs in two different cultivars of Vitis vinifera: ‘Chardonnay’ (CH) and ‘Cabernet Sauvignon’ (CS). Therefore, we investigated the genetic basis responsible for these differences by cloning and sequencing in both the cultivars the promoter regions (~2000 bp) proximal to the transcription start site of five VvWOX genes. We then introduced these promoters into Arabidopsis thaliana for expression pattern characterisation using the GUS reporter gene. In the transgenic Arabidopsis, two promoters isolated from CS (pVvWOX13C_CS and pVvWOX6_CS) induced increased expression compared to the sequence isolated in CH, confirming the data obtained in grapevine tissues. These results were corroborated by transient expression assays using the agroinfiltration approach in grapevine somatic embryos. Truncated versions of pVvWOX13C demonstrated that few nucleotide differences between the sequences isolated from CH and CS are pivotal for the transcriptional regulation of VvWOX13C. Analysis of promoters using heterologous and homologous systems appear to be effective for exploring gene modulation linked with intervarietal sequence variation in grapevine.
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Affiliation(s)
- Paolo Boccacci
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino. Strada delle Cacce 73, 10135 Torino, Italy
| | - Anita Mela
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco Unit. Largo P. Braccini 2, 10095 Grugliasco-TO, Italy
| | - Catalina Pavez Mina
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco Unit. Largo P. Braccini 2, 10095 Grugliasco-TO, Italy
| | - Walter Chitarra
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino. Strada delle Cacce 73, 10135 Torino, Italy
| | - Irene Perrone
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino. Strada delle Cacce 73, 10135 Torino, Italy
| | - Ivana Gribaudo
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco Unit. Largo P. Braccini 2, 10095 Grugliasco-TO, Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino. Strada delle Cacce 73, 10135 Torino, Italy
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Yu J, Wang L, Guo H, Liao B, King G, Zhang X. Genome evolutionary dynamics followed by diversifying selection explains the complexity of the Sesamum indicum genome. BMC Genomics 2017; 18:257. [PMID: 28340563 PMCID: PMC5364699 DOI: 10.1186/s12864-017-3599-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 02/21/2017] [Indexed: 12/26/2022] Open
Abstract
Background Whole genome duplication (WGD) and tandem duplication (TD) provide two critical sources of raw genetic material for genome complexity and evolutionary novelty. Little is known about the complexity of the Sesamum indicum genome after it diverged from a common ancestor with the paleodiploid Vitis vinifera and further experienced WGD and TD events. Results Here, we analyzed the functional divergence of different classes of inter- and intra-genome gene pairs from ancestral events to uncover multiple-layers of evolutionary dynamics acting during the process of forming the modern S. indicum genome. Comprehensive inter-genome analyses revealed that 60% and 70% of syntenic orthologous gene pairs were retained among the two subgenomes in S. indicum compared to V. vinifera, although there was no evidence of significant differences under selection pressure. For the intra-genomic analyses, 5,932 duplicated gene pairs experienced fractionation, with the remaining 1,236 duplicated gene pairs having undergone functional divergence under diversifying selection. Analysis of the TD events indicated that 2,945 paralogous gene pairs, from 1,089 tandem arrays of 2–16 genes, experienced functional divergence under diversifying selection. Sequence diversification of different classes of gene pairs revealed that most of TD events occurred after the WGD event, with others following the ancestral gene order indicating ancient TD events at some time prior to the WGD event. Our comparison-of-function analyses for different classes of gene pairs indicated that the WGD and TD evolutionary events were both responsible for introducing genes that enabled exploration of novel and complementary functionalities, whilst maintaining individual plant ruggedness. Conclusions In this study, we first investigated functional divergence of different classes of gene pairs to characterize the dynamic processes associated with each evolutionary event in S. indicum. The data demonstrated massive and distinct functional divergence among different classes of gene pairs, and provided a genome-scale view of gene function diversification explaining the complexity of the S. indicum genome. We hope this provides a biological model to study the mechanism of plant species formation, particularly in the context of the evolutionary history of flowering plants, and offers novel insights for the study of angiosperm genomes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3599-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jingyin Yu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Linhai Wang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Hui Guo
