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Schneider A, Ruffa P, Tumino G, Fontana M, Boccacci P, Raimondi S. Genetic relationships and introgression events between wild and cultivated grapevines (Vitis vinifera L.): focus on Italian Lambruscos. Sci Rep 2024; 14:12392. [PMID: 38811676 PMCID: PMC11137023 DOI: 10.1038/s41598-024-62774-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 05/21/2024] [Indexed: 05/31/2024] Open
Abstract
Research efforts on genomic structure and ecology of wild populations of Vitis vinifera L. offer insights on grape domestication processes and on the assortment evolution of the cultivated forms. Attention is also paid to the origin of traditional, long-cultivated varieties, often producing renowned and valuable wines. The genetic relationships between 283 Vitis vinifera cultivated varieties (subsp. sativa) and 65 individuals from 9 populations of the sylvestris subspecies mainly from northern Italy were explored by means of molecular markers (27 nuclear and 4 chloroplastic microsatellites). Several episodes of contamination of the wild germplasm by the pollen of specific grape cultivars were detected, implying concern for maintaining the purity of the wild form. At the same time, events of introgression from the wild subspecies resulted playing a crucial role in the emergence of several cultivated varieties with a clear admixed genome ancestry sativa-sylvestris. These included Lambruscos originated from the flat areas crossed by the Po and Adige rivers in northern Italy, while other cultivars still called Lambrusco but typical of hilly areas did not show the same admixed genome. Historical and ecological evidences suggesting an adaptative recent post-domestication process in the origin of several Italian Lambruscos are discussed.
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Affiliation(s)
- A Schneider
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Strada delle Cacce 73, 10135, Turin, Italy.
- Giovanni Dalmasso Foundation, Largo Braccini 2, 10095, Grugliasco, Turin, Italy.
| | - P Ruffa
- Department of Agricultural, Forest and Food Sciences, University of Turin (DiSAFA-UNITO), L. Braccini 2, 10095, Grugliasco, Turin, Italy
| | - G Tumino
- Plant Breeding, Wageningen University and Research (WUR), P.O. Box 9101, 6700 HB, Wageningen, The Netherlands
| | | | - P Boccacci
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - S Raimondi
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Strada delle Cacce 73, 10135, Turin, Italy
- Giovanni Dalmasso Foundation, Largo Braccini 2, 10095, Grugliasco, Turin, Italy
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2
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Breglia F, Bouby L, Wales N, Ivorra S, Fiorentino G. Disentangling the origins of viticulture in the western Mediterranean. Sci Rep 2023; 13:17284. [PMID: 37828091 PMCID: PMC10570292 DOI: 10.1038/s41598-023-44445-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 10/08/2023] [Indexed: 10/14/2023] Open
Abstract
We present direct evidence of early grape domestication in southern Italy via a multidisciplinary study of pip assemblage from one site, shedding new light on the spread of viticulture in the western Mediterranean during the Bronze Age. This consist of 55 waterlogged pips from Grotta di Pertosa, a Middle Bronze Age settlement in the south of the Italian peninsula. Direct radiocarbon dating of pips was carried out, confirming the chronological consistency of the samples with their archaeological contexts (ca. 1450-1200 BCE). The extraordinary state of conservation of the sample allowed to perform geometric morphometric (GMM) and paleogenetic analyses (aDNA) at the same time. The combination of the two methods has irrefutably shown the presence of domestic grapevines, together with wild ones, in Southern Italy during the Middle/Late Bronze Age. The results converge towards an oriental origin of the domestic grapes, most likely arriving from the Aegean area through the Mycenaeans. A parent/offspring kinship was also recognised between a domestic/wild hybrid individual and a domestic clonal group. This data point out a little known aspect of the diffusion of the first viticulture in Italy, and therefore in the western Mediterranean, which involved the hybridization between imported domestic varieties with, likely local, wild vines.
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Affiliation(s)
- Francesco Breglia
- Department of Geosciences, University of Padua, 35131, Padua, Italy.
- Laboratory of Archaeobotany and Palaeoecology, Cultural Heritage Department, University of Salento, 73100, Lecce, Italy.
| | - Laurent Bouby
- Institut des Sciences de l'Evolution, University of Montpellier, 34095, Montpellier, France
| | - Nathan Wales
- Department of Archaeology, University of York, York, YO1 7EP, UK
| | - Sarah Ivorra
- Institut des Sciences de l'Evolution, University of Montpellier, 34095, Montpellier, France
| | - Girolamo Fiorentino
- Laboratory of Archaeobotany and Palaeoecology, Cultural Heritage Department, University of Salento, 73100, Lecce, Italy
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3
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Miliordos DE, Alatzas A, Kontoudakis N, Unlubayir M, Hatzopoulos P, Lanoue A, Kotseridis Y. Benzothiadiazole Affects Grape Polyphenol Metabolism and Wine Quality in Two Greek Cultivars: Effects during Ripening Period over Two Years. PLANTS (BASEL, SWITZERLAND) 2023; 12:1179. [PMID: 36904039 PMCID: PMC10005230 DOI: 10.3390/plants12051179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 02/25/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Grape berries are one of the most important sources of phenolic compounds, either consumed fresh or as wine. A pioneer practice aiming to enrich grape phenolic content has been developed based on the application of biostimulants such as agrochemicals initially designed to induce resistance against plant pathogens. A field experiment was conducted in two growing seasons (2019-2020) to investigate the effect of benzothiadiazole on polyphenol biosynthesis during grape ripening in Mouhtaro (red-colored) and Savvatiano (white-colored) varieties. Grapevines were treated at the stage of veraison with 0.3 mM and 0.6 mM benzothiadiazole. The phenolic content of grapes, as well as the expression level of genes involved in the phenylpropanoid pathway were evaluated and showed an induction of genes specifically engaged in anthocyanins and stilbenoids biosynthesis. Experimental wines deriving from benzothiadiazole-treated grapes exhibited increased amounts of phenolic compounds in both varietal wines, as well as an enhancement in anthocyanin content of Mouhtaro wines. Taken together, benzothiadiazole can be utilized to induce the biosynthesis of secondary metabolites with oenological interest and to improve the quality characteristics of grapes produced under organic conditions.
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Affiliation(s)
- Dimitrios-Evangelos Miliordos
- Laboratory of Oenology and Alcoholic Beverage Drinks, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece
- Molecular Biology Laboratory, Department of Biotechnology, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece
- EA 2106 Biomolécules et Biotechnologie Végétales, UFR des Sciences Pharmaceutiques, Université de Tours, 31 Av. Monge, F37200 Tours, France
| | - Anastasios Alatzas
- Molecular Biology Laboratory, Department of Biotechnology, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece
| | - Nikolaos Kontoudakis
- Laboratory of Oenology and Alcoholic Beverage Drinks, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece
- Department of Agricultural Biotechnology and Oenology, International Hellenic University, 1st Km Drama-Mikrochori, 66100 Drama, Greece
| | - Marianne Unlubayir
- EA 2106 Biomolécules et Biotechnologie Végétales, UFR des Sciences Pharmaceutiques, Université de Tours, 31 Av. Monge, F37200 Tours, France
| | - Polydefkis Hatzopoulos
- Molecular Biology Laboratory, Department of Biotechnology, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece
| | - Arnaud Lanoue
- EA 2106 Biomolécules et Biotechnologie Végétales, UFR des Sciences Pharmaceutiques, Université de Tours, 31 Av. Monge, F37200 Tours, France
| | - Yorgos Kotseridis
- Laboratory of Oenology and Alcoholic Beverage Drinks, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece
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4
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Villano C, Corrado G, Basile B, Di Serio E, Mataffo A, Ferrara E, Aversano R. Morphological and Genetic Clonal Diversity within the 'Greco Bianco' Grapevine ( Vitis vinifera L.) Variety. PLANTS (BASEL, SWITZERLAND) 2023; 12:515. [PMID: 36771600 PMCID: PMC9921137 DOI: 10.3390/plants12030515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Grapevine (Vitis vinifera L.) has been propagated vegetatively for hundreds of years. Therefore, plants tend to accumulate somatic mutations that can result in an intra-varietal diversity capable of generating distinct clones. Although it is common that winemakers request specific clones or selections for planting new vineyards, relatively limited information is available on the extent, degree, and morphological impact of the clonal diversity in traditional, highly valued grapevine varieties within production areas protected by geographical denomination of origin. Here, we present a morphological and genetic investigation of the intra-varietal diversity in 'Greco Bianco', the grapevine variety used to produce the DOCG and PDO "Greco di Tufo" wine. Seventeen clones from different farms (all within the allowed production area) were phenotypically characterized using ampelographic and ampelometric traits. The clones were also genotyped with Simple Sequence Repeats (SSR) and retrotransposon-based DNA markers (REMAP). The morphological analysis indicated a uniformity in the qualitatively scored traits, and a limited variability for the quantitative traits of the bunch and of the berry composition. The molecular markers also depicted variability among clones, which was more evident with the use of REMAPs. The comparison of the discriminatory information of the three analyses indicated that they provided different estimates of the level of diversity. The evaluation described herein of the clonal variability has implications for the management and protection of clonal selections in 'Greco Bianco' and prompts for further multidisciplinary investigations on its possible role in winemaking.
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Affiliation(s)
- Clizia Villano
- Department of Agricultural Science, University of Naples Federico II, 80055 Portici, Italy
| | - Giandomenico Corrado
- Department of Agricultural Science, University of Naples Federico II, 80055 Portici, Italy
| | - Boris Basile
- Department of Agricultural Science, University of Naples Federico II, 80055 Portici, Italy
| | - Ermanno Di Serio
- Department of Agricultural Science, University of Naples Federico II, 80055 Portici, Italy
| | - Alessandro Mataffo
- Department of Agricultural Science, University of Naples Federico II, 80055 Portici, Italy
| | - Elvira Ferrara
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, 81100 Caserta, Italy
| | - Riccardo Aversano
- Department of Agricultural Science, University of Naples Federico II, 80055 Portici, Italy
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Blanco Pastor JL. Alternative modes of introgression-mediated selection shaped crop adaptation to novel climates. Genome Biol Evol 2022; 14:6647590. [PMID: 35859297 PMCID: PMC9348624 DOI: 10.1093/gbe/evac107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
Recent plant genomic studies provide fine-grained details on the evolutionary consequences of adaptive introgression during crop domestication. Modern genomic approaches and analytical methods now make it possible to better separate the introgression signal from the demographic signal thus providing a more comprehensive and complex picture of the role of introgression in local adaptation. Adaptive introgression has been fundamental for crop expansion and has involved complex patterns of gene flow. In addition to providing new and more favorable alleles of large effect, introgression during the early stages of domestication also increased allelic diversity at adaptive loci. Previous studies have largely underestimated the effect of such increased diversity following introgression. Recent genomic studies in wheat, potato, maize, grapevine, and ryegrass show that introgression of multiple genes, of as yet unknown effect, increased the effectiveness of purifying selection, and promoted disruptive or fluctuating selection in early cultivars and landraces. Historical selection processes associated with introgression from crop wild relatives provide an instructive analog for adaptation to current climate change and offer new avenues for crop breeding research that are expected to be instrumental for strengthening food security in the coming years.
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Archaeobotanical and chemical investigations on wine amphorae from San Felice Circeo (Italy) shed light on grape beverages at the Roman time. PLoS One 2022; 17:e0267129. [PMID: 35767534 PMCID: PMC9242518 DOI: 10.1371/journal.pone.0267129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 04/02/2022] [Indexed: 11/19/2022] Open
Abstract
We hereby investigate the pitch used for coating three Roman amphorae from San Felice Circeo (Italy) through a multidisciplinary study. The identification of molecular biomarkers by gas chromatography—mass spectrometry is combined with archaeobotanical evidence of pollen and plant tissues of Vitis flowers. Diterpenic chemical markers together with Pinus pollen and wood revealed Pinaceae tar coating. Aporate 3-zonocolpate pollen, identified as Vitis, together with tartaric, malic and pyruvic acids elucidate the grape-fermented nature of the content. Our conclusions open new consideration on the use of grape derivatives that cannot be supported by traditional analytical methods. Based on the finds of aporate Vitis pollen, found also in local modern and Middle Pleistocene samples, we hypothesize the use of autochthonous vines. The presence of a medicinal wine (historically reported as oenanthium) is also considered. We interrogate Vitis pollen capacity to target grapevine domestication, thereby providing innovative tools to understand such an important process. We anticipate our study to encourage a more systematic multidisciplinary approach regarding the analyses of wine amphorae.
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A Review on the Observed Climate Change in Europe and Its Impacts on Viticulture. ATMOSPHERE 2022. [DOI: 10.3390/atmos13050837] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The European climate is changing displaying profound on agriculture, thus strongly reaching the scientific community’s attention. In this review, the compilation of selected scientific research on the agroclimatic conditions’ changes and their impact on the productivity parameters (phenology timing, product quality and quantity) of grapevines and on the spatiotemporal characteristics of the viticultural areas are attempted for the first time. For this purpose, a thorough investigation through multiple search queries was conducted for the period (2005–2021). Overall, increasing (decreasing) trends in critical temperature (precipitation) parameters are the reality of the recent past with visible impacts on viticulture. The observed climate warming already enforces emerging phenomena related to the modification of the developmental rate (earlier phenological events, shortening of phenological intervals, lengthening of the growing season, earlier harvest), the alteration of product quality, the heterogeneous effects on grapevine yield and the emergence of new cool-climate viticulture areas highlighting the cultivation’s rebirth in the northern and central parts of the continent. The vulnerability of the wine-growing ecosystem urges the integration of innovative and sustainable solutions for confronting the impacts of climate change and safeguarding the production (quantity and quality) capacity of viticultural systems in Europe under a continuously changing environment.
