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Ucchesu M, Martinetto E, Sarigu M, Orrù M, Bornancin M, Bacchetta G. Morphological Characterization of Fossil Vitis L. Seeds from the Gelasian of Italy by Seed Image Analysis. PLANTS (BASEL, SWITZERLAND) 2024; 13:1417. [PMID: 38794487 PMCID: PMC11125372 DOI: 10.3390/plants13101417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/09/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024]
Abstract
The discovery of well-preserved fossil Vitis L. seeds from the Gelasian stage in Italy has provided a unique opportunity to investigate the systematics of fossilized Vitis species. Through seed image analyses and elliptical Fourier transforms of fossil Vitis seeds from the sites Buronzo-Gifflenga and Castelletto Cervo II, we pointed out a strong relationship to the group of extant Eurasian Vitis species. However, classification analyses highlighted challenges in accurately assigning the fossil grape seeds to specific modern species. Morphological comparisons with modern Vitis species revealed striking similarities between the fossil seeds and V. vinifera subsp. sylvestris, as well as several other wild species from Asia. This close morphological resemblance suggests the existence of a population of V. vinifera sensu lato in Northen Italy during the Gelasian. These findings contributed to our understanding of the evolution and the complex interplay between ancient and modern Vitis species.
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Affiliation(s)
- Mariano Ucchesu
- Institute of Evolution Sciences of Montpellier (ISEM) UMR 5554, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34090 Montpellier, France;
| | - Edoardo Martinetto
- Dipartimento di Scienze della Terra, Università di Torino, Via Valperga Caluso 35, 10125 Torino, Italy; (E.M.); (M.B.)
| | - Marco Sarigu
- Centro Conservazione Biodiversità (CCB), Dipartimento di Scienze della Vita e dell’Ambiente (DISVA), Università degli Studi di Cagliari, Viale Sant’Ignazio da Laconi, 13, 09123 Cagliari, Italy; (M.O.); (G.B.)
| | - Martino Orrù
- Centro Conservazione Biodiversità (CCB), Dipartimento di Scienze della Vita e dell’Ambiente (DISVA), Università degli Studi di Cagliari, Viale Sant’Ignazio da Laconi, 13, 09123 Cagliari, Italy; (M.O.); (G.B.)
| | - Michela Bornancin
- Dipartimento di Scienze della Terra, Università di Torino, Via Valperga Caluso 35, 10125 Torino, Italy; (E.M.); (M.B.)
| | - Gianluigi Bacchetta
- Centro Conservazione Biodiversità (CCB), Dipartimento di Scienze della Vita e dell’Ambiente (DISVA), Università degli Studi di Cagliari, Viale Sant’Ignazio da Laconi, 13, 09123 Cagliari, Italy; (M.O.); (G.B.)
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2
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Dong Y, Duan S, Xia Q, Liang Z, Dong X, Margaryan K, Musayev M, Goryslavets S, Zdunić G, Bert PF, Lacombe T, Maul E, Nick P, Bitskinashvili K, Bisztray GD, Drori E, De Lorenzis G, Cunha J, Popescu CF, Arroyo-Garcia R, Arnold C, Ergül A, Zhu Y, Ma C, Wang S, Liu S, Tang L, Wang C, Li D, Pan Y, Li J, Yang L, Li X, Xiang G, Yang Z, Chen B, Dai Z, Wang Y, Arakelyan A, Kuliyev V, Spotar G, Girollet N, Delrot S, Ollat N, This P, Marchal C, Sarah G, Laucou V, Bacilieri R, Röckel F, Guan P, Jung A, Riemann M, Ujmajuridze L, Zakalashvili T, Maghradze D, Höhn M, Jahnke G, Kiss E, Deák T, Rahimi O, Hübner S, Grassi F, Mercati F, Sunseri F, Eiras-Dias J, Dumitru AM, Carrasco D, Rodriguez-Izquierdo A, Muñoz G, Uysal T, Özer C, Kazan K, Xu M, Wang Y, Zhu S, Lu J, Zhao M, Wang L, Jiu S, Zhang Y, Sun L, Yang H, Weiss E, Wang S, Zhu Y, Li S, Sheng J, Chen W. Dual domestications and origin of traits in grapevine evolution. Science 2023; 379:892-901. [PMID: 36862793 DOI: 10.1126/science.add8655] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
We elucidate grapevine evolution and domestication histories with 3525 cultivated and wild accessions worldwide. In the Pleistocene, harsh climate drove the separation of wild grape ecotypes caused by continuous habitat fragmentation. Then, domestication occurred concurrently about 11,000 years ago in Western Asia and the Caucasus to yield table and wine grapevines. The Western Asia domesticates dispersed into Europe with early farmers, introgressed with ancient wild western ecotypes, and subsequently diversified along human migration trails into muscat and unique western wine grape ancestries by the late Neolithic. Analyses of domestication traits also reveal new insights into selection for berry palatability, hermaphroditism, muscat flavor, and berry skin color. These data demonstrate the role of the grapevines in the early inception of agriculture across Eurasia.