- Plant Genome Mapping Laboratory, the University of Georgia, Athens, GA, 30605, USA
| | - Boshou Liao
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Graham King
- Southern Cross Plant Science, Southern Cross University, PO Box 157, Lismore, NSW, 2480, Australia. .,The Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
| | - Xiurong Zhang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
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Malabarba J, Buffon V, Mariath JEA, Gaeta ML, Dornelas MC, Margis-Pinheiro M, Pasquali G, Revers LF. The MADS-box gene Agamous-like 11 is essential for seed morphogenesis in grapevine. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1493-1506. [PMID: 28369525 DOI: 10.1093/jxb/erx025] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Despite the wide appreciation of seedless grapes, little is known about the molecular mechanisms that drive the stenospermocarpic seedless-type phenotype in grapevine. In order to address the molecular mechanisms that control seedlessness in grapevine, our study aimed to characterize VviAGL11, a class D MADS-box transcription factor gene that has been proposed as the major candidate gene involved in Vitis vinifera seed morphogenesis. VviAGL11 allelic variations in seeded and seedless grapevine cultivars were determined, and its correlations with allele-specific steady-state mRNA levels were investigated. VviAGL11 relative expression was significantly higher in seeds at 2, 4, and 6 weeks after fruit set, whereas in the seedless grape its transcript levels were extremely low in all stages analyzed. In situ hybridization revealed transcript accumulation specifically in the dual endotesta layer of the seeds, which is responsible for elongation and an increase of cell number, a necessary step to determine the lignification and the final seed size. No hybridization signals were visible in the seedless grapevine tissues, and a morphoanatomical analysis showed an apparent loss of identity of the endotesta layer of the seed traces. Ectopic expression of VviAGL11 in the Arabidopsis SEEDSTICK mutant background restored the wild-type phenotype and confirmed the direct role of VviAGL11 in seed morphogenesis, suggesting that depletion of its expression is responsible for the erroneous development of a highly essential seed layer, therefore culminating in the typical apirenic phenotype.
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Affiliation(s)
- Jaiana Malabarba
- Graduate Program in Cell and Molecular Biology, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Porto Alegre, RS, 91501-970, Brazil
- Centro Nacional de Pesquisa de Uva e Vinho, Empresa Brasileira de Pesquisa Agropecuária, Rua Livramento, 515, Bento Gonçalves, RS, 95701-008, Brazil
| | - Vanessa Buffon
- Centro Nacional de Pesquisa de Uva e Vinho, Empresa Brasileira de Pesquisa Agropecuária, Rua Livramento, 515, Bento Gonçalves, RS, 95701-008, Brazil
| | - Jorge E A Mariath
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Porto Alegre, RS, 91501-970, Brazil
| | - Marcos L Gaeta
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Porto Alegre, RS, 91501-970, Brazil
| | - Marcelo C Dornelas
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, 13083-862, Brazil
| | - Márcia Margis-Pinheiro
- Graduate Program in Cell and Molecular Biology, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Porto Alegre, RS, 91501-970, Brazil
| | - Giancarlo Pasquali
- Graduate Program in Cell and Molecular Biology, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Porto Alegre, RS, 91501-970, Brazil
| | - Luís F Revers
- Centro Nacional de Pesquisa de Uva e Vinho, Empresa Brasileira de Pesquisa Agropecuária, Rua Livramento, 515, Bento Gonçalves, RS, 95701-008, Brazil
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Marrano A, Birolo G, Prazzoli ML, Lorenzi S, Valle G, Grando MS. SNP-Discovery by RAD-Sequencing in a Germplasm Collection of Wild and Cultivated Grapevines (V. vinifera L.). PLoS One 2017; 12:e0170655. [PMID: 28125640 PMCID: PMC5268455 DOI: 10.1371/journal.pone.0170655] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 01/09/2017] [Indexed: 01/27/2023] Open
Abstract