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8
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Cretazzo E, Moreno Sanz P, Lorenzi S, Benítez ML, Velasco L, Emanuelli F. Genetic Characterization by SSR Markers of a Comprehensive Wine Grape Collection Conserved at Rancho de la Merced (Andalusia, Spain). PLANTS 2022; 11:plants11081088. [PMID: 35448817 PMCID: PMC9028831 DOI: 10.3390/plants11081088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/02/2022] [Accepted: 04/13/2022] [Indexed: 11/16/2022]
Abstract
The IFAPA research center “Rancho de la Merced” (Jerez, Spain) hosts one of the oldest and most diverse grapevine germplasm repositories in Europe, and is aimed at providing feasible solutions to deal with any agronomic trait by exploring its genetic variability and by means of association and Deoxyribonucleic Acid (DNA) editing studies. In this work, we focused on a wine and dual-use grapevine subcollection that consists of 930 accessions. Genetic analysis allowed to identify 521 unique genotypes. After comparing them with several databases, matches were found for 476 genetic profiles while the remaining 45 have not been previously described. Combination with clustering analysis suggested a total pool of 481 Vitis vinifera accessions that included some table cultivars. Several synonymies, homonymies and mislabeling have also been detected. Structure analysis allowed identifying six clusters according to eco-geographic cultivation areas and one additional group including non-vinifera accessions. Diversity analysis pointed out that Spanish Mediterranean varieties are genetically closer to oriental genotypes than to European varieties typical of oceanic and continental climates. The origin of Spanish varieties is discussed in depth considering our data and previous studies. Analysis of molecular variance partition confirmed a well-structured germplasm, although differentiation among groups had a much lower effect on genetic variability than differences within groups, which are strongly related to a very high heterozygosity. A core collection that covers all allele richness is proposed. It is constituted of about 13% of total accessions, and each cluster inferred by structure analysis is represented.
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Affiliation(s)
- Enrico Cretazzo
- Área de Mejora Vegetal y Biotecnología, Instituto de Investigación y Formación Agraria, Pesquera, Alimentaria y de la Producción Ecológica (IFAPA), Centro Rancho de la Merced, 11471 Jerez de la Frontera, Spain;
- Correspondence:
| | - Paula Moreno Sanz
- Dipartimento di Biologia Cellulare, Computazionale e Integrata, University of Trento, 38122 Trento, Italy;
| | - Silvia Lorenzi
- Research and Innovation Center, Fondazione Edmund Mach (FEM), 38010 San Michele All’Adige, Italy; (S.L.); (F.E.)
| | - Miguel Lara Benítez
- Área de Mejora Vegetal y Biotecnología, Instituto de Investigación y Formación Agraria, Pesquera, Alimentaria y de la Producción Ecológica (IFAPA), Centro Rancho de la Merced, 11471 Jerez de la Frontera, Spain;
| | - Leonardo Velasco
- Área de Protección Vegetal Sostenible, Instituto de Investigación y Formación Agraria, Pesquera, Alimentaria y de la Producción Ecológica (IFAPA), Centro de Málaga, 29140 Malaga, Spain;
| | - Francesco Emanuelli
- Research and Innovation Center, Fondazione Edmund Mach (FEM), 38010 San Michele All’Adige, Italy; (S.L.); (F.E.)
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Abstract
The purpose of this work is to present the archaeological and historical background of viticulture and winemaking from ancient times to the present day in the Mediterranean basin. According to recent archaeological, archaeochemical and archaeobotanical data, winemaking emerged during the Neolithic period (c. 7th–6th millennium BC) in the South Caucasus, situated between the basins of the Black and Caspian Seas, and subsequently reached the Iberian Peninsula and Western Europe during the local beginning of Iron Age (c. 8th century BC), following the main maritime civilizations. This review summarises the most relevant findings evidencing that the expansion of wine production, besides depending on adequate pedo-climatic conditions and wine-growing practices, also required the availability of pottery vessels to properly ferment, store and transport wine without deterioration. The domestication of wild grapevines enabled the selection of more productive varieties, further sustaining the development of wine trade. Other fermented beverages such as mead and beer gradually lost their relevance and soon wine became the most valorised. Together with grapes, it became an object and a system of value for religious rituals and social celebrations throughout successive ancient Western civilizations. Moreover, wine was used for medicinal purposes and linked to a wide variety of health benefits. In everyday life, wine was a pleasant drink consumed by the elite classes and commoner populations during jubilee years, festivals, and banquets, fulfilling the social function of easy communication. In the present work, emphasis is put on the technical interpretation of the selected archaeological and historical sources that may explain present viticultural and oenological practices. Hopefully, this review will contribute to nurturing mutual understanding between archaeologists and wine professionals.
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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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11
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Abstract
The pip, as the most common grapevine archaeological remain, is extensively used to document past viticulture dynamics. This paper uses state of the art morphological analyses to analyse the largest reference collection of modern pips to date, representative of the present-day diversity of the domesticated grapevine from Western Eurasia. We tested for a costructure between the form of the modern pips and the: destination use (table/wine), geographical origins, and populational labels obtained through two molecular approaches. Significant structuring is demonstrated for each of these cofactors and for the first time it is possible to infer properties of varieties without going through the parallel with modern varieties. These results provide a unique tool that can be applied to archaeological pips in order to reconstruct the spatio-temporal dynamics of grape diversity on a large scale and to better understand viticulture history. The models obtained were then used to infer the affiliations with archaeobotanical remains recovered in Mas de Vignoles XIV (Nîmes, France). The results show a twofold shift between the Late Iron Age and the Middle Ages, from table to wine grape varieties and from eastern to western origins which correlates with previous palaeogenomic results.
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12
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Landa V, Shapira Y, David M, Karasik A, Weiss E, Reuveni Y, Drori E. Accurate classification of fresh and charred grape seeds to the varietal level, using machine learning based classification method. Sci Rep 2021; 11:13577. [PMID: 34193917 PMCID: PMC8245476 DOI: 10.1038/s41598-021-92559-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 06/10/2021] [Indexed: 11/09/2022] Open
Abstract
Grapevine (Vitis vinifera L.) currently includes thousands of cultivars. Discrimination between these varieties, historically done by ampelography, is done in recent decades mostly by genetic analysis. However, when aiming to identify archaeobotanical remains, which are mostly charred with extremely low genomic preservation, the application of the genomic approach is rarely successful. As a result, variety-level identification of most grape remains is currently prevented. Because grape pips are highly polymorphic, several attempts were made to utilize their morphological diversity as a classification tool, mostly using 2D image analysis technics. Here, we present a highly accurate varietal classification tool using an innovative and accessible 3D seed scanning approach. The suggested classification methodology is machine-learning-based, applied with the Iterative Closest Point (ICP) registration algorithm and the Linear Discriminant Analysis (LDA) technique. This methodology achieved classification results of 91% to 93% accuracy in average when trained by fresh or charred seeds to test fresh or charred seeds, respectively. We show that when classifying 8 groups, enhanced accuracy levels can be achieved using a "tournament" approach. Future development of this new methodology can lead to an effective seed classification tool, significantly improving the fields of archaeobotany, as well as general taxonomy.
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Affiliation(s)
- Vlad Landa
- Department of Computer Science, Ariel University, 40700, Ariel, Israel
| | - Yekaterina Shapira
- Department of Chemical Engineering, Biotechnology and Materials, Ariel University, 40700, Ariel, Israel
| | - Michal David
- Archaeobotanical Laboratory and National Natural History Collection of Plants' Seeds and Fruits, Institute of Archaeology, Martin (Szusz) Department of Land of Israel Studies and Archaeology, Bar-Ilan University, 5290002, Ramat-Gan, Israel
| | - Avshalom Karasik
- The National Laboratory for Digital Documentation and Research in Archaeology, Israel Antiquities Authority, Jerusalem, Israel
| | - Ehud Weiss
- Archaeobotanical Laboratory and National Natural History Collection of Plants' Seeds and Fruits, Institute of Archaeology, Martin (Szusz) Department of Land of Israel Studies and Archaeology, Bar-Ilan University, 5290002, Ramat-Gan, Israel.
| | - Yuval Reuveni
- Department of Physics, Faculty of Natural Sciences, Ariel University, Science Park, 40700, Ariel, Israel. .,Remote Sensing Lab, Eastern R&D Center, 40700, Ariel, Israel.
| | - Elyashiv Drori
- Department of Chemical Engineering, Biotechnology and Materials, Ariel University, 40700, Ariel, Israel. .,The Wine Research Center, Eastern Regional R&D Center, 40700, Ariel, Israel.
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13
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Back to the Origins: Background and Perspectives of Grapevine Domestication. Int J Mol Sci 2021; 22:ijms22094518. [PMID: 33926017 PMCID: PMC8123694 DOI: 10.3390/ijms22094518] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 01/01/2023] Open
Abstract
Domestication is a process of selection driven by humans, transforming wild progenitors into domesticated crops. The grapevine (Vitis vinifera L.), besides being one of the most extensively cultivated fruit trees in the world, is also a fascinating subject for evolutionary studies. The domestication process started in the Near East and the varieties obtained were successively spread and cultivated in different areas. Whether the domestication occurred only once, or whether successive domestication events occurred independently, is a highly debated mystery. Moreover, introgression events, breeding and intense trade in the Mediterranean basin have followed, in the last thousands of years, obfuscating the genetic relationships. Although a succession of studies has been carried out to explore grapevine origin and different evolution models are proposed, an overview of the topic remains pending. We review here the findings obtained in the main phylogenetic and genomic studies proposed in the last two decades, to clarify the fundamental questions regarding where, when and how many times grapevine domestication took place. Finally, we argue that the realization of the pan-genome of grapes could be a useful resource to discover and track the changes which have occurred in the genomes and to improve our understanding about the domestication.
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14
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Sargolzaei M, Rustioni L, Cola G, Ricciardi V, Bianco PA, Maghradze D, Failla O, Quaglino F, Toffolatti SL, De Lorenzis G. Georgian Grapevine Cultivars: Ancient Biodiversity for Future Viticulture. FRONTIERS IN PLANT SCIENCE 2021; 12:630122. [PMID: 33613611 PMCID: PMC7892605 DOI: 10.3389/fpls.2021.630122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/13/2021] [Indexed: 05/14/2023]
Abstract
Grapevine (Vitis vinifera) is one of the most widely cultivated plant species of agricultural interest, and is extensively appreciated for its fruits and the wines made from its fruits. Considering the high socio-economic impact of the wine sector all over the world, in recent years, there has been an increase in work aiming to investigate the biodiversity of grapevine germplasm available for breeding programs. Various studies have shed light on the genetic diversity characterizing the germplasm from the cradle of V. vinifera domestication in Georgia (South Caucasus). Georgian germplasm is placed in a distinct cluster from the European one and possesses a rich diversity for many different traits, including eno-carpological and phenological traits; resistance to pathogens, such as oomycetes and phytoplasmas; resistance to abiotic stresses, such as sunburn. The aim of this review is to assess the potential of Georgian cultivars as a source of useful traits for breeding programs. The unique genetic and phenotypic aspects of Georgian germplasm were unraveled, to better understand the diversity and quality of the genetic resources available to viticulturists, as valuable resources for the coming climate change scenario.
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Affiliation(s)
- Maryam Sargolzaei
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milan, Italy
| | - Laura Rustioni
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento – Centro Ecotekne, Lecce, Italy
| | - Gabriele Cola
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milan, Italy
| | - Valentina Ricciardi
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milan, Italy
| | - Piero A. Bianco
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milan, Italy
| | - David Maghradze
- Faculty of Viticulture and Winemaking, Caucasus International University, Tbilisi, Georgia
- National Wine Agency of Georgia, Tbilisi, Georgia
| | - Osvaldo Failla
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milan, Italy
| | - Fabio Quaglino
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milan, Italy
| | - Silvia L. Toffolatti
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milan, Italy
- *Correspondence: Silvia L. Toffolatti,
| | - Gabriella De Lorenzis
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milan, Italy
- Gabriella De Lorenzis,
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15
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Mercati F, De Lorenzis G, Mauceri A, Zerbo M, Brancadoro L, D'Onofrio C, Morcia C, Barbagallo MG, Bignami C, Gardiman M, de Palma L, Ruffa P, Novello V, Crespan M, Sunseri F. Integrated Bayesian Approaches Shed Light on the Dissemination Routes of the Eurasian Grapevine Germplasm. FRONTIERS IN PLANT SCIENCE 2021; 12:692661. [PMID: 34434204 PMCID: PMC8381769 DOI: 10.3389/fpls.2021.692661] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/07/2021] [Indexed: 05/12/2023]
Abstract
The domestication and spreading of grapevine as well as the gene flow history had been described in many studies. We used a high-quality 7k SNP dataset of 1,038 Eurasian grape varieties with unique profiles to assess the population genetic diversity, structure, and relatedness, and to infer the most likely migration events. Comparisons of putative scenarios of gene flow throughout Europe from Caucasus helped to fit the more reliable migration routes around the Mediterranean Basin. Approximate Bayesian computation (ABC) approach made possible to provide a response to several questions so far remaining unsolved. Firstly, the assessment of genetic diversity and population structure within a well-covered dataset of ancient Italian varieties suggested the different histories between the Northern and Southern Italian grapevines. Moreover, Italian genotypes were shown to be distinguishable from all the other Eurasian populations for the first time. The entire Eurasian panel confirmed the east-to-west gene flow, highlighting the Greek role as a "bridge" between the Western and Eastern Eurasia. Portuguese germplasm showed a greater proximity to French varieties than the Spanish ones, thus being the main route for gene flow from Iberian Peninsula to Central Europe. Our findings reconciled genetic and archaeological data for one of the most cultivated and fascinating crops in the world.
