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Péros JP, Launay A, Peyrière A, Berger G, Roux C, Lacombe T, Boursiquot JM. Species relationships within the genus Vitis based on molecular and morphological data. PLoS One 2023; 18:e0283324. [PMID: 37523393 PMCID: PMC10389703 DOI: 10.1371/journal.pone.0283324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/07/2023] [Indexed: 08/02/2023] Open
Abstract
The grape genus Vitis L. includes the domesticated V. vinifera, which is one of the most important fruit crop, and also close relatives recognized as valuable germplasm resources for improving cultivars. To resolve some standing problems in the species relationships within the Vitis genus we analyzed diversity in a set of 90 accessions comprising most of Vitis species and some putative hybrids. We discovered single nucleotide polymorphisms (SNPs) in SANGER sequences of twelve loci and genotyped accessions at a larger number of SNPs using a previously developed SNP array. Our phylogenic analyses consistently identified: three clades in North America, one in East Asia, and one in Europe corresponding to V. vinifera. Using heterozygosity measurement, haplotype reconstruction and chloroplast markers, we identified the hybrids existing within and between clades. The species relationships were better assessed after discarding these hybrids from analyses. We also studied the relationships between phylogeny and morphological traits and found that several traits significantly correlated with the phylogeny. The American clade that includes important species such as V. riparia and V. rupestris showed a major divergence with all other clades based on both DNA polymorphisms and morphological traits.
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Affiliation(s)
- Jean-Pierre Péros
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Amandine Launay
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - André Peyrière
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Gilles Berger
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Catherine Roux
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Thierry Lacombe
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Jean-Michel Boursiquot
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
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2
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Flutre T, Le Cunff L, Fodor A, Launay A, Romieu C, Berger G, Bertrand Y, Terrier N, Beccavin I, Bouckenooghe V, Roques M, Pinasseau L, Verbaere A, Sommerer N, Cheynier V, Bacilieri R, Boursiquot JM, Lacombe T, Laucou V, This P, Péros JP, Doligez A. A genome-wide association and prediction study in grapevine deciphers the genetic architecture of multiple traits and identifies genes under many new QTLs. G3 (Bethesda) 2022; 12:6575896. [PMID: 35485948 PMCID: PMC9258538 DOI: 10.1093/g3journal/jkac103] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/21/2022] [Indexed: 12/11/2022]
Abstract
To cope with the challenges facing agriculture, speeding-up breeding programs is a worthy endeavor, especially for perennial species such as grapevine, but requires understanding the genetic architecture of target traits. To go beyond the mapping of quantitative trait loci in bi-parental crosses, we exploited a diversity panel of 279 Vitis vinifera L. cultivars planted in 5 blocks in the vineyard. This panel was phenotyped over several years for 127 traits including yield components, organic acids, aroma precursors, polyphenols, and a water stress indicator. The panel was genotyped for 63k single nucleotide polymorphisms by combining an 18K microarray and genotyping-by-sequencing. The experimental design allowed to reliably assess the genotypic values for most traits. Marker densification via genotyping-by-sequencing markedly increased the proportion of genetic variance explained by single nucleotide polymorphisms, and 2 multi-single nucleotide polymorphism models identified quantitative trait loci not found by a single nucleotide polymorphism-by-single nucleotide polymorphism model. Overall, 489 reliable quantitative trait loci were detected for 41% more response variables than by a single nucleotide polymorphism-by-single nucleotide polymorphism model with microarray-only single nucleotide polymorphisms, many new ones compared with the results from bi-parental crosses. A prediction accuracy higher than 0.42 was obtained for 50% of the response variables. Our overall approach as well as quantitative trait locus and prediction results provide insights into the genetic architecture of target traits. New candidate genes and the application into breeding are discussed.
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Affiliation(s)
- Timothée Flutre
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France.,Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190 Gif-sur-Yvette, France
| | - Loïc Le Cunff
- UMT Géno-Vigne, 34398 Montpellier, France.,IFV, 30240 Le Grau-du-Roi, France
| | - Agota Fodor
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Amandine Launay
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Charles Romieu
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Gilles Berger
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Yves Bertrand
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Nancy Terrier
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France
| | | | | | - Maryline Roques
- UMT Géno-Vigne, 34398 Montpellier, France.,IFV, 30240 Le Grau-du-Roi, France
| | - Lucie Pinasseau
- SPO, Univ Montpellier, INRAE, Institut Agro, 34060 Montpellier, France
| | - Arnaud Verbaere
- SPO, Univ Montpellier, INRAE, Institut Agro, 34060 Montpellier, France
| | - Nicolas Sommerer
- SPO, Univ Montpellier, INRAE, Institut Agro, 34060 Montpellier, France
| | | | - Roberto Bacilieri
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Jean-Michel Boursiquot
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Thierry Lacombe
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Valérie Laucou
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Patrice This
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Jean-Pierre Péros
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Agnès Doligez
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
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3
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Péros JP, Cousins P, Launay A, Cubry P, Walker A, Prado E, Peressotti E, Wiedemann-Merdinoglu S, Laucou V, Merdinoglu D, This P, Boursiquot JM, Doligez A. Genetic diversity and population structure in Vitis species illustrate phylogeographic patterns in eastern North America. Mol Ecol 2021; 30:2333-2348. [PMID: 33710711 DOI: 10.1111/mec.15881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 02/22/2021] [Accepted: 03/02/2021] [Indexed: 12/21/2022]
Abstract
Geographical distribution and diversity of current plant species have been strongly shaped by climatic oscillations during the Quaternary. Analysing the resulting divergence among species and differentiation within species is crucial to understand the evolution of taxa like the Vitis genus, which provides very useful genetic resources for grapevine improvement and might reveal original recolonization patterns due to growth habit and dispersal mode. Here, we studied the genetic structure in natural populations of three species from eastern North America: Vitis aestivalis, V. cinerea and V. riparia using different marker types. Vitis aestivalis and V. cinerea showed higher diversity than V. riparia. The two former species are less differentiated, confirming an earlier divergence of V. riparia. V. aestivalis and V. riparia exhibited different genetic groups on both sides of the Appalachian Mountains that could mirror different recolonization routes from southern refugia. Genetic structure was stronger in V. cinerea, for which two varieties (var. berlandieri and var. cinerea) are morphologically recognized. Our results confirm this distinction and suggest the existence of three other lineages within var. cinerea. These discontinuities appear linked to adaptation of var. berlandieri to dry and limy areas of Texas and partially to the Mississippi River Valley. Rapid range expansions from refugia upon climate warming are also suggested by the low linkage disequilibrium values observed. Furthermore, large variation for downy mildew resistance was observed in the three species. Our findings appeared consistent with the vegetation history of eastern North America.