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Affiliation(s)
- Yang Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Shengchang Duan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Qiuju Xia
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Science and Oenology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Xiao Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Kristine Margaryan
- Institute of Molecular Biology, NAS RA, 0014 Yerevan, Armenia.,Yerevan State University, 0014 Yerevan, Armenia
| | - Mirza Musayev
- Genetic Resources Institute, Azerbaijan National Academy of Sciences, AZ1106 Baku, Azerbaijan
| | | | - Goran Zdunić
- Institute for Adriatic Crops and Karst Reclamation, 21000 Split, Croatia
| | - Pierre-François Bert
- Bordeaux University, Bordeaux Sciences Agro, INRAE, UMR EGFV, ISVV, 33882 Villenave d'Ornon, France
| | - Thierry Lacombe
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro Montpellier, 34398 Montpellier, France
| | - Erika Maul
- Julius Kühn Institute (JKI) - Federal Research Center for Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, 76833 Siebeldingen, Germany
| | - Peter Nick
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | | | - György Dénes Bisztray
- Hungarian University of Agriculture and Life Sciences (MATE), 1118 Budapest, Hungary
| | - Elyashiv Drori
- Department of Chemical Engineering, Ariel University, 40700 Ariel, Israel.,Eastern Regional R&D Center, 40700 Ariel, Israel
| | - Gabriella De Lorenzis
- Department of Agricultural and Environmental Sciences, University of Milano, 20133 Milano, Italy
| | - Jorge Cunha
- Instituto Nacional de Investigação Agrária e Veterinária, I.P./INIAV-Dois Portos, 2565-191 Torres Vedras, Portugal.,Green-it Unit, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Carmen Florentina Popescu
- National Research and Development Institute for Biotechnology in Horticulture, Stefanesti, 117715 Arges, Romania
| | - Rosa Arroyo-Garcia
- Center for Plant Biotechnology and Genomics, UPM-INIA/CSIC, Pozuelo de Alarcon, 28223 Madrid, Spain
| | | | - Ali Ergül
- Biotechnology Institute, Ankara University, 06135 Ankara, Turkey
| | - Yifan Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai JiaoTong University, Shanghai 200240, China
| | - Shufen Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Siqi Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Liu Tang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Chunping Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Dawei Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Yunbing Pan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Jingxian Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Ling Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Xuzhen Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Guisheng Xiang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Zijiang Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Baozheng Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Zhanwu Dai
- Beijing Key Laboratory of Grape Science and Oenology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Yi Wang
- Beijing Key Laboratory of Grape Science and Oenology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Arsen Arakelyan
- Institute of Molecular Biology, NAS RA, 0014 Yerevan, Armenia.,Armenian Bioinformatics Institute, 0014 Yerevan, Armenia.,Biomedicine and Pharmacy, RAU, 0051 Yerevan, Armenia
| | - Varis Kuliyev
- Institute of Bioresources, Nakhchivan Branch of the Azerbaijan National Academy of Sciences, AZ7000 Nakhchivan, Azerbaijan
| | - Gennady Spotar
- National Institute of Viticulture and Winemaking Magarach, Yalta 298600, Crimea
| | - Nabil Girollet
- Bordeaux University, Bordeaux Sciences Agro, INRAE, UMR EGFV, ISVV, 33882 Villenave d'Ornon, France
| | - Serge Delrot
- Bordeaux University, Bordeaux Sciences Agro, INRAE, UMR EGFV, ISVV, 33882 Villenave d'Ornon, France
| | - Nathalie Ollat
- Bordeaux University, Bordeaux Sciences Agro, INRAE, UMR EGFV, ISVV, 33882 Villenave d'Ornon, France
| | - Patrice This
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro Montpellier, 34398 Montpellier, France
| | - Cécile Marchal
- Vassal-Montpellier Grapevine Biological Resources Center, INRAE, 34340 Marseillan-Plage, France
| | - Gautier Sarah
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro Montpellier, 34398 Montpellier, France
| | - Valérie Laucou
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro Montpellier, 34398 Montpellier, France
| | - Roberto Bacilieri
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro Montpellier, 34398 Montpellier, France
| | - Franco Röckel
- Julius Kühn Institute (JKI) - Federal Research Center for Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, 76833 Siebeldingen, Germany
| | - Pingyin Guan
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Andreas Jung
- Historische Rebsorten-Sammlung, Rebschule (K39), 67599 Gundheim, Germany
| | - Michael Riemann