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Affiliation(s)
- Francesco Mercati
- Istituto Bioscienze e Biorisorse, Consiglio Nazionale delle Ricerche, Palermo, Italy
- *Correspondence: Francesco Mercati
| | - Gabriella De Lorenzis
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milan, Milan, Italy
| | - Antonio Mauceri
- Dipartimento Agraria, Università Mediterranea degli Studi di Reggio Calabria, Reggio Calabria, Italy
| | - Marcello Zerbo
- Istituto Bioscienze e Biorisorse, Consiglio Nazionale delle Ricerche, Palermo, Italy
| | - Lucio Brancadoro
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milan, Milan, Italy
| | - Claudio D'Onofrio
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università degli Studi di Pisa, Pisa, Italy
| | - Caterina Morcia
- CREA - Centro di Ricerca per la Genomica e la Bioinformatica, Fiorenzuola d'Arda, Italy
| | | | - Cristina Bignami
- Dipartimento di Scienze della Vita, Centro Biogest-Siteia, Università degli Studi di Modena e Reggio Emilia, Reggio Emilia, Italy
| | - Massimo Gardiman
- CREA - Centro di Ricerca per la Viticoltura ed Enologia, Conegliano, Italy
| | - Laura de Palma
- Dipartimento di Scienze Agrarie, Alimenti, Risorse Naturali e Ingegneria, Università degli Studi di Foggia, Foggia, Italy
| | - Paola Ruffa
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Torino, Italy
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Italy
| | - Vittorino Novello
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Italy
| | - Manna Crespan
- CREA - Centro di Ricerca per la Viticoltura ed Enologia, Conegliano, Italy
- Manna Crespan
| | - Francesco Sunseri
- Dipartimento Agraria, Università Mediterranea degli Studi di Reggio Calabria, Reggio Calabria, Italy
- Francesco Sunseri
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16
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Bonhomme V, Picq S, Ivorra S, Evin A, Pastor T, Bacilieri R, Lacombe T, Figueiral I, Terral JF, Bouby L. Eco-evo-devo implications and archaeobiological perspectives of trait covariance in fruits of wild and domesticated grapevines. PLoS One 2020; 15:e0239863. [PMID: 33156832 PMCID: PMC7647109 DOI: 10.1371/journal.pone.0239863] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 09/15/2020] [Indexed: 11/19/2022] Open
Abstract
The phenotypic changes that occurred during the domestication and diversification of grapevine are well known, particularly changes in seed morphology, but the functional causes and consequences behind these variations are poorly understood. Wild and domesticate grapes differ, among others, in the form of their pips: wild grapes produce roundish pips with short stalks and cultivated varieties have more elongated pips with longer stalks. Such variations of form are of first importance for archaeobotany since the pip form is, most often, the only remaining information in archaeological settings. This study aims to enlighten archaeobotanical record and grapevine pip development by better understanding how size and shape (co)variates between pip and berry in both wild and domesticated Vitis vinifera. The covariation of berry size, number of seeds per berry (“piposity”), pip size and pip shape were explored on 49 grapevine accessions sampled among Euro-Mediterranean traditional cultivars and wild grapevines. We show that for wild grapevine, the higher the piposity, the bigger the berry and the more elongated the pip. For both wild and domesticated grapevine, the longer is the pip, the more it has a “domesticated” shape. Consequences for archaeobotanical studies are tested and discussed, and these covariations allowed the inference of berry dimensions from archaeological pips from a Southern France Roman site. This systematic exploration sheds light on new aspects of pip-berry relationship, in both size and shape, on grapevine eco-evo-devo changes during domestication, and invites to explore further the functional ecology of grapevine pip and berry and notably the impact of cultivation practices and human selection on grapevine morphology.
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Affiliation(s)
- Vincent Bonhomme
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Équipe « Dynamique de la biodiversité, anthropo-écologie », CC065 Montpellier Cedex 5, France
- * E-mail:
| | - Sandrine Picq
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Équipe « Dynamique de la biodiversité, anthropo-écologie », CC065 Montpellier Cedex 5, France
- Laurentian Forestry Centre, Natural Resources Canada, Québec, Canada
| | - Sarah Ivorra
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Équipe « Dynamique de la biodiversité, anthropo-écologie », CC065 Montpellier Cedex 5, France
| | - Allowen Evin
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Équipe « Dynamique de la biodiversité, anthropo-écologie », CC065 Montpellier Cedex 5, France
| | - Thierry Pastor
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Équipe « Dynamique de la biodiversité, anthropo-écologie », CC065 Montpellier Cedex 5, France
| | - Roberto Bacilieri
- UMR AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Equipe « Diversité, Adaptation et Amélioration de la Vigne », Montpellier, France
| | - Thierry Lacombe
- UMR AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Equipe « Diversité, Adaptation et Amélioration de la Vigne », Montpellier, France
| | - Isabel Figueiral
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Équipe « Dynamique de la biodiversité, anthropo-écologie », CC065 Montpellier Cedex 5, France
| | - Jean-Frédéric Terral
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Équipe « Dynamique de la biodiversité, anthropo-écologie », CC065 Montpellier Cedex 5, France
| | - Laurent Bouby
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Équipe « Dynamique de la biodiversité, anthropo-écologie », CC065 Montpellier Cedex 5, France
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17
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Exploring the aromatic complexity of Sardinian red wines obtained from minor and rare varieties. Eur Food Res Technol 2020. [DOI: 10.1007/s00217-020-03613-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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18
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Assessment of genetic diversity of cultivated and wild Iranian grape germplasm using retrotransposon-microsatellite amplified polymorphism (REMAP) markers and pomological traits. Mol Biol Rep 2020; 47:7593-7606. [PMID: 32949305 DOI: 10.1007/s11033-020-05827-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/07/2020] [Indexed: 10/23/2022]
Abstract
Understanding the genetic diversity and relationships between genotypes is an effective step in designing effective breeding programs. Insertional polymorphisms of retrotransposons were studied in 75 cultivated and wild grape genotypes using retrotransposon-microsatellite amplified polymorphism (REMAP) technique. In the morphological part of work, seven pomological traits with a high breeding interest were also analyzed in the cultivated genotypes. A total of 328 markers were produced by 42 primer pairs, out of which 313 markers (95.43%) were polymorphic. Number of markers ranged from 4 in loci Tvv1Fa-873, Vine1-811, Gret1Ra-855 and Tvv1Fa-890 to 12 in locus Vine1Ra-841 with an average value of 7.45. Similarity values based on Dice's coefficient among all 75 grapevine genotypes varied from 0.41 to 0.77. Classification of genotypes using unweighted pair-group method using complete-linkage clustering led to six distinct groups. Some wild and cultivated varieties placed in the same groups. It seems there are close relationship between wild and cultivated genotypes and maybe wild genotypes are ancestor of native grapevines. Grouping of grapevine genotypes based on molecular marker data was not in agreement with clustering by agro-morphological data indicating that the most of multiplied sequences are confined to the non-coding regions of transposon elements. Results showed a substantial level of genetic diversity at molecular and pomological level and the potential of this diversity for future grape breeding programs.
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19
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Population genetic analysis in old Montenegrin vineyards reveals ancient ways currently active to generate diversity in Vitis vinifera. Sci Rep 2020; 10:15000. [PMID: 32929127 PMCID: PMC7490262 DOI: 10.1038/s41598-020-71918-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 08/20/2020] [Indexed: 11/08/2022] Open
Abstract
Global viticulture has evolved following market trends, causing loss of cultivar diversity and traditional practices. In Montenegro, modern viticulture co-exists with a traditional viticulture that still maintains ancient practices and exploits local cultivars. As a result, this region provides a unique opportunity to explore processes increasing genetic diversity. To evaluate the diversity of Montenegrin grapevines and the processes involved in their diversification, we collected and analyzed 419 samples in situ across the country (cultivated plants from old orchards and vines growing in the wild), and 57 local varieties preserved in a grapevine collection. We obtained 144 different genetic profiles, more than 100 corresponding to cultivated grapevines, representing a surprising diversity for one of the smallest European countries. Part of this high diversity reflects historical records indicating multiple and intense introduction events from diverse viticultural regions at different times. Another important gene pool includes many autochthonous varieties, some on the edge of extinction, linked in a complex parentage network where two varieties (Razaklija and Kratošija) played a leading role on the generation of indigenous varieties. Finally, analyses of genetic structure unveiled several putative proto-varieties, likely representing the first steps involved in the generation of new cultivars or even secondary domestication events.
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20
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Martínez-Romero E, Aguirre-Noyola JL, Taco-Taype N, Martínez-Romero J, Zuñiga-Dávila D. Plant microbiota modified by plant domestication. Syst Appl Microbiol 2020; 43:126106. [PMID: 32847781 DOI: 10.1016/j.syapm.2020.126106] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 12/19/2022]
Abstract
Human life became largely dependent on agricultural products after distinct crop-domestication events occurred around 10,000 years ago in different geographical sites. Domestication selected suitable plants for human agricultural practices with unexpected consequences on plant microbiota, which has notable effects on plant growth and health. Among other traits, domestication has changed root architecture, exudation, or defense responses that could have modified plant microbiota. Here we present the comparison of reported data on the microbiota from widely consumed cereals and legumes and their ancestors showing that different bacteria were found in domesticated and wild plant microbiomes in some cases. Considering the large variability in plant microbiota, adequate sampling efforts and function-based approaches are needed to further support differences between the microbiota from wild and domesticated plants. The study of wild plant microbiomes could provide a valuable resource of unexploited beneficial bacteria for crops.
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Affiliation(s)
| | | | - Nataly Taco-Taype
- Laboratorio de Ecología Microbiana, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
| | | | - Doris Zuñiga-Dávila
- Laboratorio de Ecología Microbiana, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
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21
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Grigoriou A, Tsaniklidis G, Hagidimitriou M, Nikoloudakis N. The Cypriot Indigenous Grapevine Germplasm Is a Multi-Clonal Varietal Mixture. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1034. [PMID: 32824004 PMCID: PMC7463456 DOI: 10.3390/plants9081034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/07/2020] [Accepted: 08/13/2020] [Indexed: 12/21/2022]
Abstract
Cypriot vineyards are considered as one among the earliest niches of viticulture and a pivotal hub for the domestication and dissemination of grapevine. The millennial presence of Vitis spp. in this Eastern Mediterranean island has given rise to a plethora of biotypes that have not been adequately characterized, despite their unique attributes and stress tolerance. This ancient germplasm also has an additional value since it survived the phylloxera outbreak; hence, it possesses a large amount of genetic diversity that has been unnoticed. In order to provide useful insights to the lineage of Cypriot vineyards, a two-year-spanning collection of centennial grapevine cultivars mostly regarded to belong to four indigenous variety clusters ("Mavro", "Xynisteri", "Maratheftiko", and "Veriko") was initiated. There were 164 accessions across the broader Commandaria wine zone sampled and characterized using a universal microsatellite primer set. Genetic analysis indicated that considered indigenous Cypriot germplasm has a polyclonal structure with a high level of heterozygosity. Moreover, several lineages or unexplored varieties may exist, since a larger than considered number of discrete genotypes was discovered. Furthermore, it was established that grapevine lineages in Cyprus were shaped across eras via clonal, as well as, sexual propagation. The special attributes of the Cypriot landscape are discussed.
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Affiliation(s)
- Apostolis Grigoriou
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol CY-3603, Cyprus;
| | - Georgios Tsaniklidis
- Institute of Olive Tree, Subtropical Plants and Viticulture, Hellenic Agricultural Organization ‘Demeter’ (NAGREF), 71003 Heraklio, Greece;
| | | | - Nikolaos Nikoloudakis
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol CY-3603, Cyprus;
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22
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Grassi F, Arroyo-Garcia R. Editorial: Origins and Domestication of the Grape. FRONTIERS IN PLANT SCIENCE 2020; 11:1176. [PMID: 32903797 PMCID: PMC7438903 DOI: 10.3389/fpls.2020.01176] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Affiliation(s)
| | - Rosa Arroyo-Garcia
- CBGP-INIA (Center for Plant Biotechnology and Genomics-National Institute of Agricultural and Food Research and Technology), Madrid, Spain
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23
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Cunha J, Ibáñez J, Teixeira-Santos M, Brazão J, Fevereiro P, Martínez-Zapater JM, Eiras‐Dias JE. Genetic Relationships Among Portuguese Cultivated and Wild Vitis vinifera L. Germplasm. FRONTIERS IN PLANT SCIENCE 2020; 11:127. [PMID: 32194583 PMCID: PMC7066319 DOI: 10.3389/fpls.2020.00127] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/28/2020] [Indexed: 05/04/2023]
Abstract
The domesticated grapevine spread along the Mediterranean basin from the primary Near East domestication area, where the greatest genetic diversity is found in its ancestor, the wild vine populations. Portuguese wild populations are on the southwestern fringe of the distribution of the Vitis vinifera L. ssp. sylvestris (C.C. Gmel.) Hegi in Europe. During the last Glacial Period they became isolated from the previous continuum that had been the territory of wild vine populations. Archaeological remains of domesticated vinifera grapevines in Portugal date back from 795 Before Common Era (BCE) in the lower Tagus river basin. In this work, 258 Portuguese vinifera varieties and sylvestris plants were characterized using 261 single nucleotide polymorphism (SNP) markers. The study of the genetic diversity of this local germplasm, its population structure and kinship, all framed in their historical and geographical backgrounds, revealed a complex network of first-degree relationships, where only Iberian varieties are involved. Some Iberian genotypes, like Alfrocheiro (Bruñal, in Spain), Sarigo (Cayetana Blanca), Mourisco Branco (Hebén), Amaral (Caiño Bravo), and Marufo (Moravia Dulce) are ancestors of a considerable fraction of all the autochthonous analyzed varieties. A part of the diversity developed was mostly local in some cases as shown by the closeness of several varieties (Vinhos Verdes) to the wild cluster in different analyses. Besides, several evidences of introgression of domesticated germplasm into wild vines was found, substantiating the high risk of genetic contamination of the sylvestris subspecies. All these findings together to the known matching between the wild maternal lineage of the Iberian Peninsula and an important number of Portuguese grapevine varieties (chlorotype A), point out that some of these varieties derive, directly or indirectly, from originally local wild populations, supporting the possible occurrence of secondary events of local domestication, or, at least, of an introgression process of wild into cultivated grapevines.