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Affiliation(s)
- Jean-Pierre Péros
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | | | - Amandine Launay
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Philippe Cubry
- UMR DIADE, University of Montpellier, IRD, Montpellier, France
| | - Andy Walker
- Department of Viticulture and Enology, University of Davis, Davis, CA, USA
| | | | | | | | - Valérie Laucou
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | | | - Patrice This
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Jean-Michel Boursiquot
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Agnès Doligez
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
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4
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Candresse T, Marais A, Faure C, Lefebvre M, Lacombe T, Boursiquot JM. Complete genome sequence of a novel grapevine-infecting member of the genus Polerovirus, grapevine polerovirus 1. Arch Virol 2020; 165:1683-1685. [PMID: 32372367 DOI: 10.1007/s00705-020-04640-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/28/2020] [Indexed: 10/24/2022]
Abstract
Double-stranded RNAs and total RNAs purified from grapevine (Vitis vinifera) phloem scrapings of two varieties held in the INRAE (France) grapevine germplasm collection were analyzed by high-throughput sequencing. BLAST annotation revealed contigs with homology to Polerovirus genus members. The full genome sequence of one isolate (KT) was determined (5651 nucleotides [nt]), and a partial sequence representing about half of the genome was assembled for a second isolate (KS) that was found to share 95% nt sequence identity with the KT isolate. The genome has a typical polerovirus organization, containing six open reading frames (ORFs) as well as a putative additional ORF3a. Based on genome organization and phylogenetic relationships, the new virus belongs to the genus Polerovirus but, similar to the recently described persimmon polerovirus 1, is characterized by a highly divergent coat-protein/readthrough domain. Considering the species demarcation criteria for the family Luteoviridae, these two isolates, together with a closely related sequence recently deposited in the GenBank database (LC507098), represent a new Polerovirus species for which the name "Grapevine polerovirus 1" is proposed.
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Affiliation(s)
- T Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, 72 Avenue Edouard Bourlaux, CS20032, 33882, Villenave d'Ornon cedex, France.
| | - A Marais
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, 72 Avenue Edouard Bourlaux, CS20032, 33882, Villenave d'Ornon cedex, France
| | - C Faure
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, 72 Avenue Edouard Bourlaux, CS20032, 33882, Villenave d'Ornon cedex, France
| | - M Lefebvre
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, 72 Avenue Edouard Bourlaux, CS20032, 33882, Villenave d'Ornon cedex, France
| | - T Lacombe
- UMR AGAP, INRAE, Montpellier SupAgro, TA A-108/03 Avenue Agropolis, 34398, Montpellier Cedex 5, France
- Centre de Ressources Biologiques de la Vigne, INRAE, 34340, Marseillan-Plage, France
| | - J M Boursiquot
- UMR AGAP, INRAE, Montpellier SupAgro, TA A-108/03 Avenue Agropolis, 34398, Montpellier Cedex 5, France
- Centre de Ressources Biologiques de la Vigne, INRAE, 34340, Marseillan-Plage, France
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5
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Riaz S, Pap D, Uretsky J, Laucou V, Boursiquot JM, Kocsis L, Andrew Walker M. Genetic diversity and parentage analysis of grape rootstocks. Theor Appl Genet 2019; 132:1847-1860. [PMID: 30848297 DOI: 10.1007/s00122-019-03320-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 02/27/2019] [Indexed: 05/06/2023]
Abstract
The maternal and paternal parentage of 36 rootstocks was determined and verified. The results of this study indicate that existing grape rootstocks are closely related to each other and have a narrow genetic background. Rootstocks are used to protect grapevines from biotic and abiotic stresses including phylloxera, nematodes, viruses, limestone-based soils, salinity and drought. The most important rootstocks were developed from three grape species between the 1890s and the 1930s in European breeding programs. In this report, we developed nuclear and chloroplast SSR fingerprint data from rootstock selections maintained in germplasm collections, compared them to develop a reference dataset, and carried out parentage analysis to resolve previously reported, and determine new, breeding records. We refined and updated the parentage of 26 rootstocks based on 21 nuclear and 14 chloroplast markers. Results indicate that 39% of the genetic background of analyzed rootstocks originated from only three accessions of three grape species: Vitis berlandieri cv. Rességuier 2, V. rupestris cv. du Lot and V. riparia cv. Gloire de Montpellier. Results determined that Rességuier 2 is the maternal parent for 14 commercial rootstocks, 9 of which are full-sibs with Gloire de Montpellier as the paternal parent. Similarly, du Lot is the paternal parent of nine rootstocks. The pedigree information for 28 rootstocks was determined or corrected in this study. The previously reported pedigree information for eight of the rootstocks was correct. The results found that the world's existing rootstocks have a narrow genetic base derived from only a few American grape species. Future rootstock breeding efforts should use a more diverse array of species to combat a changing climate and pest pressure.
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Affiliation(s)
- Summaira Riaz
- Department of Viticulture and Enology, University of California, Davis, CA, 95616, USA
| | - Daniel Pap
- Department of Viticulture and Enology, University of California, Davis, CA, 95616, USA
| | - Jake Uretsky
- Department of Viticulture and Enology, University of California, Davis, CA, 95616, USA
| | - Valérie Laucou
- Equipe DAAV, UMR AGAP, INRA, Montpellier SupAgro, CIRAD, Univ. Montpellier, 34060, Montpellier, France
| | - Jean-Michel Boursiquot
- Equipe DAAV, UMR AGAP, INRA, Montpellier SupAgro, CIRAD, Univ. Montpellier, 34060, Montpellier, France
| | - László Kocsis
- Department of Horticulture, Georgikon Faculty, University of Pannonia, Keszthely, 8360, Hungary
| | - M Andrew Walker
- Department of Viticulture and Enology, University of California, Davis, CA, 95616, USA.