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Levan Ujmajuridze
- LEPL Scientific Research Center of Agriculture, 0159 Tbilisi, Georgia
| | | | - David Maghradze
- LEPL Scientific Research Center of Agriculture, 0159 Tbilisi, Georgia
| | - Maria Höhn
- Hungarian University of Agriculture and Life Sciences (MATE), 1118 Budapest, Hungary
| | - Gizella Jahnke
- Hungarian University of Agriculture and Life Sciences (MATE), 1118 Budapest, Hungary
| | - Erzsébet Kiss
- Hungarian University of Agriculture and Life Sciences (MATE), 1118 Budapest, Hungary
| | - Tamás Deák
- Hungarian University of Agriculture and Life Sciences (MATE), 1118 Budapest, Hungary
| | - Oshrit Rahimi
- Department of Chemical Engineering, Ariel University, 40700 Ariel, Israel
| | - Sariel Hübner
- Galilee Research Institute (Migal), Tel-Hai Academic College, 12210 Upper Galilee, Israel
| | - Fabrizio Grassi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milano, Italy.,NBFC, National Biodiversity Future Center, 90133 Palermo, Italy
| | - Francesco Mercati
- Institute of Biosciences and Bioresources, National Research Council, 90129 Palermo, Italy
| | - Francesco Sunseri
- Department AGRARIA, University Mediterranea of Reggio Calabria, Reggio 89122 Calabria, Italy
| | - José Eiras-Dias
- Instituto Nacional de Investigação Agrária e Veterinária, I.P./INIAV-Dois Portos, 2565-191 Torres Vedras, Portugal.,Green-it Unit, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Anamaria Mirabela Dumitru
- National Research and Development Institute for Biotechnology in Horticulture, Stefanesti, 117715 Arges, Romania
| | - David Carrasco
- Center for Plant Biotechnology and Genomics, UPM-INIA/CSIC, Pozuelo de Alarcon, 28223 Madrid, Spain
| | | | | | - Tamer Uysal
- Viticulture Research Institute, Ministry of Agriculture and Forestry, 59200 Tekirdağ, Turkey
| | - Cengiz Özer
- Viticulture Research Institute, Ministry of Agriculture and Forestry, 59200 Tekirdağ, Turkey
| | - Kemal Kazan
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Meilong Xu
- Institute of Horticulture, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan 750002, China
| | - Yunyue Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Shusheng Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Jiang Lu
- Center for Viticulture and Oenology, School of Agriculture and Biology, Shanghai JiaoTong University, Shanghai 200240, China
| | - Maoxiang Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai JiaoTong University, Shanghai 200240, China
| | - Lei Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai JiaoTong University, Shanghai 200240, China
| | - Songtao Jiu
- Department of Plant Science, School of Agriculture and Biology, Shanghai JiaoTong University, Shanghai 200240, China
| | - Ying Zhang
- Zhengzhou Fruit Research Institutes, CAAS, Zhengzhou 450009, China
| | - Lei Sun
- Zhengzhou Fruit Research Institutes, CAAS, Zhengzhou 450009, China
| | | | - Ehud Weiss
- The Martin (Szusz) Department of Land of Israel Studies and Archaeology, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai JiaoTong University, Shanghai 200240, China
| | - Youyong Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Science and Oenology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Jun Sheng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Wei Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
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3
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Cordero-Bueso G, Vigentini I, Foschino R, Maghradze D, Ruiz-Muñoz M, Benitez-Trujillo F, Cantoral JM. Culturable Yeast Diversity of Grape Berries from Vitis vinifera ssp. sylvestris (Gmelin) Hegi. J Fungi (Basel) 2022; 8:410. [PMID: 35448641 PMCID: PMC9025944 DOI: 10.3390/jof8040410] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 02/04/2023] Open
Abstract
Vitis vinifera L. ssp. sylvestris (Gmelin) Hegi is recognized as the dioecious parental generation of today's cultivars. Climatic change and the arrival of pathogens and pests in Europe led it to be included on the International Union for Conservation of Nature (IUCN) Red List of Threatened Species in 1997. The present work focused on the study of culturable yeast occurrence and diversity of grape berries collected from wild vines. Sampling was performed in 29 locations of Azerbaijan, Georgia, Italy, Romania, and Spain. In total, 3431 yeast colonies were isolated and identified as belonging to 49 species, including Saccharomyces cerevisiae, by 26S rDNA D1/D2 domains and ITS region sequencing. Isolates of S. cerevisiae were also analyzed by SSR-PCR obtaining 185 different genotypes. Classical ecology indices were used to obtain the richness (S), the biodiversity (H'), and the dominance (D) of the species studied. This study highlights the biodiversity potential of natural environments that still represent a fascinating source of solutions to common problems in winemaking.