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Affiliation(s)
- Jorge Cunha
- Instituto Nacional de Investigação Agrária e Veterinária, Dois Portos, Portugal
- Green-it Unit, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- *Correspondence: Jorge Cunha,
| | - Javier Ibáñez
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino, (Consejo Superior de Investigaciones Científicas, Universidad de La Rioja, Gobierno de La Rioja), Logroño, Spain
| | | | - João Brazão
- Instituto Nacional de Investigação Agrária e Veterinária, Dois Portos, Portugal
- Green-it Unit, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Pedro Fevereiro
- Green-it Unit, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Departamento de Biologia Vegetal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - José M. Martínez-Zapater
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino, (Consejo Superior de Investigaciones Científicas, Universidad de La Rioja, Gobierno de La Rioja), Logroño, Spain
| | - José E. Eiras‐Dias
- Instituto Nacional de Investigação Agrária e Veterinária, Dois Portos, Portugal
- Green-it Unit, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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D’Onofrio C, Tumino G, Gardiman M, Crespan M, Bignami C, de Palma L, Barbagallo MG, Muganu M, Morcia C, Novello V, Schneider A, Terzi V. Parentage Atlas of Italian Grapevine Varieties as Inferred From SNP Genotyping. FRONTIERS IN PLANT SCIENCE 2020; 11:605934. [PMID: 33584749 PMCID: PMC7874015 DOI: 10.3389/fpls.2020.605934] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 12/22/2020] [Indexed: 05/11/2023]
Abstract
The Italian grape germplasm is characterized by a high level of richness in terms of varieties number, with nearly 600 wine grape varieties listed in the Italian National Register of Grapevine Varieties and with a plethora of autochthonous grapes. In the present study an extended SNP genotyping has been carried out on Italian germplasm of cultivated Vitis vinifera subsp. sativa and Vitis hybrids. Several hundred Italian varieties maintained in the repositories of scientific Institutions and about one thousand additional varieties derived from previous studies on European, Southern Italy, Magna Graecia and Georgian germplasm were considered. The large genotyping data obtained were used to check the presence of homonyms and synonyms, determine parental relationships, and identify the main ancestors of traditional Italian cultivars and closely-related accessions. The parentage among a set of 1,232 unique varieties has been assessed. A total of 92 new parent-offspring (PO) pairs and 14 new PO trios were identified. The resulted parentage network suggested that the traditional Italian grapevine germplasm originates largely from a few central varieties geographically distributed into several areas of genetic influence: "Strinto porcino" and its offspring "Sangiovese", "Mantonico bianco" and "Aglianico" mainly as founder varieties of South-Western Italy (IT-SW); Italian Adriatic Coast (IT-AC); and Central Italy with most varieties being offsprings of "Visparola", "Garganega" and "Bombino bianco"; "Termarina (Sciaccarello)" "Orsolina" and "Uva Tosca" as the main varieties of North-Western Italy (IT-NW) and Central Italy. The pedigree reconstruction by full-sib and second-degree relationships highlighted the key role of some cultivars, and, in particular, the centrality of "Visparola" in the origin of Italian germplasm appeared clear. An hypothetical migration of this variety within the Italian Peninsula from South to North along the eastern side, as well as of "Sangiovese" from South to Central Italy along the Western side might be supposed. Moreover, it was also highlighted that, among the main founders of muscat varieties, "Moscato bianco" and "Zibibbo (Muscat of Alexandria)" have spread over the whole Italy, with a high contribution by the former to germplasm of the North-Western of the peninsula.
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Affiliation(s)
- Claudio D’Onofrio
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
- *Correspondence: Claudio D’Onofrio,
| | - Giorgio Tumino
- CREA Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Massimo Gardiman
- CREA Research Centre for Viticulture and Enology, Conegliano, Italy
| | - Manna Crespan
- CREA Research Centre for Viticulture and Enology, Conegliano, Italy
| | - Cristina Bignami
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Laura de Palma
- Department of Sciences of Agriculture, Food, Natural Resources and Engineering, University of Foggia, Foggia, Italy
| | | | - Massimo Muganu
- Department of Agriculture and Forest Sciences, University of Tuscia, Viterbo, Italy
| | - Caterina Morcia
- CREA Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Vittorino Novello
- Department of Agriculture, Forestry and Food Sciences, University of Turin, Turin, Italy
| | - Anna Schneider
- Research Council of Italy, Institute for Sustainable Plant Protection, Turin, Italy
| | - Valeria Terzi
- CREA Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
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De Lorenzis G, Mercati F, Bergamini C, Cardone MF, Lupini A, Mauceri A, Caputo AR, Abbate L, Barbagallo MG, Antonacci D, Sunseri F, Brancadoro L. SNP genotyping elucidates the genetic diversity of Magna Graecia grapevine germplasm and its historical origin and dissemination. BMC PLANT BIOLOGY 2019; 19:7. [PMID: 30612542 PMCID: PMC6322315 DOI: 10.1186/s12870-018-1576-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/27/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Magna Graecia is the ancient name for the modern geopolitical region of South Italy extensively populated by Greek colonizers, shown by archeological and historical evidence to be the oldest wine growing region of Italy, crucial for the spread of specialized viticulture around Mediterranean shores. Here, the genetic diversity of Magna Graecia grape germplasm was assessed and its role in grapevine propagation around the Mediterranean basin was underlined. RESULTS A large collection of grapevines from Magna Graecia was compared with germplasm from Georgia to the Iberian Peninsula using the 18 K SNP array. A high level of genetic diversity of the analyzed germplasm was determined; clustering, structure analysis and DAPC (Discriminant Analysis of Principal Components) highlighted the genetic relationships among genotypes from South Italy and the Eastern Mediterranean (Greece). Gene flow from east (Georgia) to west (Iberian Peninsula) was identified throughout the large number of detected admixed samples. Pedigree analysis showed a complex and well-structured network of first degree relationships, where the cultivars from Magna Graecia were mainly involved. CONCLUSIONS This study provided evidence that Magna Graecia germplasm was shaped by historical events that occurred in the area due to the robust link between South Italian and Greek genotypes, as well as, by the availability of different thermal resources for cultivars growing in such different winegrowing areas. The uniqueness of this ampelographic platform was mainly an outcome of complex natural or human-driven crosses involving elite cultivars.
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Affiliation(s)
| | - Francesco Mercati
- Istituto di Bioscienze e Biorisorse CNR, Corso Calatafimi 414, 90120 Palermo, Italy
| | - Carlo Bergamini
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria, Centro di ricerca Viticoltura ed Enologia, CREA-VE, via Casamassima 148, 70010 Turi, Bari Italy
| | - Maria Francesca Cardone
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria, Centro di ricerca Viticoltura ed Enologia, CREA-VE, via Casamassima 148, 70010 Turi, Bari Italy
| | - Antonio Lupini
- Dipartimento AGRARIA, località Feo di Vito snc, 89121 Reggio Calabria, Italy
| | - Antonio Mauceri
- Dipartimento AGRARIA, località Feo di Vito snc, 89121 Reggio Calabria, Italy
| | - Angelo Raffaele Caputo
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria, Centro di ricerca Viticoltura ed Enologia, CREA-VE, via Casamassima 148, 70010 Turi, Bari Italy
| | - Loredana Abbate
- Istituto di Bioscienze e Biorisorse CNR, Corso Calatafimi 414, 90120 Palermo, Italy
| | | | - Donato Antonacci
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria, Centro di ricerca Viticoltura ed Enologia, CREA-VE, via Casamassima 148, 70010 Turi, Bari Italy
| | - Francesco Sunseri
- Dipartimento AGRARIA, località Feo di Vito snc, 89121 Reggio Calabria, Italy
| | - Lucio Brancadoro
- Dipartimento di Scienze Agrarie ed Ambientali, via Celoria 2, 20133 Milan, Italy
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De Michele R, La Bella F, Gristina AS, Fontana I, Pacifico D, Garfi G, Motisi A, Crucitti D, Abbate L, Carimi F. Phylogenetic Relationship Among Wild and Cultivated Grapevine in Sicily: A Hotspot in the Middle of the Mediterranean Basin. FRONTIERS IN PLANT SCIENCE 2019; 10:1506. [PMID: 31850016 PMCID: PMC6888813 DOI: 10.3389/fpls.2019.01506] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 10/29/2019] [Indexed: 05/09/2023]
Abstract
Grapevine (Vitis vinifera ssp. sativa) is a perennial crop especially important for wine and fruit production. The species is highly polymorphic with thousands of different varieties selected by farmers and clonally propagated. However, it is still debated whether grapevine domestication from its wild ancestor (V. vinifera ssp. sylvestris) has been a single event or rather it occurred on multiple occasions during the diffusion of its cultivation across the Mediterranean. Located in the center of the Basin, Sicily is its largest island and has served as a hotspot for all civilizations that have crossed the Mediterranean throughout history. Hundreds of unique grapevine cultivars are still cultivated in Sicily and its surrounding minor islands, though most of them are menaced by extinction. Wild grapevine is also present with isolated populations thriving along riverbanks. With the aim to evaluate the phylogenetic relationships among Sicilian varieties, and to assess the possible contribution of indigenous wild populations to the genetic makeup of cultivated grapevine, we analyzed 170 domestic cultivars and 125 wild plants, collected from 10 different populations, with 23 SSR markers. We also compared our data with published dataset from Eurasia. Results show that Sicilian wild populations are related to the cultivated Sicilian and Italian germplasm, suggesting events of introgression and/or domestication of local varieties.
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Molecular characterization of a diverse Iranian table grapevine germplasm using REMAP markers: population structure, linkage disequilibrium and association mapping of berry yield and quality traits. Biologia (Bratisl) 2018. [DOI: 10.2478/s11756-018-0158-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Riaz S, De Lorenzis G, Velasco D, Koehmstedt A, Maghradze D, Bobokashvili Z, Musayev M, Zdunic G, Laucou V, Andrew Walker M, Failla O, Preece JE, Aradhya M, Arroyo-Garcia R. Genetic diversity analysis of cultivated and wild grapevine (Vitis vinifera L.) accessions around the Mediterranean basin and Central Asia. BMC PLANT BIOLOGY 2018; 18:137. [PMID: 29945553 PMCID: PMC6020434 DOI: 10.1186/s12870-018-1351-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 06/13/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND The mountainous region between the Caucasus and China is considered to be the center of domestication for grapevine. Despite the importance of Central Asia in the history of grape growing, information about the extent and distribution of grape genetic variation in this region is limited in comparison to wild and cultivated grapevines from around the Mediterranean basin. The principal goal of this work was to survey the genetic diversity and relationships among wild and cultivated grape germplasm from the Caucasus, Central Asia, and the Mediterranean basin collectively to understand gene flow, possible domestication events and adaptive introgression. RESULTS A total of 1378 wild and cultivated grapevines collected around the Mediterranean basin and from Central Asia were tested with a set of 20 nuclear SSR markers. Genetic data were analyzed (Cluster analysis, Principal Coordinate Analysis and STRUCTURE) to identify groups, and the results were validated by Nei's genetic distance, pairwise FST analysis and assignment tests. All of these analyses identified three genetic groups: G1, wild accessions from Croatia, France, Italy and Spain; G2, wild accessions from Armenia, Azerbaijan and Georgia; and G3, cultivars from Spain, France, Italy, Georgia, Iran, Pakistan and Turkmenistan, which included a small group of wild accessions from Georgia and Croatia. Wild accessions from Georgia clustered with cultivated grape from the same area (proles pontica), but also with Western Europe (proles occidentalis), supporting Georgia as the ancient center of grapevine domestication. In addition, cluster analysis indicated that Western European wild grapes grouped with cultivated grapes from the same area, suggesting that the cultivated proles occidentalis contributed more to the early development of wine grapes than the wild vines from Eastern Europe. CONCLUSIONS The analysis of genetic relationships among the tested genotypes provided evidence of genetic relationships between wild and cultivated accessions in the Mediterranean basin and Central Asia. The genetic structure indicated a considerable amount of gene flow, which limited the differentiation between the two subspecies. The results also indicated that grapes with mixed ancestry occur in the regions where wild grapevines were domesticated.