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6
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Bigard A, Berhe DT, Maoddi E, Sire Y, Boursiquot JM, Ojeda H, Péros JP, Doligez A, Romieu C, Torregrosa L. Vitis vinifera L. Fruit Diversity to Breed Varieties Anticipating Climate Changes. Front Plant Sci 2018; 9:455. [PMID: 29765379 PMCID: PMC5938353 DOI: 10.3389/fpls.2018.00455] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 03/22/2018] [Indexed: 05/04/2023]
Abstract
The wine industry is facing critical issues due to climate changes since production is established on very tight Genotype × Environment interaction bases. While, some cultivation practices may reduce adverse effects of abiotic stresses on the vines, e.g., the use of irrigation to mitigate drought, the deleterious impacts of warming on fruit development are difficult to manage. Elevated temperature alters grapevine fruit growth and composition, with a critical increase of the sugars/organic acids ratio. Select grapes with improved metabolite balances to offset high temperature effects is a valuable option to sustain viticulture. Unfortunately, the lack of knowledge about the genetic diversity for fruit traits impacted by temperature impairs the design of breeding programs. This study aimed to assess the variation in berry volume, main sugars and organic acids amounts in genetic resources. Fruit phenotyping focused on two critical stages of development: the end of green lag phase when organic acidity reaches its maximum, and the ripe stage when sugar unloading and water uptake stop. For that purpose, we studied a panel of 33 genotypes, including 12 grapevine varieties and 21 microvine offspring. To determine the date of sampling for each critical stage, fruit texture and growth were carefully monitored. Analyses at both stages revealed large phenotypic variation for malic and tartaric acids, as well as for sugars and berry size. At ripe stage, fruit fresh weight ranged from 1.04 to 5.25 g and sugar concentration from 751 to 1353 mmol.L-1. The content in organic acids varied both in quantity (from 80 to 361 meq.L-1) and in composition, with malic to tartaric acid ratio ranging from 0.13 to 3.62. At the inter-genotypic level, data showed no link between berry growth and osmoticum accumulation per fruit unit, suggesting that berry water uptake is not dependent only on fruit osmotic potential. Diversity among varieties for berry size, sugar accumulation and malic to tartaric acid ratio could be exploited through cross-breeding. This provides interesting prospects for improving grapevine to mitigate some adverse effects of climate warming on grapevine fruit volume and quality.
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Affiliation(s)
- Antoine Bigard
- AGAP, University of Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- UE INRA de Pech-Rouge, University of Montpellier, INRA, Montpellier, France
| | - Dargie T Berhe
- UE INRA de Pech-Rouge, University of Montpellier, INRA, Montpellier, France
- SNNPRS, Dilla University, Dilla, Ethiopia
| | - Eleonora Maoddi
- AGAP, University of Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Yannick Sire
- UE INRA de Pech-Rouge, University of Montpellier, INRA, Montpellier, France
| | | | - Hernan Ojeda
- UE INRA de Pech-Rouge, University of Montpellier, INRA, Montpellier, France
- UE INRA de Vassal, Grapevine Biological Resource Centre, University of Montpellier, INRA, Montpellier, France
| | - Jean-Pierre Péros
- AGAP, University of Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Agnès Doligez
- AGAP, University of Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Charles Romieu
- AGAP, University of Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Laurent Torregrosa
- AGAP, University of Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- UE INRA de Pech-Rouge, University of Montpellier, INRA, Montpellier, France
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7
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Laucou V, Launay A, Bacilieri R, Lacombe T, Adam-Blondon AF, Bérard A, Chauveau A, de Andrés MT, Hausmann L, Ibáñez J, Le Paslier MC, Maghradze D, Martinez-Zapater JM, Maul E, Ponnaiah M, Töpfer R, Péros JP, Boursiquot JM. Extended diversity analysis of cultivated grapevine Vitis vinifera with 10K genome-wide SNPs. PLoS One 2018; 13:e0192540. [PMID: 29420602 PMCID: PMC5805323 DOI: 10.1371/journal.pone.0192540] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 01/25/2018] [Indexed: 12/18/2022] Open
Abstract
Grapevine is a very important crop species that is mainly cultivated worldwide for fruits, wine and juice. Identification of the genetic bases of performance traits through association mapping studies requires a precise knowledge of the available diversity and how this diversity is structured and varies across the whole genome. An 18k SNP genotyping array was evaluated on a panel of Vitis vinifera cultivars and we obtained a data set with no missing values for a total of 10207 SNPs and 783 different genotypes. The average inter-SNP spacing was ~47 kbp, the mean minor allele frequency (MAF) was 0.23 and the genetic diversity in the sample was high (He = 0.32). Fourteen SNPs, chosen from those with the highest MAF values, were sufficient to identify each genotype in the sample. Parentage analysis revealed 118 full parentages and 490 parent-offspring duos, thus confirming the close pedigree relationships within the cultivated grapevine. Structure analyses also confirmed the main divisions due to an eastern-western gradient and human usage (table vs. wine). Using a multivariate approach, we refined the structure and identified a total of eight clusters. Both the genetic diversity (He, 0.26-0.32) and linkage disequilibrium (LD, 28.8-58.2 kbp) varied between clusters. Despite the short span LD, we also identified some non-recombining haplotype blocks that may complicate association mapping. Finally, we performed a genome-wide association study that confirmed previous works and also identified new regions for important performance traits such as acidity. Taken together, all the results contribute to a better knowledge of the genetics of the cultivated grapevine.