Whole-genome comparisons of Vitis vinifera subsp. sativa and V. vinifera subsp. sylvestris are expected to provide a better estimate of the valuable genetic diversity still present in grapevine, and help to reconstruct the evolutionary history of a major crop worldwide. To this aim, the increase of molecular marker density across the grapevine genome is fundamental. Here we describe the SNP discovery in a grapevine germplasm collection of 51 cultivars and 44 wild accessions through a novel protocol of restriction-site associated DNA (RAD) sequencing. By resequencing 1.1% of the grapevine genome at a high coverage, we recovered 34K BamHI unique restriction sites, of which 6.8% were absent in the ‘PN40024’ reference genome. Moreover, we identified 37,748 single nucleotide polymorphisms (SNPs), 93% of which belonged to the 19 assembled chromosomes with an average of 1.8K SNPs per chromosome. Nearly half of the SNPs fell in genic regions mostly assigned to the functional categories of metabolism and regulation, whereas some nonsynonymous variants were identified in genes related with the detection and response to environmental stimuli. SNP validation was carried-out, showing the ability of RAD-seq to accurately determine genotypes in a highly heterozygous species. To test the usefulness of our SNP panel, the main diversity statistics were evaluated, highlighting how the wild grapevine retained less genetic variability than the cultivated form. Furthermore, the analysis of Linkage Disequilibrium (LD) in the two subspecies separately revealed how the LD decays faster within the domesticated grapevine compared to its wild relative. Being the first application of RAD-seq in a diverse grapevine germplasm collection, our approach holds great promise for exploiting the genetic resources available in one of the most economically important fruit crops.
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Affiliation(s)
- Annarita Marrano
- Department of Genomics and Biology of Fruit Crops, Grapevine Genetics and Breeding, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trentino, Italy
- * E-mail:
| | - Giovanni Birolo
- CRIBI Biotechnology Centre, University of Padua, Padua, Italy
| | - Maria Lucia Prazzoli
- Department of Genomics and Biology of Fruit Crops, Grapevine Genetics and Breeding, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trentino, Italy
| | - Silvia Lorenzi
- Department of Genomics and Biology of Fruit Crops, Grapevine Genetics and Breeding, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trentino, Italy
| | - Giorgio Valle
- CRIBI Biotechnology Centre, University of Padua, Padua, Italy
- Department of Biology, University of Padua, Padua, Italy
| | - Maria Stella Grando
- Department of Genomics and Biology of Fruit Crops, Grapevine Genetics and Breeding, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trentino, Italy
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Minio A, Lin J, Gaut BS, Cantu D. How Single Molecule Real-Time Sequencing and Haplotype Phasing Have Enabled Reference-Grade Diploid Genome Assembly of Wine Grapes. FRONTIERS IN PLANT SCIENCE 2017; 8:826. [PMID: 28567052 PMCID: PMC5434136 DOI: 10.3389/fpls.2017.00826] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 05/02/2017] [Indexed: 05/23/2023]
Affiliation(s)
- Andrea Minio
- Department of Viticulture and Enology, University of California, DavisDavis, CA, United States
| | - Jerry Lin
- Department of Viticulture and Enology, University of California, DavisDavis, CA, United States
| | - Brandon S. Gaut
- Department of Ecology and Evolutionary Biology, University of California, IrvineIrvine, CA, United States
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, DavisDavis, CA, United States
- *Correspondence: Dario Cantu
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Serrano A, Espinoza C, Armijo G, Inostroza-Blancheteau C, Poblete E, Meyer-Regueiro C, Arce A, Parada F, Santibáñez C, Arce-Johnson P. Omics Approaches for Understanding Grapevine Berry Development: Regulatory Networks Associated with Endogenous Processes and Environmental Responses. FRONTIERS IN PLANT SCIENCE 2017; 8:1486. [PMID: 28936215 PMCID: PMC5594091 DOI: 10.3389/fpls.2017.01486] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/10/2017] [Indexed: 05/21/2023]
Abstract