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Affiliation(s)
- Summaira Riaz
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
| | - Gabriella De Lorenzis
- Department of Agricultural and Environmental Sciences, via Celoria 2, 20133 Milan, Italy
| | - Dianne Velasco
- Plant Sciences Department, UC Davis, Davis, CA 95616 USA
| | - Anne Koehmstedt
- USDA-ARS, National Clonal Germplasm Repository, University of California, Davis, CA 95616 USA
| | - David Maghradze
- Institute of Horticulture, Viticulture, and Oenology, Agricultural University of Georgia, Tbilisi, Georgia
| | - Zviad Bobokashvili
- Department of Fruit Crops, Genetic Resources Institute, Azerbaijan National Academy of Sciences, AZ1106, Baku, Azerbaijan
| | - Mirza Musayev
- Department of Fruit Crops, Genetic Resources Institute, Azerbaijan National Academy of Sciences, AZ1106, Baku, Azerbaijan
| | - Goran Zdunic
- Institute for Adriatic Crops and Karst Reclimation, Split, Croatia
| | | | - M. Andrew Walker
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
| | - Osvaldo Failla
- Department of Agricultural and Environmental Sciences, via Celoria 2, 20133 Milan, Italy
| | - John E. Preece
- USDA-ARS, National Clonal Germplasm Repository, University of California, Davis, CA 95616 USA
| | - Mallikarjuna Aradhya
- USDA-ARS, National Clonal Germplasm Repository, University of California, Davis, CA 95616 USA
| | - Rosa Arroyo-Garcia
- Dpto. Biotecnología, CBGP-INIA, Campus de Montegancedo, Autovía M40 km 38, Pozuelo de Alarcón, 28223 Madrid, Spain
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Butorac L, Hančević K, Lukšić K, Škvorc Ž, Leko M, Maul E, Zdunić G. Assessment of wild grapevine (Vitis vinifera ssp. sylvestris) chlorotypes and accompanying woody species in the Eastern Adriatic region. PLoS One 2018; 13:e0199495. [PMID: 29928046 PMCID: PMC6013236 DOI: 10.1371/journal.pone.0199495] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/10/2018] [Indexed: 11/19/2022] Open
Abstract
The Eastern Adriatic region, encompassing Croatia and Bosnia and Herzegovina, is considered an important area of natural populations of wild grapevines (Vitis vinifera ssp. sylvestris). The wild grapevine arises in the Eastern Adriatic region in a contact zone of the EU-Mediterranean and the sub-Mediterranean characterized by typical karst relief. This study focuses on the chloroplast DNA (cpDNA) analysis of wild grapevines and the biodiversity of accompanying woody species to better understand the genetic variation of the sylvestris populations of the Eastern Adriatic region and to investigate how this variation fits within today's wild grapevine distribution in the European continent. The allelic variation at nine cpDNA microsatellite loci of wild individuals was used to characterize haplotype diversity in 53 individuals from four population sites. All individuals were grouped into two chlorotypes: A and D, D being the rare haplotype among wild populations on the European continent. In total, 52 woody plant species were identified. However, the studied vegetation structures have been affected by permanent human pressure on natural resources and the preservation status of the collection sites. Based on our results, we conclude that the investigated areas were probably shelter zones for wild grapevine preservation during the unfavorable glaciation era.
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Affiliation(s)
| | | | - Katarina Lukšić
- Institute for Adriatic Crops and Karst Reclamation, Split, Croatia
| | - Željko Škvorc
- Faculty of Forestry, University of Zagreb, Zagreb, Croatia
| | - Mario Leko
- Federal Agromediterranean Institute, Mostar, Bosnia and Herzegovina
| | - Erika Maul
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Grapevine Breeding, Siebeldingen, Germany
| | - Goran Zdunić
- Institute for Adriatic Crops and Karst Reclamation, Split, Croatia
- * E-mail:
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Laucou V, Launay A, Bacilieri R, Lacombe T, Adam-Blondon AF, Bérard A, Chauveau A, de Andrés MT, Hausmann L, Ibáñez J, Le Paslier MC, Maghradze D, Martinez-Zapater JM, Maul E, Ponnaiah M, Töpfer R, Péros JP, Boursiquot JM. Extended diversity analysis of cultivated grapevine Vitis vinifera with 10K genome-wide SNPs. PLoS One 2018; 13:e0192540. [PMID: 29420602 PMCID: PMC5805323 DOI: 10.1371/journal.pone.0192540] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 01/25/2018] [Indexed: 12/18/2022] Open
Abstract
Grapevine is a very important crop species that is mainly cultivated worldwide for fruits, wine and juice. Identification of the genetic bases of performance traits through association mapping studies requires a precise knowledge of the available diversity and how this diversity is structured and varies across the whole genome. An 18k SNP genotyping array was evaluated on a panel of Vitis vinifera cultivars and we obtained a data set with no missing values for a total of 10207 SNPs and 783 different genotypes. The average inter-SNP spacing was ~47 kbp, the mean minor allele frequency (MAF) was 0.23 and the genetic diversity in the sample was high (He = 0.32). Fourteen SNPs, chosen from those with the highest MAF values, were sufficient to identify each genotype in the sample. Parentage analysis revealed 118 full parentages and 490 parent-offspring duos, thus confirming the close pedigree relationships within the cultivated grapevine. Structure analyses also confirmed the main divisions due to an eastern-western gradient and human usage (table vs. wine). Using a multivariate approach, we refined the structure and identified a total of eight clusters. Both the genetic diversity (He, 0.26-0.32) and linkage disequilibrium (LD, 28.8-58.2 kbp) varied between clusters. Despite the short span LD, we also identified some non-recombining haplotype blocks that may complicate association mapping. Finally, we performed a genome-wide association study that confirmed previous works and also identified new regions for important performance traits such as acidity. Taken together, all the results contribute to a better knowledge of the genetics of the cultivated grapevine.
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Affiliation(s)
- Valérie Laucou
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Amandine Launay
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Roberto Bacilieri
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Thierry Lacombe
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.,INRA Unité Expérimentale de Vassal, Centre de Ressources Biologiques de la Vigne, Marseillan-plage, France
| | | | - Aurélie Bérard
- EPGV, Univ Paris-Saclay, CEA, IG-CNG, INRA, Evry, France
| | | | | | - Ludger Hausmann
- JKI, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Javier Ibáñez
- ICVV, CSIC, Universidad de La Rioja, Gobierno de la Rioja, Logroño, Spain
| | | | | | | | - Erika Maul
- JKI, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Maharajah Ponnaiah
- EPGV, Univ Paris-Saclay, CEA, IG-CNG, INRA, Evry, France.,LBD, Univ UPMC, CNRS, INSERM, Paris, France
| | - Reinhard Töpfer
- JKI, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Jean-Pierre Péros
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Jean-Michel Boursiquot
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.,INRA Unité Expérimentale de Vassal, Centre de Ressources Biologiques de la Vigne, Marseillan-plage, France
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Aversano R, Basile B, Buonincontri MP, Carucci F, Carputo D, Frusciante L, Di Pasquale G. Dating the beginning of the Roman viticultural model in the Western Mediterranean: The case study of Chianti (Central Italy). PLoS One 2017; 12:e0186298. [PMID: 29140987 PMCID: PMC5687709 DOI: 10.1371/journal.pone.0186298] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 09/28/2017] [Indexed: 11/19/2022] Open
Abstract
Although domestication of the grapevine (Vitis vinifera L.) has been extensively documented, the history of genotype selection and evolution of vineyard management remain relatively neglected fields of study. The find of 454 waterlogged grapevine pips from a well-dated Etrusco-Roman site in the Chianti district (Tuscany, Central Italy) is an extraordinary chance to gain insights into the progress of viticulture occurring in a key historical period in one of the world's most famous wine regions. The molecular and geometrical analyses of grape seeds showed (a) the presence in the site of different grapevine individuals and (b) a sudden increase in pip size, occurring at around 200 BC, whic explainable by the selection and introduction of new varieties. In this period, the Etruscans settlers in Chianti were stimulated by northward-expanding Roman culture to use novel vineyard management practices. We hypothesize that one of the most important innovations may have been the introduction of pruning, inducing vine physiological conditions more favorable to pip growth. Such changes were the consequence of specific entrepreneurial choices made by the Romans in a period of economic investment in grape cultivation and wine making to satisfy the increased trade demand after the conquest of the Central-Western Mediterranean basin.
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Affiliation(s)
- Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Boris Basile
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | | | - Francesca Carucci
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Domenico Carputo
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Luigi Frusciante
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Gaetano Di Pasquale
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 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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Drori E, Rahimi O, Marrano A, Henig Y, Brauner H, Salmon-Divon M, Netzer Y, Prazzoli ML, Stanevsky M, Failla O, Weiss E, Grando MS. Collection and characterization of grapevine genetic resources (Vitis vinifera) in the Holy Land, towards the renewal of ancient winemaking practices. Sci Rep 2017; 7:44463. [PMID: 28303928 PMCID: PMC5358690 DOI: 10.1038/srep44463] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/08/2017] [Indexed: 11/10/2022] Open
Abstract
The importance and extent of wine consumption in all life aspects at the Holy Land is well documented. The Muslim influence in this region led to the abandonment of winemaking practices, and possible loss of indigenous wine varieties. Here we present a country wide collection of the local grapevine population including wild and cultivated forms, and its characterization by genetic, ampelographic and enological methods. The ampelographic analysis shows clear differences between Sativa and Sylvestris groups in flower, leaf and cluster parameters, and that most Sativa belong to proles orientalis. Genetic population analysis was conducted by analyzing 22 common SSR markers, determining first the unique genotypes, and internally assessing the population’s structure, showing the existence of two distinct Sativa and Sylvestris populations, and a third mixed one. Likewise, the relationship between the Israeli grapevine population and grapevine populations in Europe and parts of Asia was investigated, showing that the Israeli Sativa and Sylvestris populations cluster closely together, suggesting a common genetic source. Lastly, the enological characteristics of selected Sativa and Sylvestris genotypes are presented, demonstrating their potential for quality wine production. This research significantly contributes toward the re-establishment of indigenous and traditional local grapevine varieties into the modern international wine industry.
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Affiliation(s)
- Elyashiv Drori
- Department of Chemical Engineering and Biotechnology, Ariel University, Ariel, Israel.,Agriculture and Oenology Research Dept., Eastern R&D center, Ariel, Israel
| | - Oshrit Rahimi
- Agriculture and Oenology Research Dept., Eastern R&D center, Ariel, Israel
| | - Annarita Marrano
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, (TN) Italy
| | - Yakov Henig
- Agriculture and Oenology Research Dept., Eastern R&D center, Ariel, Israel
| | - Hodaya Brauner
- Agriculture and Oenology Research Dept., Eastern R&D center, Ariel, Israel
| | | | - Yishay Netzer
- Department of Chemical Engineering and Biotechnology, Ariel University, Ariel, Israel.,Agriculture and Oenology Research Dept., Eastern R&D center, Ariel, Israel
| | - Maria Lucia Prazzoli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, (TN) Italy
| | - Maria Stanevsky
- Agriculture and Oenology Research Dept., Eastern R&D center, Ariel, Israel
| | - Osvaldo Failla
- Department of Agricultural and Environmental Sciences, University of Milan, Italy
| | - Ehud Weiss
- The Martin (Szusz) Department of Land of Israel Studies and Archaeology, Bar-Ilan University, Ramat-Gan, Israel
| | - Maria Stella Grando
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, (TN) Italy.,Center Agriculture Food Environment, University of Trento, San Michele all'Adige (TN) Italy
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34
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Cantos M, Arroyo-García R, García JL, Lara M, Morales R, López MÁ, Gallardo A, Ocete CA, Rodríguez Á, Valle JM, Vaca R, González-Maestro M, Bánáti H, Ocete R. Current distribution and characterization of the wild grapevine populations in Andalusia (Spain). C R Biol 2017; 340:164-177. [PMID: 28256414 DOI: 10.1016/j.crvi.2017.01.004] [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: 12/16/2016] [Revised: 01/25/2017] [Accepted: 01/26/2017] [Indexed: 10/20/2022]
Abstract
For decades, human activities have gradually destroyed the natural habitats of wild grapevine, Vitis vinifera L. subsp. sylvestris (Gmelin) Hegi, and nowadays this species is endangered in southern Europe. In this paper, 94 populations of this species have been localized and characterized in the Andalusian region in the Iberian Peninsula between 1989 and 2013. Location, ecological aspects, and sanitary characteristics are described. Must properties and in vitro tolerance to calcareous conditions were also checked. The paper also contains a global description of female and male individuals. Two hundred individuals from six river basin populations have been sampled, and their genetic structure analyzed by using 25 nuclear microsatellites loci to investigate the gene diversity of wild grape populations in Andalusia at two levels: total individuals and at river basin populations. Also, the genetic relationship of wild and cultivated accessions has been tested. Wild grapevine is considered the ancestor of the cultivated varieties and should be preserved as this material could be used to start breeding programs of cultivated varieties and also to restore riverbank forests, which constitute one of the worst preserved ecosystems in the area.