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Affiliation(s)
- Valérie Laucou
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Amandine Launay
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Roberto Bacilieri
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Thierry Lacombe
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.,INRA Unité Expérimentale de Vassal, Centre de Ressources Biologiques de la Vigne, Marseillan-plage, France
| | | | - Aurélie Bérard
- EPGV, Univ Paris-Saclay, CEA, IG-CNG, INRA, Evry, France
| | | | | | - Ludger Hausmann
- JKI, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Javier Ibáñez
- ICVV, CSIC, Universidad de La Rioja, Gobierno de la Rioja, Logroño, Spain
| | | | | | | | - Erika Maul
- JKI, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Maharajah Ponnaiah
- EPGV, Univ Paris-Saclay, CEA, IG-CNG, INRA, Evry, France.,LBD, Univ UPMC, CNRS, INSERM, Paris, France
| | - Reinhard Töpfer
- JKI, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Jean-Pierre Péros
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Jean-Michel Boursiquot
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.,INRA Unité Expérimentale de Vassal, Centre de Ressources Biologiques de la Vigne, Marseillan-plage, France
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8
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Chalak L, Touma JA, Touma S, Rahme S, Azzi R, Guiberteau F, Boursiquot JM. Erratum to: Assessment of the Lebanese grapevine germplasm reveals a substantial diversity and a high potential for selection. BIO Web of Conferences 2016. [DOI: 10.1051/bioconf/20160701045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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9
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Champ J, Lorieul T, Bonnet P, Maghnaoui N, Sereno C, Dessup T, Boursiquot JM, Audeguin L, Lacombe T, Joly A. Categorizing plant images at the variety level: Did you say fine-grained? Pattern Recognit Lett 2016. [DOI: 10.1016/j.patrec.2016.05.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Boursiquot JM, Laucou V, Llorente A, Lacombe T. Identification of grapevine accessions from Argentina introduced in the ampelographic collection of Domaine de Vassal. BIO Web of Conferences 2015. [DOI: 10.1051/bioconf/20140301019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Riaz S, Boursiquot JM, Dangl GS, Lacombe T, Laucou V, Tenscher AC, Walker MA. Identification of mildew resistance in wild and cultivated Central Asian grape germplasm. BMC Plant Biol 2013; 13:149. [PMID: 24093598 PMCID: PMC3851849 DOI: 10.1186/1471-2229-13-149] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 09/30/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND Cultivated grapevines, Vitis vinifera subsp. sativa, evolved from their wild relative, V. vinifera subsp. sylvestris. They were domesticated in Central Asia in the absence of the powdery mildew fungus, Erysiphe necator, which is thought to have originated in North America. However, powdery mildew resistance has previously been discovered in two Central Asian cultivars and in Chinese Vitis species. RESULTS A set of 380 unique genotypes were evaluated with data generated from 34 simple sequence repeat (SSR) markers. The set included 306 V. vinifera cultivars, 40 accessions of V. vinifera subsp. sylvestris, and 34 accessions of Vitis species from northern Pakistan, Afghanistan and China. Based on the presence of four SSR alleles previously identified as linked to the powdery mildew resistance locus, Ren1, 10 new mildew resistant genotypes were identified in the test set: eight were V. vinifera cultivars and two were V. vinifera subsp. sylvestris based on flower and seed morphology. Sequence comparison of a 620 bp region that includes the Ren1-linked allele (143 bp) of the co-segregating SSR marker SC8-0071-014, revealed that the ten newly identified genotypes have sequences that are essentially identical to the previously identified mildew resistant V. vinifera cultivars: 'Kishmish vatkana' and 'Karadzhandal'. Kinship analysis determined that three of the newly identified powdery mildew resistant accessions had a relationship with 'Kishmish vatkana' and 'Karadzhandal', and that six were not related to any other accession in this study set. Clustering procedures assigned accessions into three groups: 1) Chinese species; 2) a mixed group of cultivated and wild V. vinifera; and 3) table grape cultivars, including nine of the powdery mildew resistant accessions. Gene flow was detected among the groups. CONCLUSIONS This study provides evidence that powdery mildew resistance is present in V. vinifera subsp. sylvestris, the dioecious wild progenitor of the cultivated grape. Four first-degree parent progeny relationships were discovered among the hermaphroditic powdery mildew resistant cultivars, supporting the existence of intentional grape breeding efforts. Although several Chinese grape species are resistant to powdery mildew, no direct genetic link to the resistance found in V. vinifera could be established.
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Affiliation(s)
- Summaira Riaz
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA
| | - Jean-Michel Boursiquot
- UMR AGAP, Equipe Diversité et Adaptation de la Vigne et des Espèces Méditerranéennes, Montpellier SupAgro, 2 Place Viala, Montpellier 34060, France
| | - Gerald S Dangl
- Foundation Plant Services, University of California, Davis, CA 95616, USA
| | - Thierry Lacombe
- UMR AGAP, Equipe Diversité et Adaptation de la Vigne et des Espèces Méditerranéennes, INRA, 2 Place Viala, Montpellier 34060, France
| | - Valerie Laucou
- UMR AGAP, Equipe Diversité et Adaptation de la Vigne et des Espèces Méditerranéennes, INRA, 2 Place Viala, Montpellier 34060, France
| | - Alan C Tenscher
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA
| | - M Andrew Walker
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA
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Bacilieri R, Lacombe T, Le Cunff L, Di Vecchi-Staraz M, Laucou V, Genna B, Péros JP, This P, Boursiquot JM. Genetic structure in cultivated grapevines is linked to geography and human selection. BMC Plant Biol 2013; 13:25. [PMID: 23394135 PMCID: PMC3598926 DOI: 10.1186/1471-2229-13-25] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 01/31/2013] [Indexed: 05/19/2023]
Abstract
BACKGROUND Grapevine (Vitis vinifera subsp. vinifera) is one of the most important and ancient horticultural plants in the world. Domesticated about 8-10,000 years ago in the Eurasian region, grapevine evolved from its wild relative (V. vinifera subsp. sylvestris) into very diverse and heterozygous cultivated forms. In this work we study grapevine genetic structure in a large sample of cultivated varieties, to interpret the wide diversity at morphological and molecular levels and link it to cultivars utilization, putative geographic origin and historical events. RESULTS We analyzed the genetic structure of cultivated grapevine using a dataset of 2,096 multi-locus genotypes defined by 20 microsatellite markers. We used the Bayesian approach implemented in the STRUCTURE program and a hierarchical clustering procedure based on Ward's method to assign individuals to sub-groups. The analysis revealed three main genetic groups defined by human use and geographic origin: a) wine cultivars from western regions, b) wine cultivars from the Balkans and East Europe, and c) a group mainly composed of table grape cultivars from Eastern Mediterranean, Caucasus, Middle and Far East countries. A second structure level revealed two additional groups, a geographic group from the Iberian Peninsula and Maghreb, and a group comprising table grapes of recent origins from Italy and Central Europe. A large number of admixed genotypes were also identified. Structure clusters regrouped together a large proportion of family-related genotypes. In addition, Ward's method revealed a third level of structure, corresponding either to limited geographic areas, to particular grape use or to family groups created through artificial selection and breeding. CONCLUSIONS This study provides evidence that the cultivated compartment of Vitis vinifera L. is genetically structured. Genetic relatedness of cultivars has been shaped mostly by human uses, in combination with a geographical effect. The finding of a large portion of admixed genotypes may be the trace of both large human-mediated exchanges between grape-growing regions throughout history and recent breeding.