Grapevine fruit development is a dynamic process that can be divided into three stages: formation (I), lag (II), and ripening (III), in which physiological and biochemical changes occur, leading to cell differentiation and accumulation of different solutes. These stages can be positively or negatively affected by multiple environmental factors. During the last decade, efforts have been made to understand berry development from a global perspective. Special attention has been paid to transcriptional and metabolic networks associated with the control of grape berry development, and how external factors affect the ripening process. In this review, we focus on the integration of global approaches, including proteomics, metabolomics, and especially transcriptomics, to understand grape berry development. Several aspects will be considered, including seed development and the production of seedless fruits; veraison, at which anthocyanin accumulation begins in the berry skin of colored varieties; and hormonal regulation of berry development and signaling throughout ripening, focusing on the transcriptional regulation of hormone receptors, protein kinases, and genes related to secondary messenger sensing. Finally, berry responses to different environmental factors, including abiotic (temperature, water-related stress and UV-B radiation) and biotic (fungi and viruses) stresses, and how they can significantly modify both, development and composition of vine fruit, will be discussed. Until now, advances have been made due to the application of Omics tools at different molecular levels. However, the potential of these technologies should not be limited to the study of single-level questions; instead, data obtained by these platforms should be integrated to unravel the molecular aspects of grapevine development. Therefore, the current challenge is the generation of new tools that integrate large-scale data to assess new questions in this field, and to support agronomical practices.
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Affiliation(s)
- Alejandra Serrano
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Carmen Espinoza
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Grace Armijo
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Claudio Inostroza-Blancheteau
- Núcleo de Investigación en Producción Alimentaría, Facultad de Recursos Naturales, Escuela de Agronomía, Universidad Católica de TemucoTemuco, Chile
| | - Evelyn Poblete
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Carlos Meyer-Regueiro
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Anibal Arce
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Francisca Parada
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Claudia Santibáñez
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
- Ecophysiology and Functional Genomic of Grapevine, Institut des Sciences de la Vigne et du Vin, Institut National de la Recherche Agronomique, Université de BordeauxBordeaux, France
| | - Patricio Arce-Johnson
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
- *Correspondence: Patricio Arce-Johnson,
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Mercenaro L, Nieddu G, Porceddu A, Pezzotti M, Camiolo S. Sequence Polymorphisms and Structural Variations among Four Grapevine ( Vitis vinifera L.) Cultivars Representing Sardinian Agriculture. FRONTIERS IN PLANT SCIENCE 2017; 8:1279. [PMID: 28775732 PMCID: PMC5517397 DOI: 10.3389/fpls.2017.01279] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/06/2017] [Indexed: 05/04/2023]
Abstract
The genetic diversity among grapevine (Vitis vinifera L.) cultivars that underlies differences in agronomic performance and wine quality reflects the accumulation of single nucleotide polymorphisms (SNPs) and small indels as well as larger genomic variations. A combination of high throughput sequencing and mapping against the grapevine reference genome allows the creation of comprehensive sequence variation maps. We used next generation sequencing and bioinformatics to generate an inventory of SNPs and small indels in four widely cultivated Sardinian grape cultivars (Bovale sardo, Cannonau, Carignano and Vermentino). More than 3,200,000 SNPs were identified with high statistical confidence. Some of the SNPs caused the appearance of premature stop codons and thus identified putative pseudogenes. The analysis of SNP distribution along chromosomes led to the identification of large genomic regions with uninterrupted series of homozygous SNPs. We used a digital comparative genomic hybridization approach to identify 6526 genomic regions with significant differences in copy number among the four cultivars compared to the reference sequence, including 81 regions shared between all four cultivars and 4953 specific to single cultivars (representing 1.2 and 75.9% of total copy number variation, respectively). Reads mapping at a distance that was not compatible with the insert size were used to identify a dataset of putative large deletions with cultivar Cannonau revealing the highest number. The analysis of genes mapping to these regions provided a list of candidates that may explain some of the phenotypic differences among the Bovale sardo, Cannonau, Carignano and Vermentino cultivars.