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Affiliation(s)
- Manuel Cantos
- Instituto de Recursos Naturales y Agrobiología de Sevilla (CSIC), avenue Reina Mercedes 10, 41012 Sevilla, Spain.
| | - Rosa Arroyo-García
- Centro de Biotecnología y Genómica de Plantas, UPM-INIA, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - José Luis García
- Instituto de Recursos Naturales y Agrobiología de Sevilla (CSIC), avenue Reina Mercedes 10, 41012 Sevilla, Spain
| | - Miguel Lara
- IFAPA Rancho de la Merced, Ctra. de Trebujena km. 3.2, 11431 Jerez de la Frontera, Cádiz, Spain
| | - Ramón Morales
- Real Jardín Botánico (CSIC), Plaza de Murillo 2, 28014 Madrid, Spain
| | - María Ángeles López
- Laboratorio Entomología Aplicada, Universidad de Sevilla, avenue Reina Mercedes 6, 41012 Sevilla, Spain
| | - Antonio Gallardo
- Laboratorio Entomología Aplicada, Universidad de Sevilla, avenue Reina Mercedes 6, 41012 Sevilla, Spain
| | - Carlos Alvar Ocete
- Laboratorio Entomología Aplicada, Universidad de Sevilla, avenue Reina Mercedes 6, 41012 Sevilla, Spain
| | - Álvaro Rodríguez
- Escuela Universitaria de Ingeniería, Universidad del País Vasco, Vitoria-Gasteiz, Spain
| | - José Manuel Valle
- Escuela Universitaria de Ingeniería, Universidad del País Vasco, Vitoria-Gasteiz, Spain
| | - Ramón Vaca
- Macià Batle Wineries, 07320 Santa María del Camí, Illes Balears, Spain
| | - Magdalena González-Maestro
- Instituto de Recursos Naturales y Agrobiología de Sevilla (CSIC), avenue Reina Mercedes 10, 41012 Sevilla, Spain
| | - Hajnalka Bánáti
- Department of Ecotoxicology, Central Environmental and Food Science Research Institute, Herman Ottó út 15, 1022 Budapest, Hungary
| | - Rafael Ocete
- Laboratorio Entomología Aplicada, Universidad de Sevilla, avenue Reina Mercedes 6, 41012 Sevilla, Spain
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35
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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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36
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Decroocq S, Cornille A, Tricon D, Babayeva S, Chague A, Eyquard JP, Karychev R, Dolgikh S, Kostritsyna T, Liu S, Liu W, Geng W, Liao K, Asma BM, Akparov Z, Giraud T, Decroocq V. New insights into the history of domesticated and wild apricots and its contribution to Plum pox virus resistance. Mol Ecol 2016; 25:4712-29. [PMID: 27480465 DOI: 10.1111/mec.13772] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 07/14/2016] [Accepted: 07/25/2016] [Indexed: 12/01/2022]
Abstract
Studying domesticated species and their wild relatives allows understanding of the mechanisms of population divergence and adaptation, and identifying valuable genetic resources. Apricot is an important fruit in the Northern hemisphere, where it is threatened by the Plum pox virus (PPV), causing the sharka disease. The histories of apricot domestication and of its resistance to sharka are however still poorly understood. We used 18 microsatellite markers to genotype a collection of 230 wild trees from Central Asia and 142 cultivated apricots as representatives of the worldwide cultivated apricot germplasm; we also performed experimental PPV inoculation tests. The genetic markers revealed highest levels of diversity in Central Asian and Chinese wild and cultivated apricots, confirming an origin in this region. In cultivated apricots, Chinese accessions were differentiated from more Western accessions, while cultivated apricots were differentiated from wild apricots. An approximate Bayesian approach indicated that apricots likely underwent two independent domestication events, with bottlenecks, from the same wild population. Central Asian native apricots exhibited genetic subdivision and high frequency of resistance to sharka. Altogether, our results contribute to the understanding of the domestication history of cultivated apricot and point to valuable genetic diversity in the extant genetic resources of wild apricots.
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Affiliation(s)
- Stéphane Decroocq
- UMR 1332 BFP, Equipe de virologie, INRA, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France.,UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Amandine Cornille
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala, Sweden
| | - David Tricon
- UMR 1332 BFP, Equipe de virologie, INRA, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France.,UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Sevda Babayeva
- Genetic Resources Institute of ANAS, Azadlig ave. 155, AZ1106, Baku, Azerbaijan
| | - Aurélie Chague
- UMR 1332 BFP, Equipe de virologie, INRA, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France.,UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Jean-Philippe Eyquard
- UMR 1332 BFP, Equipe de virologie, INRA, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France.,UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Raul Karychev
- Kazakh Research Institute of Horticulture and Viticulture, 238-a Gagarin Avenue, 480060, Almaty, Kazakhstan
| | - Svetlana Dolgikh
- Kazakh Research Institute of Horticulture and Viticulture, 238-a Gagarin Avenue, 480060, Almaty, Kazakhstan
| | - Tatiana Kostritsyna
- Botanical Garden of National Academy of Sciences, Akhunbaeva street 1a, 720064, Bishkek, Kyrgyzstan
| | - Shuo Liu
- UMR 1332 BFP, Equipe de virologie, INRA, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France.,UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France.,Liaoning Institute of Pomology, Tiedong Street, Xiongyue Town, Bayuquan District, Yingkou City, Liaoning, 115009, China
| | - Weisheng Liu
- Liaoning Institute of Pomology, Tiedong Street, Xiongyue Town, Bayuquan District, Yingkou City, Liaoning, 115009, China
| | - Wenjuan Geng
- College of Horticulture & Forestry Sciences, Xinjiang Agricultural University, 311 NongDaDong Road, 830052, Urumqi City, Xinjiang, China
| | - Kang Liao
- College of Horticulture & Forestry Sciences, Xinjiang Agricultural University, 311 NongDaDong Road, 830052, Urumqi City, Xinjiang, China
| | - Bayram M Asma
- Department of Horticulture, Inonu University, Malatya, 44210, Turkey
| | - Zeynal Akparov
- Genetic Resources Institute of ANAS, Azadlig ave. 155, AZ1106, Baku, Azerbaijan
| | - Tatiana Giraud
- Ecologie Systematique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France.
| | - Véronique Decroocq
- UMR 1332 BFP, Equipe de virologie, INRA, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France. .,UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France.
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37
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Akagi T, Hanada T, Yaegaki H, Gradziel TM, Tao R. Genome-wide view of genetic diversity reveals paths of selection and cultivar differentiation in peach domestication. DNA Res 2016; 23:271-82. [PMID: 27085183 PMCID: PMC4909313 DOI: 10.1093/dnares/dsw014] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 03/02/2016] [Indexed: 01/19/2023] Open
Abstract
Domestication and cultivar differentiation are requisite processes for establishing cultivated crops. These processes inherently involve substantial changes in population structure, including those from artificial selection of key genes. In this study, accessions of peach (Prunus persica) and its wild relatives were analysed genome-wide to identify changes in genetic structures and gene selections associated with their differentiation. Analysis of genome-wide informative single-nucleotide polymorphism loci revealed distinct changes in genetic structures and delineations among domesticated peach and its wild relatives and among peach landraces and modern fruit (F) and modern ornamental (O-A) cultivars. Indications of distinct changes in linkage disequilibrium extension/decay and of strong population bottlenecks or inbreeding were identified. Site frequency spectrum- and extended haplotype homozygosity-based evaluation of genome-wide genetic diversities supported selective sweeps distinguishing the domesticated peach from its wild relatives and each F/O-A cluster from the landrace clusters. The regions with strong selective sweeps harboured promising candidates for genes subjected to selection. Further sequence-based evaluation further defined the candidates and revealed their characteristics. All results suggest opportunities for identifying critical genes associated with each differentiation by analysing genome-wide genetic diversity in currently established populations. This approach obviates the special development of genetic populations, which is particularly difficult for long-lived tree crops.
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Affiliation(s)
- Takashi Akagi
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kita-shirakawa, Oiwake-cho, Kyoto 606-8502, Japan
| | - Toshio Hanada
- Apple Research Division, NARO Institute of Fruit Tree Science, Morioka 020-0123, Japan
| | - Hideaki Yaegaki
- Breeding and Pest Management Division, NARO Institute, Tsukuba, Ibaragi 305-8605, Japan
| | - Thomas M Gradziel
- Department of Plant Sciences, University of California Davis, CA 95616, USA
| | - Ryutaro Tao
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kita-shirakawa, Oiwake-cho, Kyoto 606-8502, Japan
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38
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Tello J, Torres-Pérez R, Grimplet J, Carbonell-Bejerano P, Martínez-Zapater JM, Ibáñez J. Polymorphisms and minihaplotypes in the VvNAC26 gene associate with berry size variation in grapevine. BMC PLANT BIOLOGY 2015; 15:253. [PMID: 26499326 PMCID: PMC4618959 DOI: 10.1186/s12870-015-0622-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 09/18/2015] [Indexed: 05/09/2023]
Abstract
BACKGROUND Domestication and selection of Vitis vinifera L. for table and wine grapes has led to a large level of berry size diversity in current grapevine cultivars. Identifying the genetic basis for this natural variation is paramount both for breeding programs and for elucidating which genes contributed to crop evolution during domestication and selection processes. The gene VvNAC26, which encodes a NAC domain-containing transcription factor, has been related to the early development of grapevine flowers and berries. It was selected as candidate gene for an association study to elucidate its possible participation in the natural variation of reproductive traits in cultivated grapevine. METHODS A grapevine collection of 114 varieties was characterized during three consecutive seasons for different berry and bunch traits. The promoter and coding regions of VvNAC26 gene (VIT_01s0026g02710) were sequenced in all the varieties of the collection, and the existing polymorphisms (SNP and INDEL) were detected. The corresponding haplotypes were inferred and used for a phylogenetic analysis. The possible associations between genotypic and phenotypic data were analyzed independently for each season data, using different models and significance thresholds. RESULTS A total of 30 non-rare polymorphisms were detected in the VvNAC26 sequence, and 26 different haplotypes were inferred. Phylogenetic analysis revealed their clustering in two major haplogroups with marked phenotypic differences in berry size between varieties harboring haplogroup-specific alleles. After correcting the statistical models for the effect of the population genetic stratification, we found a set of polymorphisms associated with berry size explaining between 8.4 and 21.7% (R(2)) of trait variance, including those generating the differentiation between both haplogroups. Haplotypes built from only three polymorphisms (minihaplotypes) were also associated with this trait (R(2): 17.5 - 26.6%), supporting the involvement of this gene in the natural variation for berry size. CONCLUSIONS Our results suggest the participation of VvNAC26 in the determination of the grape berry final size. Different VvNAC26 polymorphisms and their combination showed to be associated with different features of the fruit. The phylogenetic relationships between the VvNAC26 haplotypes and the association results indicate that this nucleotide variation may have contributed to the differentiation between table and wine grapes.
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Affiliation(s)
- Javier Tello
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Carretera LO-20 salida 13, Finca La Grajera, 26007, Logroño, Spain.
| | - Rafael Torres-Pérez
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Carretera LO-20 salida 13, Finca La Grajera, 26007, Logroño, Spain.
| | - Jérôme Grimplet
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Carretera LO-20 salida 13, Finca La Grajera, 26007, Logroño, Spain.
| | - Pablo Carbonell-Bejerano
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Carretera LO-20 salida 13, Finca La Grajera, 26007, Logroño, Spain.
| | - José Miguel Martínez-Zapater
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Carretera LO-20 salida 13, Finca La Grajera, 26007, Logroño, Spain.
| | - Javier Ibáñez
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Carretera LO-20 salida 13, Finca La Grajera, 26007, Logroño, Spain.
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39
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Potenza E, Racchi ML, Sterck L, Coller E, Asquini E, Tosatto SCE, Velasco R, Van de Peer Y, Cestaro A. Exploration of alternative splicing events in ten different grapevine cultivars. BMC Genomics 2015; 16:706. [PMID: 26380971 PMCID: PMC4574008 DOI: 10.1186/s12864-015-1922-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 09/11/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The complex dynamics of gene regulation in plants are still far from being fully understood. Among many factors involved, alternative splicing (AS) in particular is one of the least well documented. For many years, AS has been considered of less relevant in plants, especially when compared to animals, however, since the introduction of next generation sequencing techniques the number of plant genes believed to be alternatively spliced has increased exponentially. RESULTS Here, we performed a comprehensive high-throughput transcript sequencing of ten different grapevine cultivars, which resulted in the first high coverage atlas of the grape berry transcriptome. We also developed findAS, a software tool for the analysis of alternatively spliced junctions. We demonstrate that at least 44% of multi-exonic genes undergo AS and a large number of low abundance splice variants is present within the 131.622 splice junctions we have annotated from Pinot noir. CONCLUSIONS Our analysis shows that ~70% of AS events have relatively low expression levels, furthermore alternative splice sites seem to be enriched near the constitutive ones in some extent showing the noise of the splicing mechanisms. However, AS seems to be extensively conserved among the 10 cultivars.
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Affiliation(s)
- Emilio Potenza
- Fondazione Edmund Mach, Via E. Mach 1, 38010 S., Michele all'Adige, TN, Italy. .,Department of Agri-Food Production and Environmental Sciences, Università degli Studi di Firenze, Firenze, 50121, Italy. .,Department of Plant Systems Biology, VIB, Ghent, Belgium. .,Department of Biomedical Sciences, Università degli Studi di Padova, Padova, 35131, Italy.
| | - Milvia Luisa Racchi
- Department of Agri-Food Production and Environmental Sciences, Università degli Studi di Firenze, Firenze, 50121, Italy.
| | - Lieven Sterck
- Department of Plant Systems Biology, VIB, Ghent, Belgium. .,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
| | - Emanuela Coller
- Fondazione Edmund Mach, Via E. Mach 1, 38010 S., Michele all'Adige, TN, Italy.
| | - Elisa Asquini
- Fondazione Edmund Mach, Via E. Mach 1, 38010 S., Michele all'Adige, TN, Italy.