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Affiliation(s)
- Roberto Bacilieri
- Institut National de la Recherche Agronomique, UMR 1334 AGAP Amélioration génétique et adaptation de plantes, équipe DAVEM, 2 Place P. Viala, 34060, Montpellier, France
| | - Thierry Lacombe
- Institut National de la Recherche Agronomique, UMR 1334 AGAP Amélioration génétique et adaptation de plantes, équipe DAVEM, 2 Place P. Viala, 34060, Montpellier, France
- INRA - Domaine de Vassal. Ancienne route de Sète, 34340, Marseillan Plage, France
| | - Loïc Le Cunff
- Institut Français de la Vigne et du Vin - Unité Mixte Technologique Géno-Vigne, 2 Place P. Viala, 34060, Montpellier, France
| | - Manuel Di Vecchi-Staraz
- Institut National de la Recherche Agronomique, UMR 1334 AGAP Amélioration génétique et adaptation de plantes, équipe DAVEM, 2 Place P. Viala, 34060, Montpellier, France
| | - Valérie Laucou
- Institut National de la Recherche Agronomique, UMR 1334 AGAP Amélioration génétique et adaptation de plantes, équipe DAVEM, 2 Place P. Viala, 34060, Montpellier, France
| | - Blaise Genna
- INRA - Domaine de Vassal. Ancienne route de Sète, 34340, Marseillan Plage, France
| | - Jean-Pierre Péros
- Institut National de la Recherche Agronomique, UMR 1334 AGAP Amélioration génétique et adaptation de plantes, équipe DAVEM, 2 Place P. Viala, 34060, Montpellier, France
| | - Patrice This
- Institut National de la Recherche Agronomique, UMR 1334 AGAP Amélioration génétique et adaptation de plantes, équipe DAVEM, 2 Place P. Viala, 34060, Montpellier, France
| | - Jean-Michel Boursiquot
- Montpellier SupAgro, UMR 1334 AGAP Amélioration génétique et adaptation de plantes, équipe DAVEM, 2 Place P. Viala, 34060, Montpellier, France
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13
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Lacombe T, Boursiquot JM, Laucou V, Di Vecchi-Staraz M, Péros JP, This P. Large-scale parentage analysis in an extended set of grapevine cultivars (Vitis vinifera L.). Theor Appl Genet 2013; 126:401-14. [PMID: 23015217 DOI: 10.1007/s00122-012-1988-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 09/15/2012] [Indexed: 05/06/2023]
Abstract
Inheritance of nuclear microsatellite markers (nSSR) has been proved to be a powerful tool to verify or uncover the parentage of grapevine cultivars. The aim of the present study was to undertake an extended parentage analysis using a large sample of Vitis vinifera cultivars held in the INRA "Domaine de Vassal" Grape Germplasm Repository (France). A dataset of 2,344 unique genotypes (i.e. cultivars without synonyms, clones or mutants) identified using 20 nSSR was analysed with FAMOZ software. Parentages showing a logarithm of odds score higher than 18 were validated in relation to the historical data available. The analysis first revealed the full parentage of 828 cultivars resulting in: (1) 315 original full parentages uncovered for traditional cultivars, (2) 100 full parentages confirming results established with molecular markers in prior papers and 32 full parentages that invalidated prior results, (3) 255 full parentages confirming pedigrees as disclosed by the breeders and (4) 126 full parentages that invalidated breeders' data. Second, incomplete parentages were determined in 1,087 cultivars due to the absence of complementary parents in our cultivar sample. Last, a group of 276 genotypes showed no direct relationship with any other cultivar in the collection. Compiling these results from the largest set of parentage data published so far both enlarges and clarifies our knowledge of the genetic constitution of cultivated V. vinifera germplasm. It also allows the identification of the main genitors involved in varietal assortment evolution and grapevine breeding.
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Affiliation(s)
- Thierry Lacombe
- UMR AGAP, Equipe Diversité et Adaptation de la Vigne et des Espèces Méditerranéennes, INRA, 2 Place Viala, 34060 Montpellier, France.
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Carrier G, Le Cunff L, Dereeper A, Legrand D, Sabot F, Bouchez O, Audeguin L, Boursiquot JM, This P. Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L. PLoS One 2012; 7:e32973. [PMID: 22427919 PMCID: PMC3299709 DOI: 10.1371/journal.pone.0032973] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 02/06/2012] [Indexed: 12/22/2022] Open
Abstract
Through multiple vegetative propagation cycles, clones accumulate mutations in somatic cells that are at the origin of clonal phenotypic diversity in grape. Clonal diversity provided clones such as Cabernet-Sauvignon N°470, Chardonnay N° 548 and Pinot noir N° 777 which all produce wines of superior quality. The economic impact of clonal selection is therefore very high: since approx. 95% of the grapevines produced in French nurseries originate from the French clonal selection. In this study we provide the first broad description of polymorphism in different clones of a single grapevine cultivar, Pinot noir, in the context of vegetative propagation. Genome sequencing was performed using 454 GS-FLX methodology without a priori, in order to identify and quantify for the first time molecular polymorphisms responsible for clonal variability in grapevine. New generation sequencing (NGS) was used to compare a large portion of the genome of three Pinot noir clones selected for their phenotypic differences. Reads obtained with NGS and the sequence of Pinot noir ENTAV-INRA® 115 sequenced by Velasco et al., were aligned on the PN40024 reference sequence. We then searched for molecular polymorphism between clones. Three types of polymorphism (SNPs, Indels, mobile elements) were found but insertion polymorphism generated by mobile elements of many families displayed the highest mutational event with respect to clonal variation. Mobile elements inducing insertion polymorphism in the genome of Pinot noir were identified and classified and a list is presented in this study as potential markers for the study of clonal variation. Among these, the dynamic of four mobile elements with a high polymorphism level were analyzed and insertion polymorphism was confirmed in all the Pinot clones registered in France.