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Affiliation(s)
- Luca Mercenaro
- Dipartimento di Agraria, Università degli Studi di SassariSassari, Italy
| | - Giovanni Nieddu
- Dipartimento di Agraria, Università degli Studi di SassariSassari, Italy
| | - Andrea Porceddu
- Dipartimento di Agraria, Università degli Studi di SassariSassari, Italy
| | - Mario Pezzotti
- Dipartimento di Biotecnologie, Università degli Studi di VeronaVerona, Italy
| | - Salvatore Camiolo
- Dipartimento di Agraria, Università degli Studi di SassariSassari, Italy
- *Correspondence: Salvatore Camiolo,
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49
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Adam-Blondon AF, Alaux M, Pommier C, Cantu D, Cheng ZM, Cramer GR, Davies C, Delrot S, Deluc L, Di Gaspero G, Grimplet J, Fennell A, Londo JP, Kersey P, Mattivi F, Naithani S, Neveu P, Nikolski M, Pezzotti M, Reisch BI, Töpfer R, Vivier MA, Ware D, Quesneville H. Towards an open grapevine information system. HORTICULTURE RESEARCH 2016; 3:16056. [PMID: 27917288 PMCID: PMC5120350 DOI: 10.1038/hortres.2016.56] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/10/2016] [Accepted: 10/21/2016] [Indexed: 05/26/2023]
Abstract
Viticulture, like other fields of agriculture, is currently facing important challenges that will be addressed only through sustained, dedicated and coordinated research. Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature, in many domains of study, including grapevine research, there is a need to improve the findability, accessibility, interoperability and reusability (FAIR-ness) of these data. Considering the heterogeneous nature of the data produced, the transnational nature of the scientific community and the experience gained elsewhere, we have formed an open working group, in the framework of the International Grapevine Genome Program (www.vitaceae.org), to construct a coordinated federation of information systems holding grapevine data distributed around the world, providing an integrated set of interfaces supporting advanced data modeling, rich semantic integration and the next generation of data mining tools. To achieve this goal, it will be critical to develop, implement and adopt appropriate standards for data annotation and formatting. The development of this system, the GrapeIS, linking genotypes to phenotypes, and scientific research to agronomical and oeneological data, should provide new insights into grape biology, and allow the development of new varieties to meet the challenges of biotic and abiotic stress, environmental change, and consumer demand.