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, Università degli Studi di Padova, Padova, 35131, Italy.
| | - Riccardo Velasco
- Fondazione Edmund Mach, Via E. Mach 1, 38010 S., Michele all'Adige, TN, Italy.
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, Ghent, Belgium. .,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. .,Department of Genetics, Genomics Research Institute, University of Pretoria, Pretoria, South Africa.
| | - Alessandro Cestaro
- Fondazione Edmund Mach, Via E. Mach 1, 38010 S., Michele all'Adige, TN, Italy.
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40
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Zehdi-Azouzi S, Cherif E, Moussouni S, Gros-Balthazard M, Abbas Naqvi S, Ludeña B, Castillo K, Chabrillange N, Bouguedoura N, Bennaceur M, Si-Dehbi F, Abdoulkader S, Daher A, Terral JF, Santoni S, Ballardini M, Mercuri A, Ben Salah M, Kadri K, Othmani A, Littardi C, Salhi-Hannachi A, Pintaud JC, Aberlenc-Bertossi F. Genetic structure of the date palm (Phoenix dactylifera) in the Old World reveals a strong differentiation between eastern and western populations. ANNALS OF BOTANY 2015; 116:101-12. [PMID: 26113618 PMCID: PMC4479755 DOI: 10.1093/aob/mcv068] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/02/2015] [Accepted: 04/13/2015] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND AIMS Date palms (Phoenix dactylifera, Arecaceae) are of great economic and ecological value to the oasis agriculture of arid and semi-arid areas. However, despite the availability of a large date palm germplasm spreading from the Atlantic shores to Southern Asia, improvement of the species is being hampered by a lack of information on global genetic diversity and population structure. In order to contribute to the varietal improvement of date palms and to provide new insights on the influence of geographic origins and human activity on the genetic structure of the date palm, this study analysed the diversity of the species. METHODS Genetic diversity levels and population genetic structure were investigated through the genotyping of a collection of 295 date palm accessions ranging from Mauritania to Pakistan using a set of 18 simple sequence repeat (SSR) markers and a plastid minisatellite. KEY RESULTS Using a Bayesian clustering approach, the date palm genotypes can be structured into two different gene pools: the first, termed the Eastern pool, consists of accessions from Asia and Djibouti, whilst the second, termed the Western pool, consists of accessions from Africa. These results confirm the existence of two ancient gene pools that have contributed to the current date palm diversity. The presence of admixed genotypes is also noted, which points at gene flows between eastern and western origins, mostly from east to west, following a human-mediated diffusion of the species. CONCLUSIONS This study assesses the distribution and level of genetic diversity of accessible date palm resources, provides new insights on the geographic origins and genetic history of the cultivated component of this species, and confirms the existence of at least two domestication origins. Furthermore, the strong genetic structure clearly established here is a prerequisite for any breeding programme exploiting the effective polymorphism related to each gene pool.
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Affiliation(s)
- Salwa Zehdi-Azouzi
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Emira Cherif
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe D
| | - Souhila Moussouni
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Muriel Gros-Balthazard
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe D
| | - Summar Abbas Naqvi
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Bertha Ludeña
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe D
| | - Karina Castillo
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Nathalie Chabrillange
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Nadia Bouguedoura
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Malika Bennaceur
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Farida Si-Dehbi
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Sabira Abdoulkader
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Abdourahman Daher
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Jean-Frederic Terral
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Sylvain Santoni
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Marco Ballardini
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Antonio Mercuri
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Mohamed Ben Salah
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Karim Kadri
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Ahmed Othmani
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Claudio Littardi
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Amel Salhi-Hannachi
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Jean-Christophe Pintaud
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Frédérique Aberlenc-Bertossi
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
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De Lorenzis G, Chipashvili R, Failla O, Maghradze D. Study of genetic variability in Vitis vinifera L. germplasm by high-throughput Vitis18kSNP array: the case of Georgian genetic resources. BMC PLANT BIOLOGY 2015; 15:154. [PMID: 26099513 PMCID: PMC4477415 DOI: 10.1186/s12870-015-0510-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 04/28/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Georgia, in the Caucasian region, is considered the first domestication centre of grapevine. This country is characterized by high morphological variability of cultivated (Vitis vinifera L. subsp. sativa (DC.) Hegi) and wild (Vitis vinifera L. subsp. sylvestris (Gmel.) Hegi) compartments. The main objective of this study was to investigate the level of genetic diversity obtained by the novel custom Vitis18kSNP array, in order to analyse 71 grapevine accessions representative of wild and cultivated Georgian germplasms. RESULTS The number of loci successfully amplified was 15,317 out of 18,775 SNP and 79 % of loci resulted polymorphic. Sixty-eight unique profiles were identified, 42 for the sativa and 26 for the sylvestris compartment. Cluster analysis highlighted two main groups, one for cultivars and another for wild individuals, while a genetic structure according to accession taxonomic status and cultivar geographical origin was revealed by multivariate analysis, differentiating clearly the genotypes into 3 main groups, two groups including cultivars and one for wild individuals, even though a considerable overlapping area was observed. CONCLUSIONS Pattern of genetic diversity structure presented an additional proof that grapevine domestication events took place in the Caucasian region contributing to the crop evolution. Our results demonstrated a moderate differentiation between sativa and sylvestris compartments, even though a connection between several samples of both subspecies may be assumed for the occurrence of cross hybridization events among native wild populations and the cultivated accessions. Nevertheless, first degree relationships have not been discovered between wild and cultivated individuals.
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Affiliation(s)
- Gabriella De Lorenzis
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milan, Italy.
| | - Ramaz Chipashvili
- Institute of Viticulture and Oenology, Agricultural University of Georgia, Tbilisi, Georgia.
| | - Osvaldo Failla
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milan, Italy.
| | - David Maghradze
- Institute of Viticulture and Oenology, Agricultural University of Georgia, Tbilisi, Georgia.
- National Wine Agency of Georgia, Tbilisi, Georgia.
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De Lorenzis G, Chipashvili R, Failla O, Maghradze D. Study of genetic variability in Vitis vinifera L. germplasm by high-throughput Vitis18kSNP array: the case of Georgian genetic resources. BMC PLANT BIOLOGY 2015. [PMID: 26099513 DOI: 10.5061/dryad.521h5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND Georgia, in the Caucasian region, is considered the first domestication centre of grapevine. This country is characterized by high morphological variability of cultivated (Vitis vinifera L. subsp. sativa (DC.) Hegi) and wild (Vitis vinifera L. subsp. sylvestris (Gmel.) Hegi) compartments. The main objective of this study was to investigate the level of genetic diversity obtained by the novel custom Vitis18kSNP array, in order to analyse 71 grapevine accessions representative of wild and cultivated Georgian germplasms. RESULTS The number of loci successfully amplified was 15,317 out of 18,775 SNP and 79 % of loci resulted polymorphic. Sixty-eight unique profiles were identified, 42 for the sativa and 26 for the sylvestris compartment. Cluster analysis highlighted two main groups, one for cultivars and another for wild individuals, while a genetic structure according to accession taxonomic status and cultivar geographical origin was revealed by multivariate analysis, differentiating clearly the genotypes into 3 main groups, two groups including cultivars and one for wild individuals, even though a considerable overlapping area was observed. CONCLUSIONS Pattern of genetic diversity structure presented an additional proof that grapevine domestication events took place in the Caucasian region contributing to the crop evolution. Our results demonstrated a moderate differentiation between sativa and sylvestris compartments, even though a connection between several samples of both subspecies may be assumed for the occurrence of cross hybridization events among native wild populations and the cultivated accessions. Nevertheless, first degree relationships have not been discovered between wild and cultivated individuals.
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Affiliation(s)
- Gabriella De Lorenzis
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milan, Italy.
| | - Ramaz Chipashvili
- Institute of Viticulture and Oenology, Agricultural University of Georgia, Tbilisi, Georgia.
| | - Osvaldo Failla
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milan, Italy.
| | - David Maghradze
- Institute of Viticulture and Oenology, Agricultural University of Georgia, Tbilisi, Georgia.
- National Wine Agency of Georgia, Tbilisi, Georgia.
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Karataş DD, Karataş H, Laucou V, Sarikamiş G, Riahi L, Bacilieri R, This P. Genetic diversity of wild and cultivated grapevine accessions from southeast Turkey. Hereditas 2015; 151:73-80. [PMID: 25363274 DOI: 10.1111/hrd2.00039] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 06/27/2014] [Indexed: 11/27/2022] Open
Abstract
Wild grapevine genetic diversity in southeast Turkey has not been documented to date. In the present work, in order to clarify the relationships between wild and cultivated grape accessions from southeastern Turkey, 22 nuclear and three chloroplast microsatellite loci were used on 21 wild grapevine Vitis vinifera L. ssp. sylvestris (Gmelin) and 13 cultivated grapevine Vitis vinifera ssp. sativa accessions. The number of alleles per SSR locus ranged from 4 (VVIn16) to 20 (VVIv67) and the mean allele number per locus was 10.09. Expected locus heterozygosity ranged from 0.586 (locus VVIb01) to 0.898 (locus (VVIv67)). The three cpSSR molecular markers presented variation in size both in cultivars and in wild Turkish accessions. Two size variants were detected for cpSSR3 (106 and 107 bp) for cpSSR5 (104 and 105 bp), and for cpSSR10 (115 and 116 bp). The six alleles in wild grapevines fell into three haplotypes B, C and D. A genetic structure according to accessions taxonomic status (wild or cultivated) was revealed by UPGMA analysis. This highlighted a clear separation between domesticated and wild accessions in Turkish germplasm. The results pointed out the need to further collect and characterize this wild and cultivated grapevine germplasm.
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Abstract
Grapevine is a high value vegetatively propagated fruit crop that suffers from numerous viruses, including some that seriously affect the profitability of vineyards. Nowadays, 64 viruses belonging to different genera and families have been reported in grapevines and new virus species will likely be described in the future. Three viral diseases namely leafroll, rugose wood, and infectious degeneration are of major economic importance worldwide. The viruses associated with these diseases are transmitted by mealybugs, scale and soft scale insects, or dagger nematodes. Here, we review control measures of the major grapevine viral diseases. More specifically, emphasis is laid on (i) approaches for the production of clean stocks and propagative material through effective sanitation, robust diagnosis, as well as local and regional certification efforts, (ii) the management of vectors of viruses using cultural, biological, and chemical methods, and (iii) the production of resistant grapevines mainly through the application of genetic engineering. The benefits and limitations of the different control measures are discussed with regard to accomplishments and future research directions.
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Affiliation(s)
- Varvara I Maliogka
- Faculty of agriculture, Forestry and Natural Environment, School of Agriculture, Plant Pathology Lab, Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | | | - Marc Fuchs
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, New York State Agricultural Experiment Station, Geneva, New York, USA
| | - Nikolaos I Katis
- Faculty of agriculture, Forestry and Natural Environment, School of Agriculture, Plant Pathology Lab, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Fodor A, Segura V, Denis M, Neuenschwander S, Fournier-Level A, Chatelet P, Homa FAA, Lacombe T, This P, Le Cunff L. Genome-wide prediction methods in highly diverse and heterozygous species: proof-of-concept through simulation in grapevine. PLoS One 2014; 9:e110436. [PMID: 25365338 PMCID: PMC4217727 DOI: 10.1371/journal.pone.0110436] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 09/19/2014] [Indexed: 11/20/2022] Open
Abstract
Nowadays, genome-wide association studies (GWAS) and genomic selection (GS) methods which use genome-wide marker data for phenotype prediction are of much potential interest in plant breeding. However, to our knowledge, no studies have been performed yet on the predictive ability of these methods for structured traits when using training populations with high levels of genetic diversity. Such an example of a highly heterozygous, perennial species is grapevine. The present study compares the accuracy of models based on GWAS or GS alone, or in combination, for predicting simple or complex traits, linked or not with population structure. In order to explore the relevance of these methods in this context, we performed simulations using approx 90,000 SNPs on a population of 3,000 individuals structured into three groups and corresponding to published diversity grapevine data. To estimate the parameters of the prediction models, we defined four training populations of 1,000 individuals, corresponding to these three groups and a core collection. Finally, to estimate the accuracy of the models, we also simulated four breeding populations of 200 individuals. Although prediction accuracy was low when breeding populations were too distant from the training populations, high accuracy levels were obtained using the sole core-collection as training population. The highest prediction accuracy was obtained (up to 0.9) using the combined GWAS-GS model. We thus recommend using the combined prediction model and a core-collection as training population for grapevine breeding or for other important economic crops with the same characteristics.