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Affiliation(s)
- Grégory Carrier
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France.
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15
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Mejía N, Soto B, Guerrero M, Casanueva X, Houel C, de los Ángeles Miccono M, Ramos R, Le Cunff L, Boursiquot JM, Hinrichsen P, Adam-Blondon AF. Molecular, genetic and transcriptional evidence for a role of VvAGL11 in stenospermocarpic seedlessness in grapevine. BMC Plant Biol 2011; 11:57. [PMID: 21447172 PMCID: PMC3076230 DOI: 10.1186/1471-2229-11-57] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 03/29/2011] [Indexed: 05/19/2023]
Abstract
BACKGROUND Stenospermocarpy is a mechanism through which certain genotypes of Vitis vinifera L. such as Sultanina produce berries with seeds reduced in size. Stenospermocarpy has not yet been characterized at the molecular level. RESULTS Genetic and physical maps were integrated with the public genomic sequence of Vitis vinifera L. to improve QTL analysis for seedlessness and berry size in experimental progeny derived from a cross of two seedless genotypes. Major QTLs co-positioning for both traits on chromosome 18 defined a 92-kb confidence interval. Functional information from model species including Vitis suggested that VvAGL11, included in this confidence interval, might be the main positional candidate gene responsible for seed and berry development.Characterization of VvAGL11 at the sequence level in the experimental progeny identified several SNPs and INDELs in both regulatory and coding regions. In association analyses performed over three seasons, these SNPs and INDELs explained up to 78% and 44% of the phenotypic variation in seed and berry weight, respectively. Moreover, genetic experiments indicated that the regulatory region has a larger effect on the phenotype than the coding region. Transcriptional analysis lent additional support to the putative role of VvAGL11's regulatory region, as its expression is abolished in seedless genotypes at key stages of seed development. These results transform VvAGL11 into a functional candidate gene for further analyses based on genetic transformation.For breeding purposes, intragenic markers were tested individually for marker assisted selection, and the best markers were those closest to the transcription start site. CONCLUSION We propose that VvAGL11 is the major functional candidate gene for seedlessness, and we provide experimental evidence suggesting that the seedless phenotype might be caused by variations in its promoter region. Current knowledge of the function of its orthologous genes, its expression profile in Vitis varieties and the strong association between its sequence variation and the degree of seedlessness together indicate that the D-lineage MADS-box gene VvAGL11 corresponds to the Seed Development Inhibitor locus described earlier as a major locus for seedlessness. These results provide new hypotheses for further investigations of the molecular mechanisms involved in seed and berry development.
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Affiliation(s)
- Nilo Mejía
- Biotechnology Unit, La Platina Experimental Station, INIA, Av. Santa Rosa 11610, 8831314, Santiago, Chile
| | - Braulio Soto
- Biotechnology Unit, La Platina Experimental Station, INIA, Av. Santa Rosa 11610, 8831314, Santiago, Chile
| | - Marcos Guerrero
- Biotechnology Unit, La Platina Experimental Station, INIA, Av. Santa Rosa 11610, 8831314, Santiago, Chile
| | - Ximena Casanueva
- Biotechnology Unit, La Platina Experimental Station, INIA, Av. Santa Rosa 11610, 8831314, Santiago, Chile
| | - Cléa Houel
- UMR INRA CNRS University of Evry on Plant Genomics, 2 rue Gaston Crémieux, BP 5708, 91057, Evry, France
| | | | - Rodrigo Ramos
- Biotechnology Unit, La Platina Experimental Station, INIA, Av. Santa Rosa 11610, 8831314, Santiago, Chile
| | - Loïc Le Cunff
- INRA - Montpellier SupAgro, UMR 1097, Equipe Diversité Génétique et Génomique Vigne, 2 place P. Viala, F-34060 Montpellier Cedex 1, France
| | - Jean-Michel Boursiquot
- INRA - Montpellier SupAgro, UMR 1097, Equipe Diversité Génétique et Génomique Vigne, 2 place P. Viala, F-34060 Montpellier Cedex 1, France
| | - Patricio Hinrichsen
- Biotechnology Unit, La Platina Experimental Station, INIA, Av. Santa Rosa 11610, 8831314, Santiago, Chile
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16
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Carrier G, Santoni S, Rodier-Goud M, Canaguier A, Kochko AD, Dubreuil-Tranchant C, This P, Boursiquot JM, Le Cunff L. An efficient and rapid protocol for plant nuclear DNA preparation suitable for next generation sequencing methods. Am J Bot 2011; 98:e13-5. [PMID: 21613076 DOI: 10.3732/ajb.1000371] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
PREMISE OF THE STUDY In this study, we developed a nuclear DNA extraction protocol for Next Generation Sequencers (NGS). METHODS AND RESULTS We applied this extraction method to grapevines and coffee trees, which are known to contain many secondary metabolites. The nuclear DNA obtained was sequenced by the 454/GS-FLX method. We obtained excellent results, with less than 4% cytoplasmic DNA, in a similar way to a BAC (Bacterial Artificial Chromosome)-building protocol. We also compared our protocol with a classic DNA extraction using specific cytoplasmic DNA amplification. Results showed a lower cytoplasmic DNA contamination with the new protocol. CONCLUSIONS The method presented here is fast and economical. The DNA obtained is of high quality, with a low level of cytoplasmic DNA contamination, and very efficient for the construction of sequencing libraries.