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Affiliation(s)
- A-F Adam-Blondon
- URGI, UR1164 INRA, Université Paris-Saclay, Versailles 78026, France
| | - M Alaux
- URGI, UR1164 INRA, Université Paris-Saclay, Versailles 78026, France
| | - C Pommier
- URGI, UR1164 INRA, Université Paris-Saclay, Versailles 78026, France
| | - D Cantu
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA
| | - Z-M Cheng
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
| | - GR Cramer
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
| | - C Davies
- CSIRO Agriculture and Food, Waite Campus, WIC West Building, PMB2, Glen Osmond, South Australia 5064, Australia
| | - S Delrot
- Université de Bordeaux, ISVV, EGFV, UMR 1287, F-33140 Villenave d’Ornon, France
| | - L Deluc
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - G Di Gaspero
- Istituto di Genomica Applicata, Udine 33100, Italy
| | - J Grimplet
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño 26006, Spain
| | - A Fennell
- Plant Science Department, South Dakota State University, BioSNTR, Brookings, SD 57007, USA
| | - JP Londo
- United States Department of Agriculture-Agricultural Research Service-Grape Genetics Research Unit, Geneva, NY 14456, USA
| | - P Kersey
- European Molecular Biology Laboratory, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - F Mattivi
- Dipartimento Qualità Alimentare e Nutrizione, Centro Ricerca ed Innovazione Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige, Italia
| | - S Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - P Neveu
- UMR Mistea, INRA, Montpellier 34060, France
| | - M Nikolski
- University of Bordeaux, CBiB, Bordeaux 33000, France
- University of Bordeaux, CNRS/LaBRI, Talence 33405, France
| | - M Pezzotti
- Department of Biotechnology, Università degli Studi di Verona, Verona 37134, Italy
| | - BI Reisch
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - R Töpfer
- JKI Institute for Grapevine Breeding Geilweilerhof, Siebeldingen 76833, Germany
| | - MA Vivier
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch University, Stellenbosch, Matieland 7602, South Africa
| | - D Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- US Department of Agriculture-Agricultural Research Service, NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14853, USA
| | - H Quesneville
- URGI, UR1164 INRA, Université Paris-Saclay, Versailles 78026, France
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50
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Cardone MF, D'Addabbo P, Alkan C, Bergamini C, Catacchio CR, Anaclerio F, Chiatante G, Marra A, Giannuzzi G, Perniola R, Ventura M, Antonacci D. Inter-varietal structural variation in grapevine genomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:648-661. [PMID: 27419916 DOI: 10.1111/tpj.13274] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 07/12/2016] [Accepted: 07/13/2016] [Indexed: 05/10/2023]
Abstract
Grapevine (Vitis vinifera L.) is one of the world's most important crop plants, which is of large economic value for fruit and wine production. There is much interest in identifying genomic variations and their functional effects on inter-varietal, phenotypic differences. Using an approach developed for the analysis of human and mammalian genomes, which combines high-throughput sequencing, array comparative genomic hybridization, fluorescent in situ hybridization and quantitative PCR, we created an inter-varietal atlas of structural variations and single nucleotide variants (SNVs) for the grapevine genome analyzing four economically and genetically relevant table grapevine varieties. We found 4.8 million SNVs and detected 8% of the grapevine genome to be affected by genomic variations. We identified more than 700 copy number variation (CNV) regions and more than 2000 genes subjected to CNV as potential candidates for phenotypic differences between varieties.
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Affiliation(s)
- Maria Francesca Cardone
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Unità di ricerca per l'uva da tavola e la vitivinicoltura in ambiente mediterraneo, Research Unit for viticulture and enology in Southern Italy, Turi (BA), Italy
| | - Pietro D'Addabbo
- Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy
| | - Can Alkan
- Department of Computer Engineering, Bilkent University, Ankara, TR-06800, Turkey
| | - Carlo Bergamini
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Unità di ricerca per l'uva da tavola e la vitivinicoltura in ambiente mediterraneo, Research Unit for viticulture and enology in Southern Italy, Turi (BA), Italy
| | | | - Fabio Anaclerio
- Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy
| | - Giorgia Chiatante
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Unità di ricerca per l'uva da tavola e la vitivinicoltura in ambiente mediterraneo, Research Unit for viticulture and enology in Southern Italy, Turi (BA), Italy
- Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy
| | - Annamaria Marra
- Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy
| | - Giuliana Giannuzzi
- Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Rocco Perniola
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Unità di ricerca per l'uva da tavola e la vitivinicoltura in ambiente mediterraneo, Research Unit for viticulture and enology in Southern Italy, Turi (BA), Italy
| | - Mario Ventura
- Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy
| | - Donato Antonacci
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Unità di ricerca per l'uva da tavola e la vitivinicoltura in ambiente mediterraneo, Research Unit for viticulture and enology in Southern Italy, Turi (BA), Italy
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