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Affiliation(s)
- Gustavo Cordero-Bueso
- Department of Biomedicine, Biotechnology and Public Health, University of Cádiz, 11009 Cádiz, Spain; (M.R.-M.); (J.M.C.)
| | - Ileana Vigentini
- Department of Food, Environmental and Nutritional Sciences, University of Milan, 20122 Milan, Italy; (I.V.); (R.F.)
| | - Roberto Foschino
- Department of Food, Environmental and Nutritional Sciences, University of Milan, 20122 Milan, Italy; (I.V.); (R.F.)
| | - David Maghradze
- Department of Agriculture, Faculty of Viticulture and Winemaking, Caucasus International University, 0141 Tbilisi, Georgia;
| | - Marina Ruiz-Muñoz
- Department of Biomedicine, Biotechnology and Public Health, University of Cádiz, 11009 Cádiz, Spain; (M.R.-M.); (J.M.C.)
| | | | - Jesús M. Cantoral
- Department of Biomedicine, Biotechnology and Public Health, University of Cádiz, 11009 Cádiz, Spain; (M.R.-M.); (J.M.C.)
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4
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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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5
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Liang Z, Duan S, Sheng J, Zhu S, Ni X, Shao J, Liu C, Nick P, Du F, Fan P, Mao R, Zhu Y, Deng W, Yang M, Huang H, Liu Y, Ding Y, Liu X, Jiang J, Zhu Y, Li S, He X, Chen W, Dong Y. Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses. Nat Commun 2019; 10:1190. [PMID: 30867414 PMCID: PMC6416300 DOI: 10.1038/s41467-019-09135-8] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 02/21/2019] [Indexed: 01/27/2023] Open
Abstract
Understanding the Vitis species at the genomic level is important for cultivar improvement of grapevine. Here we report whole-genome genetic variation at single-base resolution of 472 Vitis accessions, which cover 48 out of 60 extant Vitis species from a wide geographic distribution. The variation helps to identify a recent dramatic expansion and contraction of effective population size in the domesticated grapevines and that cultivars from the pan-Black Sea region have a unique demographic history in comparison to the other domesticated cultivars. We also find selective sweeps for berry edibility and stress resistance improvement. Furthermore, we find associations between candidate genes and important agronomic traits, such as berry shape and aromatic compounds. These results demonstrate resource value of the resequencing data for illuminating the evolutionary biology of Vitis species and providing targets for grapevine genetic improvement. Despite the importance of grapevine cultivation in human history and the economic values of cultivar improvement, large-scale genomic variation data are lacking. Here the authors resequence 472 Vitis accessions and use the identified genetic variations for domestication history, demography, and GWAS analyses.
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Affiliation(s)
- Zhenchang Liang
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Shengchang Duan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,Nowbio Biotechnology Company, Kunming, 650201, China
| | - Jun Sheng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, 650201, China.,Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Shusheng Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Xuemei Ni
- BGI, BGI-Shenzhen, Shenzhen, 518120, China.,BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jianhui Shao
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Chonghuai Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Peter Nick
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, 76128, Germany
| | - Fei Du
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Peige Fan
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ruzhi Mao
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Yifan Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Weiping Deng
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Min Yang
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Huichuan Huang
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Yixiang Liu
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Yiqing Ding
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianju Liu
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianfu Jiang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Youyong Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, 650201, China.,Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiahong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China. .,Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China.
| | - Wei Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China. .,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, 650201, China.
| | - Yang Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China. .,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, 650201, China.