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Affiliation(s)
- Agota Fodor
- UMT Geno-Vigne, IFV-INRA-Montpellier Supagro, Montpellier, France; UMR AGAP, INRA, Montpellier, France
| | | | | | - Samuel Neuenschwander
- University of Lausanne, Department of Ecology and Evolution, Lausanne, Switzerland; University of Lausanne, Swiss Institute of Bioinformatics, Vital-IT, Lausanne, Switzerland
| | | | | | | | | | - Patrice This
- UMT Geno-Vigne, IFV-INRA-Montpellier Supagro, Montpellier, France; UMR AGAP, INRA, Montpellier, France
| | - Loic Le Cunff
- UMT Geno-Vigne, IFV-INRA-Montpellier Supagro, Montpellier, France; UMR AGAP, INRA, Montpellier, France
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Santos S, Oliveira M, Amorim A, van Asch B. A forensic perspective on the genetic identification of grapevine (Vitis vinifera L.) varieties using STR markers. Electrophoresis 2014; 35:3201-7. [PMID: 25146979 DOI: 10.1002/elps.201400107] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 08/10/2014] [Accepted: 08/12/2014] [Indexed: 11/07/2022]
Abstract
The grapevine (Vitis vinifera subsp. vinifera) is one of the most important agricultural crops worldwide. A long interest in the historical origins of ancient and cultivated current grapevines, as well as the need to establish phylogenetic relationships and parentage, solve homonymies and synonymies, fingerprint cultivars and clones, and assess the authenticity of plants and wines has encouraged the development of genetic identification methods. STR analysis is currently the most commonly used method for these purposes. A large dataset of grapevines genotypes for many cultivars worldwide has been produced in the last decade using a common set of recommended dinucleotide nuclear STRs. This type of marker has been replaced by long core-repeat loci in standardized state-of-the-art human forensic genotyping. The first steps toward harmonized grapevine genotyping have already been taken to bring the genetic identification methods closer to human forensic STR standards by previous authors. In this context, we bring forward a set of basic suggestions that reinforce the need to (i) guarantee trueness-to-type of the sample; (ii) use the long core-repeat markers; (iii) verify the specificity and amplification consistency of PCR primers; (iv) sequence frequent alleles and use these standardized allele ladders; (v) consider mutation rates when evaluating results of STR-based parentage and pedigree analysis; (vi) genotype large and representative samples in order to obtain allele frequency databases; (vii) standardize genotype data by establishing allele nomenclature based on repeat number to facilitate information exchange and data compilation.
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Affiliation(s)
- Sara Santos
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal; Faculdade de Ciências da Universidade do Porto, Porto, Portugal
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Picq S, Santoni S, Lacombe T, Latreille M, Weber A, Ardisson M, Ivorra S, Maghradze D, Arroyo-Garcia R, Chatelet P, This P, Terral JF, Bacilieri R. A small XY chromosomal region explains sex determination in wild dioecious V. vinifera and the reversal to hermaphroditism in domesticated grapevines. BMC PLANT BIOLOGY 2014; 14:229. [PMID: 25179565 PMCID: PMC4167142 DOI: 10.1186/s12870-014-0229-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 08/18/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND In Vitis vinifera L., domestication induced a dramatic change in flower morphology: the wild sylvestris subspecies is dioecious while hermaphroditism is largely predominant in the domesticated subsp. V. v. vinifera. The characterisation of polymorphisms in genes underlying the sex-determining chromosomal region may help clarify the history of domestication in grapevine and the evolution of sex chromosomes in plants. In the genus Vitis, sex determination is putatively controlled by one major locus with three alleles, male M, hermaphrodite H and female F, with an allelic dominance M > H > F. Previous genetic studies located the sex locus on chromosome 2. We used DNA polymorphisms of geographically diverse V. vinifera genotypes to confirm the position of this locus, to characterise the genetic diversity and traces of selection in candidate genes, and to explore the origin of hermaphroditism. RESULTS In V. v. sylvestris, a sex-determining region of 154.8 kb, also present in other Vitis species, spans less than 1% of chromosome 2. It displays haplotype diversity, linkage disequilibrium and differentiation that typically correspond to a small XY sex-determining region with XY males and XX females. In male alleles, traces of purifying selection were found for a trehalose phosphatase, an exostosin and a WRKY transcription factor, with strikingly low polymorphism levels between distant geographic regions. Both diversity and network analysis revealed that H alleles are more closely related to M than to F alleles. CONCLUSIONS Hermaphrodite alleles appear to derive from male alleles of wild grapevines, with successive recombination events allowing import of diversity from the X into the Y chromosomal region and slowing down the expansion of the region into a full heteromorphic chromosome. Our data are consistent with multiple domestication events and show traces of introgression from other Asian Vitis species into the cultivated grapevine gene pool.
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Affiliation(s)
- Sandrine Picq
- />Centre de Bio-Archéologie et d’Ecologie CBAE (UMR 5059 CNRS/Université Montpellier 2/EPHE/INRAP). Equipe Interactions, Biodiversité, Sociétés, Institut de Botanique, 163 rue Auguste Broussonet, 34090 Montpellier, France
| | - Sylvain Santoni
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Thierry Lacombe
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Muriel Latreille
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Audrey Weber
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Morgane Ardisson
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Sarah Ivorra
- />Centre de Bio-Archéologie et d’Ecologie CBAE (UMR 5059 CNRS/Université Montpellier 2/EPHE/INRAP). Equipe Interactions, Biodiversité, Sociétés, Institut de Botanique, 163 rue Auguste Broussonet, 34090 Montpellier, France
| | - David Maghradze
- />Institute of Horticulture, Viticulture and Oenology, Agrarian University of Georgia, University Campus at Digomi, David Aghmashenebeli Alley, 13-th km. 0159, Tbilisi, Georgia
| | - Rosa Arroyo-Garcia
- />CBGP-INIA. Dpto Biotecnología, Campus de Montegancedo, Autovía M40, km38, 28223 Pozuelo de Alarcón, Madrid Spain
| | - Philippe Chatelet
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Patrice This
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Jean-Frédéric Terral
- />Centre de Bio-Archéologie et d’Ecologie CBAE (UMR 5059 CNRS/Université Montpellier 2/EPHE/INRAP). Equipe Interactions, Biodiversité, Sociétés, Institut de Botanique, 163 rue Auguste Broussonet, 34090 Montpellier, France
- />Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier, France
| | - Roberto Bacilieri
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
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Genotyping of Vitis vinifera L. within the Slovak national collection of genetic resources. Open Life Sci 2014. [DOI: 10.2478/s11535-014-0314-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractMicrosatellites were used as a very effective tool for genetic diversity analysis and characterization of 51 grapevine (Vitis vinifera L.) accessions from the national collection of genetic resources. Genetic diversity was relatively high, 8.91 alleles were detected per analysed microsatellite locus in average, and fifty-one accessions were distinguished into 45 groups. Distribution of recent Slovak cultivars across the dendrogram accented both their genetic diversity and the effectiveness of the national breeding program in maintaining genetic diversity and generating new genetic variants. Each cultivar was different from the others and twelve of them contained 77.6% of the total genetic diversity of the whole analysed set. Microsatellite patterns were also able to confirm parentage in selected Slovak cultivars. An unusual phenomenon of triallelism was also detected in one of the analysed accessions. The present study has initiated molecular characterization within the national grapevine genetic resource collection and their comparison with well-established international cultivars.
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Doligez A, Bertrand Y, Farnos M, Grolier M, Romieu C, Esnault F, Dias S, Berger G, François P, Pons T, Ortigosa P, Roux C, Houel C, Laucou V, Bacilieri R, Péros JP, This P. New stable QTLs for berry weight do not colocalize with QTLs for seed traits in cultivated grapevine (Vitis vinifera L.). BMC PLANT BIOLOGY 2013; 13:217. [PMID: 24350702 PMCID: PMC3878267 DOI: 10.1186/1471-2229-13-217] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 12/10/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND In grapevine, as in other fruit crops, fruit size and seed content are key components of yield and quality; however, very few Quantitative Trait Loci (QTLs) for berry weight and seed content (number, weight, and dry matter percentage) have been discovered so far. To identify new stable QTLs for marker-assisted selection and candidate gene identification, we performed simultaneous QTL detection in four mapping populations (seeded or seedless) with various genetic backgrounds. RESULTS For berry weight, we identified five new QTLs, on linkage groups (LGs) 1, 8, 11, 17 and 18, in addition to the known major QTL on LG 18. The QTL with the largest effect explained up to 31% of total variance and was found in two genetically distant populations on LG 17, where it colocalized with a published putative domestication locus. For seed traits, besides the major QTLs on LG 18 previously reported, we found four new QTLs explaining up to 51% of total variance, on LGs 4, 5, 12 and 14. The previously published QTL for seed number on LG 2 was found related in fact to sex. We found colocalizations between seed and berry weight QTLs only for the major QTL on LG 18 in a seedless background, and on LGs 1 and 13 in a seeded background. Candidate genes belonging to the cell number regulator CNR or cytochrome P450 families were found under the berry weight QTLs on LGs 1, 8, and 17. The involvement of these gene families in fruit weight was first described in tomato using a QTL-cloning approach. Several other interesting candidate genes related to cell wall modifications, water import, auxin and ethylene signalling, transcription control, or organ identity were also found under berry weight QTLs. CONCLUSION We discovered a total of nine new QTLs for berry weight or seed traits in grapevine, thereby increasing more than twofold the number of reliable QTLs for these traits available for marker assisted selection or candidate gene studies. The lack of colocalization between berry and seed QTLs suggests that these traits may be partly dissociated.
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Affiliation(s)
- Agnès Doligez
- INRA, UMR AGAP, Batiment 21 2 place Viala, F-34060 Montpellier Cedex 1, France
| | - Yves Bertrand
- INRA, UMR AGAP, Batiment 21 2 place Viala, F-34060 Montpellier Cedex 1, France
| | - Marc Farnos
- INRA, UMR AGAP, Batiment 21 2 place Viala, F-34060 Montpellier Cedex 1, France
| | - Michel Grolier
- INRA, UMR AGAP, Batiment 21 2 place Viala, F-34060 Montpellier Cedex 1, France
| | - Charles Romieu
- INRA, UMR AGAP, Batiment 21 2 place Viala, F-34060 Montpellier Cedex 1, France
| | - Florence Esnault
- INRA, UMR AGAP, Batiment 21 2 place Viala, F-34060 Montpellier Cedex 1, France
| | - Sonia Dias
- INRA, UMR AGAP, Batiment 21 2 place Viala, F-34060 Montpellier Cedex 1, France
| | - Gilles Berger
- INRA, UMR AGAP, Batiment 21 2 place Viala, F-34060 Montpellier Cedex 1, France
| | - Pierre François
- INRA, UMR AGAP, Batiment 21 2 place Viala, F-34060 Montpellier Cedex 1, France
| | - Thierry Pons
- INRA, UMR AGAP, Batiment 21 2 place Viala, F-34060 Montpellier Cedex 1, France
| | - Patrick Ortigosa
- INRA, UMR AGAP, Batiment 21 2 place Viala, F-34060 Montpellier Cedex 1, France
| | - Catherine Roux
- INRA, UMR AGAP, Batiment 21 2 place Viala, F-34060 Montpellier Cedex 1, France
| | - Cléa Houel
- INRA, UMR AGAP, Batiment 21 2 place Viala, F-34060 Montpellier Cedex 1, France
| | - Valérie Laucou
- INRA, UMR AGAP, Batiment 21 2 place Viala, F-34060 Montpellier Cedex 1, France
| | - Roberto Bacilieri
- INRA, UMR AGAP, Batiment 21 2 place Viala, F-34060 Montpellier Cedex 1, France
| | - Jean-Pierre Péros
- INRA, UMR AGAP, Batiment 21 2 place Viala, F-34060 Montpellier Cedex 1, France
| | - Patrice This
- INRA, UMR AGAP, Batiment 21 2 place Viala, F-34060 Montpellier Cedex 1, France
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Nicolè S, Barcaccia G, Erickson DL, Kress JW, Lucchin M. The coding region of the UFGT gene is a source of diagnostic SNP markers that allow single-locus DNA genotyping for the assessment of cultivar identity and ancestry in grapevine (Vitis vinifera L.). BMC Res Notes 2013; 6:502. [PMID: 24298902 PMCID: PMC4222114 DOI: 10.1186/1756-0500-6-502] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 11/23/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Vitis vinifera L. is one of society's most important agricultural crops with a broad genetic variability. The difficulty in recognizing grapevine genotypes based on ampelographic traits and secondary metabolites prompted the development of molecular markers suitable for achieving variety genetic identification. FINDINGS Here, we propose a comparison between a multi-locus barcoding approach based on six chloroplast markers and a single-copy nuclear gene sequencing method using five coding regions combined with a character-based system with the aim of reconstructing cultivar-specific haplotypes and genotypes to be exploited for the molecular characterization of 157 V. vinifera accessions. The analysis of the chloroplast target regions proved the inadequacy of the DNA barcoding approach at the subspecies level, and hence further DNA genotyping analyses were targeted on the sequences of five nuclear single-copy genes amplified across all of the accessions. The sequencing of the coding region of the UFGT nuclear gene (UDP-glucose: flavonoid 3-0-glucosyltransferase, the key enzyme for the accumulation of anthocyanins in berry skins) enabled the discovery of discriminant SNPs (1/34 bp) and the reconstruction of 130 V. vinifera distinct genotypes. Most of the genotypes proved to be cultivar-specific, and only few genotypes were shared by more, although strictly related, cultivars. CONCLUSION On the whole, this technique was successful for inferring SNP-based genotypes of grapevine accessions suitable for assessing the genetic identity and ancestry of international cultivars and also useful for corroborating some hypotheses regarding the origin of local varieties, suggesting several issues of misidentification (synonymy/homonymy).
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Affiliation(s)
- Silvia Nicolè
- Laboratory of Plant Genetics and Genomics, DAFNAE, University of Padova, Campus of Agripolis - Viale Università 16, 35020 Padova, Legnaro, Italy
| | - Gianni Barcaccia
- Laboratory of Plant Genetics and Genomics, DAFNAE, University of Padova, Campus of Agripolis - Viale Università 16, 35020 Padova, Legnaro, Italy
| | - David L Erickson
- Department of Botany and Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012 USA
| | - John W Kress
- Department of Botany and Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012 USA
| | - Margherita Lucchin
- Laboratory of Plant Genetics and Genomics, DAFNAE, University of Padova, Campus of Agripolis - Viale Università 16, 35020 Padova, Legnaro, Italy
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