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Affiliation(s)
- Gregory Carrier
- UMT Geno-Vigne, IFV-INRA-Montpellier Supagro, 2 place Viala, Montpellier, France.
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17
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Emanuelli F, Battilana J, Costantini L, Le Cunff L, Boursiquot JM, This P, Grando MS. A candidate gene association study on muscat flavor in grapevine (Vitis vinifera L.). BMC Plant Biol 2010; 10:241. [PMID: 21062440 PMCID: PMC3095323 DOI: 10.1186/1471-2229-10-241] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 11/09/2010] [Indexed: 05/20/2023]
Abstract
BACKGROUND The sweet, floral flavor typical of Muscat varieties (Muscats), due to high levels of monoterpenoids (geraniol, linalool and nerol), is highly distinct and has been greatly appreciated both in table grapes and in wine since ancient times. Muscat flavor determination in grape (Vitis vinifera L.) has up to now been studied by evaluating monoterpenoid levels through QTL analysis. These studies have revealed co-localization of 1-deoxy-D-xylulose 5-phosphate synthase (VvDXS) with the major QTL positioned on chromosome 5. RESULTS We resequenced VvDXS in an ad hoc association population of 148 grape varieties, which included muscat-flavored, aromatic and neutral accessions as well as muscat-like aromatic mutants and non-aromatic offsprings of Muscats. Gene nucleotide diversity and intragenic linkage disequilibrium (LD) were evaluated. Structured association analysis revealed three SNPs in moderate LD to be significantly associated with muscat-flavored varieties. We identified a putative causal SNP responsible for a predicted non-neutral substitution and we discuss its possible implications for flavor metabolism. Network analysis revealed a major star-shaped cluster of reconstructed haplotypes unique to muscat-flavored varieties. Moreover, muscat-like aromatic mutants displayed unique non-synonymous mutations near the mutated site of Muscat genotypes. CONCLUSIONS This study is a crucial step forward in understanding the genetic regulation of muscat flavor in grapevine and it also sheds light on the domestication history of Muscats. VvDXS appears to be a possible human-selected locus in grapevine domestication and post-domestication. The putative causal SNP identified in Muscat varieties as well as the unique mutations identifying the muscat-like aromatic mutants under study may be immediately applied in marker-assisted breeding programs aimed at enhancing fragrance and aroma complexity respectively in table grape and wine cultivars.
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Affiliation(s)
- Francesco Emanuelli
- Research and Innovation Center, Fondazione Edmund Mach-Istituto Agrario di San Michele all'Adige, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Juri Battilana
- Research and Innovation Center, Fondazione Edmund Mach-Istituto Agrario di San Michele all'Adige, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Laura Costantini
- Research and Innovation Center, Fondazione Edmund Mach-Istituto Agrario di San Michele all'Adige, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Loïc Le Cunff
- INRA UMR 1097 Diversité et Adaptation des Plantes Cultivées, 2 place Viala, 34060, Montpellier, France
- UMT GenoVigne®, IFV-INRA-Montpellier Supagro, 2 place Viala, 34060, Montpellier, France
| | - Jean-Michel Boursiquot
- INRA UMR 1097 Diversité et Adaptation des Plantes Cultivées, 2 place Viala, 34060, Montpellier, France
| | - Patrice This
- INRA UMR 1097 Diversité et Adaptation des Plantes Cultivées, 2 place Viala, 34060, Montpellier, France
| | - Maria S Grando
- Research and Innovation Center, Fondazione Edmund Mach-Istituto Agrario di San Michele all'Adige, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
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Le Cunff L, Fournier-Level A, Laucou V, Vezzulli S, Lacombe T, Adam-Blondon AF, Boursiquot JM, This P. Construction of nested genetic core collections to optimize the exploitation of natural diversity in Vitis vinifera L. subsp. sativa. BMC Plant Biol 2008; 8:31. [PMID: 18384667 PMCID: PMC2375891 DOI: 10.1186/1471-2229-8-31] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Accepted: 04/02/2008] [Indexed: 05/03/2023]
Abstract
BACKGROUND The first high quality draft of the grape genome sequence has just been published. This is a critical step in accessing all the genes of this species and increases the chances of exploiting the natural genetic diversity through association genetics. However, our basic knowledge of the extent of allelic variation within the species is still not sufficient. Towards this goal, we constructed nested genetic core collections (G-cores) to capture the simple sequence repeat (SSR) diversity of the grape cultivated compartment (Vitis vinifera L. subsp. sativa) from the world's largest germplasm collection (Domaine de Vassal, INRA Hérault, France), containing 2262 unique genotypes. RESULTS Sub-samples of 12, 24, 48 and 92 varieties of V. vinifera L. were selected based on their genotypes for 20 SSR markers using the M-strategy. They represent respectively 58%, 73%, 83% and 100% of total SSR diversity. The capture of allelic diversity was analyzed by sequencing three genes scattered throughout the genome on 233 individuals: 41 single nucleotide polymorphisms (SNPs) were identified using the G-92 core (one SNP for every 49 nucleotides) while only 25 were observed using a larger sample of 141 individuals selected on the basis of 50 morphological traits, thus demonstrating the reliability of the approach. CONCLUSION The G-12 and G-24 core-collections displayed respectively 78% and 88% of the SNPs respectively, and are therefore of great interest for SNP discovery studies. Furthermore, the nested genetic core collections satisfactorily reflected the geographic and the genetic diversity of grape, which are also of great interest for the study of gene evolution in this species.