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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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Liu J, Guo X, Chen D, Li J, Yue B, Zeng X. Diversification and historical demography of the rapid racerunner (Eremias velox) in relation to geological history and Pleistocene climatic oscillations in arid Central Asia. Mol Phylogenet Evol 2019; 130:244-258. [DOI: 10.1016/j.ympev.2018.10.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 10/21/2018] [Accepted: 10/22/2018] [Indexed: 10/28/2022]
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8
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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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9
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Després L, Henniaux C, Rioux D, Capblancq T, Zupan S, čelik T, Sielezniew M, Bonato L, Ficetola GF. Inferring the biogeography and demographic history of an endangered butterfly in Europe from multilocus markers. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly160] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | | | - Delphine Rioux
- Université Grenoble Alpes, LECA UMR5553, CNRS, Grenoble, France
| | | | - Sara Zupan
- University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Koper, Slovenia
| | - Tatjana čelik
- Research Centre of the Slovenian Academy of Sciences and Arts, Jovan Hadži Institute of Biology, Ljubljana, Slovenia
| | - Marcin Sielezniew
- Laboratory of Insect Evolutionary Biology and Ecology, Institute of Biology, University of Bialystok, Białystok, Poland
| | - Lucio Bonato
- Department of Biology, Università degli Studi di Padova, Padova, Italy
| | - Gentile Francesco Ficetola
- Université Grenoble Alpes, LECA UMR5553, CNRS, Grenoble, France
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milano, Italy
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10
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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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11
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Arnold C, Bachmann O, Schnitzler A. Insights into the Vitis complex in the Danube floodplain (Austria). Ecol Evol 2017; 7:7796-7806. [PMID: 29043035 PMCID: PMC5632635 DOI: 10.1002/ece3.3187] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/20/2017] [Accepted: 05/30/2017] [Indexed: 11/24/2022] Open
Abstract
European grapevine populations quickly disappeared from most of their range, massively killed by the spread of North American grapevine pests and diseases. Nowadays taxonomic pollution represents a new threat. A large Vitis complex involves escaped cultivars, rootstocks, and wild grapevines. The study aimed to provide insight into the Vitis complex in the Danube region through field and genetic analyses. Among the five other major rivers in Europe which still host wild grapevine populations, the Danube floodplain is the only one benefiting from an extensive protected forest area (93 km²) and an relatively active dynamic flood pulse. The Donau‐Auen National Park also regroups the largest wild grapevine population in Europe. Ninety‐two percent of the individuals collected in the park were true wild grapevines, and 8% were hybrids and introgressed individuals of rootstocks, wild grapevines, and cultivars. These three groups are interfertile acting either as pollen donor or receiver. Hybrids were established within and outside the dykes, mostly in anthropized forest edges. The best‐developed individuals imply rootstock genes. They establish in the most erosive parts of the floodplain. 42% of the true wild grapevines lived at the edges of forest/meadow, 33.3% at the edges forest/channels, and 23.9% in forest gaps. DBH (Diameter Breast Height) varied significantly with the occurrence of flooding. Clones were found in both true wild and hybrids/introgressed grapevines. The process of cloning seemed to be prevented in places where flooding dynamics is reduced. The current global distribution of true wild grapevines shows a strong tendency toward clustering, in sites where forestry practices were the most extensive. However, the reduced flooding activity is a danger for long‐term sustainability of the natural wild grapevine population.
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Affiliation(s)
- Claire Arnold
- Unicentre, University of Lausanne Lausanne Switzerland
| | - Olivier Bachmann
- Laboratory of Evolutionary Botany University of Neuchâtel Neuchâtel Switzerland.,Laboratory of Plant Ecology University of Basel Basel Switzerland
| | - Annik Schnitzler
- Laboratoire Interdisciplinaire des Environnements Continentaux LIEC - UMR 7360 CNRS University of Lorraine Metz France
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12
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An ancient Mediterranean melting pot: investigating the uniparental genetic structure and population history of sicily and southern Italy. PLoS One 2014; 9:e96074. [PMID: 24788788 PMCID: PMC4005757 DOI: 10.1371/journal.pone.0096074] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 04/03/2014] [Indexed: 11/19/2022] Open
Abstract
Due to their strategic geographic location between three different continents, Sicily and Southern Italy have long represented a major Mediterranean crossroad where different peoples and cultures came together over time. However, its multi-layered history of migration pathways and cultural exchanges, has made the reconstruction of its genetic history and population structure extremely controversial and widely debated. To address this debate, we surveyed the genetic variability of 326 accurately selected individuals from 8 different provinces of Sicily and Southern Italy, through a comprehensive evaluation of both Y-chromosome and mtDNA genomes. The main goal was to investigate the structuring of maternal and paternal genetic pools within Sicily and Southern Italy, and to examine their degrees of interaction with other Mediterranean populations. Our findings show high levels of within-population variability, coupled with the lack of significant genetic sub-structures both within Sicily, as well as between Sicily and Southern Italy. When Sicilian and Southern Italian populations were contextualized within the Euro-Mediterranean genetic space, we observed different historical dynamics for maternal and paternal inheritances. Y-chromosome results highlight a significant genetic differentiation between the North-Western and South-Eastern part of the Mediterranean, the Italian Peninsula occupying an intermediate position therein. In particular, Sicily and Southern Italy reveal a shared paternal genetic background with the Balkan Peninsula and the time estimates of main Y-chromosome lineages signal paternal genetic traces of Neolithic and post-Neolithic migration events. On the contrary, despite showing some correspondence with its paternal counterpart, mtDNA reveals a substantially homogeneous genetic landscape, which may reflect older population events or different demographic dynamics between males and females. Overall, both uniparental genetic structures and TMRCA estimates confirm the role of Sicily and Southern Italy as an ancient Mediterranean melting pot for genes and cultures.
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13
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Boattini A, Martinez-Cruz B, Sarno S, Harmant C, Useli A, Sanz P, Yang-Yao D, Manry J, Ciani G, Luiselli D, Quintana-Murci L, Comas D, Pettener D. Uniparental markers in Italy reveal a sex-biased genetic structure and different historical strata. PLoS One 2013; 8:e65441. [PMID: 23734255 PMCID: PMC3666984 DOI: 10.1371/journal.pone.0065441] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 04/24/2013] [Indexed: 11/18/2022] Open
Abstract
Located in the center of the Mediterranean landscape and with an extensive coastal line, the territory of what is today Italy has played an important role in the history of human settlements and movements of Southern Europe and the Mediterranean Basin. Populated since Paleolithic times, the complexity of human movements during the Neolithic, the Metal Ages and the most recent history of the two last millennia (involving the overlapping of different cultural and demic strata) has shaped the pattern of the modern Italian genetic structure. With the aim of disentangling this pattern and understanding which processes more importantly shaped the distribution of diversity, we have analyzed the uniparentally-inherited markers in ∼900 individuals from an extensive sampling across the Italian peninsula, Sardinia and Sicily. Spatial PCAs and DAPCs revealed a sex-biased pattern indicating different demographic histories for males and females. Besides the genetic outlier position of Sardinians, a North West–South East Y-chromosome structure is found in continental Italy. Such structure is in agreement with recent archeological syntheses indicating two independent and parallel processes of Neolithisation. In addition, date estimates pinpoint the importance of the cultural and demographic events during the late Neolithic and Metal Ages. On the other hand, mitochondrial diversity is distributed more homogeneously in agreement with older population events that might be related to the presence of an Italian Refugium during the last glacial period in Europe.
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Affiliation(s)
- Alessio Boattini
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Begoña Martinez-Cruz
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
| | - Stefania Sarno
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Christine Harmant
- Institut Pasteur, Human Evolutionary Genetics Unit, Department of Genomes and Genetics, Paris, France
- Centre National de la Recherche Scientifique, Paris, France
| | - Antonella Useli
- Dipartimento di Scienze della Natura e del Territorio, Università di Sassari, Sassari, Italy
| | - Paula Sanz
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
| | - Daniele Yang-Yao
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Jeremy Manry
- Institut Pasteur, Human Evolutionary Genetics Unit, Department of Genomes and Genetics, Paris, France
- Centre National de la Recherche Scientifique, Paris, France
| | - Graziella Ciani
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Donata Luiselli
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Lluis Quintana-Murci
- Institut Pasteur, Human Evolutionary Genetics Unit, Department of Genomes and Genetics, Paris, France
- Centre National de la Recherche Scientifique, Paris, France
| | - David Comas
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
- * E-mail: (DC); (DP)
| | - Davide Pettener
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
- * E-mail: (DC); (DP)
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14
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Orrù M, Mattana E, Pritchard HW, Bacchetta G. Thermal thresholds as predictors of seed dormancy release and germination timing: altitude-related risks from climate warming for the wild grapevine Vitis vinifera subsp. sylvestris. ANNALS OF BOTANY 2012; 110:1651-60. [PMID: 23071219 PMCID: PMC3503498 DOI: 10.1093/aob/mcs218] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 08/23/2012] [Indexed: 05/05/2023]
Abstract
BACKGROUND AND AIMS The importance of thermal thresholds for predicting seed dormancy release and germination timing under the present climate conditions and simulated climate change scenarios was investigated. In particular, Vitis vinifera subsp. sylvestris was investigated in four Sardinian populations over the full altitudinal range of the species (from approx. 100 to 800 m a.s.l). METHODS Dried and fresh seeds from each population were incubated in the light at a range of temperatures (10-25 and 25/10 °C), without any pre-treatment and after a warm (3 months at 25 °C) or a cold (3 months at 5 °C) stratification. A thermal time approach was then applied to the germination results for dried seeds and the seed responses were modelled according to the present climate conditions and two simulated scenarios of the Intergovernmental Panel on Climate Change (IPCC): B1 (+1·8 °C) and A2 (+3·4 °C). KEY RESULTS Cold stratification released physiological dormancy, while very few seeds germinated without treatments or after warm stratification. Fresh, cold-stratified seeds germinated significantly better (>80 %) at temperatures ≥20 °C than at lower temperatures. A base temperature for germination (T(b)) of 9·0-11·3 °C and a thermal time requirement for 50 % of germination (θ(50)) ranging from 33·6 °Cd to 68·6 °Cd were identified for non-dormant cold-stratified seeds, depending on the populations. This complex combination of thermal requirements for dormancy release and germination allowed prediction of field emergence from March to May under the present climatic conditions for the investigated populations. CONCLUSIONS The thermal thresholds for seed germination identified in this study (T(b) and θ(50)) explained the differences in seed germination detected among populations. Under the two simulated IPCC scenarios, an altitude-related risk from climate warming is identified, with lowland populations being more threatened due to a compromised seed dormancy release and a narrowed seed germination window.