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Affiliation(s)
- Loïc Le Cunff
- UMR 1097 DIA-PC, Equipe « génétique Vigne », INRA-Supagro, 2 place Viala, F-34060 Montpellier, France
| | - Alexandre Fournier-Level
- UMR 1097 DIA-PC, Equipe « génétique Vigne », INRA-Supagro, 2 place Viala, F-34060 Montpellier, France
| | - Valérie Laucou
- UMR 1097 DIA-PC, Equipe « génétique Vigne », INRA-Supagro, 2 place Viala, F-34060 Montpellier, France
| | - Silvia Vezzulli
- IASMA Research Center, 38010 San Michele all'Adige (TN), Italy
| | - Thierry Lacombe
- UMR 1097 DIA-PC, Equipe « génétique Vigne », INRA-Supagro, 2 place Viala, F-34060 Montpellier, France
| | - Anne-Françoise Adam-Blondon
- UMR 1165 INRA-CNRS-Université d'Evry Génomique Végétale, 2, rue Gaston Crémieux CP 5708, F-91057 EVRY cedex, France
| | - Jean-Michel Boursiquot
- UMR 1097 DIA-PC, Equipe « génétique Vigne », INRA-Supagro, 2 place Viala, F-34060 Montpellier, France
| | - Patrice This
- UMR 1097 DIA-PC, Equipe « génétique Vigne », INRA-Supagro, 2 place Viala, F-34060 Montpellier, France
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Aradhya MK, Dangl GS, Prins BH, Boursiquot JM, Walker MA, Meredith CP, Simon CJ. Genetic structure and differentiation in cultivated grape, Vitis vinifera L. Genet Res (Camb) 2003; 81:179-92. [PMID: 12929909 DOI: 10.1017/s0016672303006177] [Citation(s) in RCA: 193] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
222 cultivated (Vitis vinifera) and 22 wild (V. vinifera ssp. sylvestris) grape accessions were analysed for genetic diversity and differentiation at eight microsatellite loci. A total of 94 alleles were detected, with extensive polymorphism among the accessions. Multivariate relationships among accessions revealed 16 genetic groups structured into three clusters, supporting the classical eco-geographic grouping of grape cultivars: occidentalis, pontica and orientalis. French cultivars appeared to be distinct and showed close affinity to the wild progenitor, ssp. sylvestris from south-western France (Pyrenees) and Tunisia, probably reflecting the origin and domestication history of many of the old wine cultivars from France. There was appreciable level of differentiation between table and wine grape cultivars, and the Muscat types were somewhat distinct within the wine grapes. Contingency chi2 analysis indicated significant heterogeneity in allele frequencies among groups at all loci. The observed heterozygosities for different groups ranged from 0.625 to 0.9 with an overall average of 0.771. Genetic relationships among groups suggested hierarchical differentiation within cultivated grape. The gene diversity analysis indicated narrow divergence among groups and that most variation was found within groups (approximately 85%). Partitioning of diversity suggested that the remaining variation is somewhat structured hierarchically at different levels of differentiation. The overall organization of genetic diversity suggests that the germplasm of cultivated grape represents a single complex gene pool and that its structure is determined by strong artificial selection and a vegetative mode of reproduction.
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Affiliation(s)
- Mallikarjuna K Aradhya
- National Clonal Germplasm Repository, US Department of Agriculture, One Shields Avenue, University of California, Davis, CA 95616, USA
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Lacombe T, Laucou V, Di Vecchi M, Bordenave L, Bourse T, Siret R, David J, Boursiquot JM, Bronner A, Merdinoglu D, This P. INVENTORY AND CHARACTERIZATION OF VITIS VINIFERA SSP. SILVESTRIS IN FRANCE. ACTA ACUST UNITED AC 2003. [DOI: 10.17660/actahortic.2003.603.73] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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This P, Roux C, Parra P, Siret R, Bourse T, Adam AF, Yvon M, Lacombe T, David J, Boursiquot JM. Caractérisation de la diversité d’une population de vignes sauvages du Pic Saint-Loup (Hérault) et relations avec le compartiment cultivé. Genet Sel Evol 2001. [DOI: 10.1186/bf03500885] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Siret R, Boursiquot JM, Merle MH, Cabanis JC, This P. Toward the authentication of varietal wines by the analysis of grape (Vitis vinifera L.) residual DNA in must and wine using microsatellite markers. J Agric Food Chem 2000; 48:5035-5040. [PMID: 11052774 DOI: 10.1021/jf991168a] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In an attempt to develop a technique for the identification of grape cultivars in commercial wines, a method for the extraction of DNA from must and experimental wines was adapted and optimal PCR conditions for the amplification of this DNA were established. DNA was analyzed during the fermentation process for six cultivars (Chardonnay, Clairette blanche, Grenache noir, Merlot, Muscat blanc à petits grains, and Syrah). The extractions were performed on solid parts in suspension as well as on the aqueous fraction. Expected profiles for these cultivars were obtained with DNA extracted from the solid parts during all of the fermentation process and for the wine. The analysis of DNA extracted from aqueous fractions was less reproducible, and microsatellite amplifications were obtained only in the case of Clairette blanche, Merlot, and Syrah wines. Results demonstrate that the purification process is adequate for the analysis but that the DNA concentration represents the main limiting factor. Technical improvements of the method are discussed.
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Affiliation(s)
- R Siret
- Laboratoire Interrégional de la Direction Générale de la Concurrence, de la Consommation et de la Répression des Fraudes (DGCCRF), 205 Rue de la croix verte, parc Euromédecine, 34196 Montpellier, France.
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Bowers J, Boursiquot JM, This P, Chu K, Johansson H, Meredith C. Historical Genetics: The Parentage of Chardonnay, Gamay, and Other Wine Grapes of Northeastern France. Science 1999; 285:1562-1565. [PMID: 10477519 DOI: 10.1126/science.285.5433.1562] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The origins of the classic European wine grapes (Vitis vinifera) have been the subject of much speculation. In a search for parental relationships, microsatellite loci were analyzed in more than 300 grape cultivars. Sixteen wine grapes that have long been grown in northeastern France, including 'Chardonnay', 'Gamay noir', 'Aligoté', and 'Melon', have microsatellite genotypes consistent with their being the progeny of a single pair of parents, 'Pinot' and 'Gouais blanc', both of which were widespread in this region in the Middle Ages. Parentage analysis at 32 microsatellite loci provides statistical support for these relationships.
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Affiliation(s)
- J Bowers
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA. Unité de Formation et de Recherche de Viticulture, Ecole Nationale Supérieure Agronomique, 34060 Montpellier, France. Unité de Recherches de Génétique et d'Amélioration des Plantes-Viticulture, Institut National de la Recherche Agronomique, 34060 Montpellier, France
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