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Affiliation(s)
- Martino Orrù
- Centro Conservazione Biodiversità (CCB), Dipartimento di Scienze della Vita e dell'Ambiente, Università degli Studi di Cagliari, Viale Sant'Ignazio da Laconi, 13, Cagliari, 09123, Italy
| | - Efisio Mattana
- Centro Conservazione Biodiversità (CCB), Dipartimento di Scienze della Vita e dell'Ambiente, Università degli Studi di Cagliari, Viale Sant'Ignazio da Laconi, 13, Cagliari, 09123, Italy
| | - Hugh W. Pritchard
- Seed Conservation Department, Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, West Sussex RH17 6TN, UK
| | - Gianluigi Bacchetta
- Centro Conservazione Biodiversità (CCB), Dipartimento di Scienze della Vita e dell'Ambiente, Università degli Studi di Cagliari, Viale Sant'Ignazio da Laconi, 13, Cagliari, 09123, Italy
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Computer vision as a method complementary to molecular analysis: Grapevine cultivar seeds case study. C R Biol 2012; 335:602-15. [DOI: 10.1016/j.crvi.2012.08.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 08/07/2012] [Accepted: 08/07/2012] [Indexed: 11/13/2022]
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Molecular phylogenetics and historical biogeography of the west-palearctic common toads (Bufo bufo species complex). Mol Phylogenet Evol 2011; 63:113-30. [PMID: 22214922 DOI: 10.1016/j.ympev.2011.12.019] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 12/18/2011] [Accepted: 12/20/2011] [Indexed: 11/20/2022]
Abstract
In most pan-Eurasiatic species complexes, two phenomena have been traditionally considered key processes of their cladogenesis and biogeography. First, it is hypothesized that the origin and development of the Central Asian Deserts generated a biogeographic barrier that fragmented past continuous distributions in Eastern and Western domains. Second, Pleistocene glaciations have been proposed as the main process driving the regional diversification within each of these domains. The European common toad and its closest relatives provide an interesting opportunity to examine the relative contributions of these paleogeographic and paleoclimatic events to the phylogeny and biogeography of a widespread Eurasiatic group. We investigate this issue by applying a multiproxy approach combining information from molecular phylogenies, a multiple correspondence analysis of allozyme data and species distribution models. Our study includes 304 specimens from 164 populations, covering most of the distributional range of the Bufo bufo species complex in the Western Palearctic. The phylogenies (ML and Bayesian analyses) were based on a total of 1988 bp of mitochondrial DNA encompassing three genes (tRNAval, 16S and ND1). A dataset with 173 species of the family Bufonidae was assembled to estimate the separation of the two pan-Eurasiatic species complexes of Bufo and to date the main biogeographic events within the Bufo bufo species complex. The allozyme study included sixteen protein systems, corresponding to 21 presumptive loci. Finally, the distribution models were based on maximum entropy. Our distribution models show that Eastern and Western species complexes are greatly isolated by the Central Asian Deserts, and our dating estimates place this divergence during the Middle Miocene, a moment in which different sources of evidence document a major upturn of the aridification rate of Central Asia. This climate-driven process likely separated the Eastern and Western species. At the level of the Western Palearctic, our dating estimates place most of the deepest phylogenetic structure before the Pleistocene, indicating that Pleistocene glaciations did not have a major role in splitting the major lineages. At a shallow level, the glacial dynamics contributed unevenly to the genetic structuring of populations, with a strong influence in the European-Caucasian populations, and a more relaxed effect in the Iberian populations.
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De Andrés MT, Benito A, Pérez-Rivera G, Ocete R, Lopez MA, Gaforio L, Muñoz G, Cabello F, Martínez Zapater JM, Arroyo-García R. Genetic diversity of wild grapevine populations in Spain and their genetic relationships with cultivated grapevines. Mol Ecol 2011; 21:800-16. [PMID: 22151598 DOI: 10.1111/j.1365-294x.2011.05395.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The wild grapevine, Vitis vinifera L. ssp. sylvestris (Gmelin) Hegi, considered as the ancestor of the cultivated grapevine, is native from Eurasia. In Spain, natural populations of V. vinifera ssp. sylvestris can still be found along river banks. In this work, we have performed a wide search of wild grapevine populations in Spain and characterized the amount and distribution of their genetic diversity using 25 nuclear SSR loci. We have also analysed the possible coexistence in the natural habitat of wild grapevines with naturalized grapevine cultivars and rootstocks. In this way, phenotypic and genetic analyses identified 19% of the collected samples as derived from cultivated genotypes, being either naturalized cultivars or hybrid genotypes derived from spontaneous crosses between wild and cultivated grapevines. The genetic diversity of wild grapevine populations was similar than that observed in the cultivated group. The molecular analysis showed that cultivated germplasm and wild germplasm are genetically divergent with low level of introgression. Using a model-based approach implemented in the software structure, we identified four genetic groups, with two of them fundamentally represented among cultivated genotypes and two among wild accessions. The analyses of genetic relationships between wild and cultivated grapevines could suggest a genetic contribution of wild accessions from Spain to current Western cultivars.
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Affiliation(s)
- M T De Andrés
- Departamento de Investigación Agroalimentaria, IMIDRA, Finca El Encín, Apto 127, 28800 Alcalá de Henares, Madrid, Spain
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Zecca G, Abbott JR, Sun WB, Spada A, Sala F, Grassi F. The timing and the mode of evolution of wild grapes (Vitis). Mol Phylogenet Evol 2011; 62:736-47. [PMID: 22138159 DOI: 10.1016/j.ympev.2011.11.015] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 11/04/2011] [Accepted: 11/17/2011] [Indexed: 10/14/2022]
Abstract
Wild grapes are woody climbers, found mostly in temperate regions of the northern hemisphere, comprising the genus Vitis. Despite its importance, the evolutionary history of Vitis is still contentious. Past studies have led to conflicting hypotheses about the phylogeny, speciation events, and biogeographic history of the genus. Here we investigate the evolutionary history of Vitis using data from four chloroplast spacers (trnH-psbA, trnK-rps16, trnF-nahJ, and rpl32-trnL) and the nuclear gene RPB2-I, and we explore mechanisms that could have shaped the observed distribution of current species. Maximum likelihood and Bayesian analyses provided similar results, strongly supporting the presence of two subgenera and suggesting a species clustering within subgenus Vitis that mainly mirrors the disjunction between the Old and New World. Vitis vinifera subsp. sylvestris was found to be sister to the Asian species while three major clades were found in the American species. A network approach confirmed the main geographic groups and highlighted different chloroplast haplotype patterns between Asian and American species. Molecular dating analysis provided the time boundaries to discuss our results. Our study shows wild grape diversification to be a continuous and complex process that concerned the Tertiary as well as the Quaternary, most likely involving both geographical and climatic forces. Local variations in extent and timing of these forces were discussed based on observed differences between groups. In the context of the Tertiary-Quaternary debate, we provide evidence in favor of the "continuous hypothesis" to explain present diversity. Finally, two directions for future research are highlighted: (i) was the earliest grape American or Asian? and (ii) are all modern grape species real?
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Affiliation(s)
- Giovanni Zecca
- Botanical Garden, Department of Biology, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy.
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Houel C, Bounon R, Chaïb J, Guichard C, Péros JP, Bacilieri R, Dereeper A, Canaguier A, Lacombe T, N'Diaye A, Le Paslier MC, Vernerey MS, Coriton O, Brunel D, This P, Torregrosa L, Adam-Blondon AF. Patterns of sequence polymorphism in the fleshless berry locus in cultivated and wild Vitis vinifera accessions. BMC PLANT BIOLOGY 2010; 10:284. [PMID: 21176183 PMCID: PMC3022909 DOI: 10.1186/1471-2229-10-284] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 12/22/2010] [Indexed: 05/19/2023]
Abstract
BACKGROUND Unlike in tomato, little is known about the genetic and molecular control of fleshy fruit development of perennial fruit trees like grapevine (Vitis vinifera L.). Here we present the study of the sequence polymorphism in a 1 Mb grapevine genome region at the top of chromosome 18 carrying the fleshless berry mutation (flb) in order, first to identify SNP markers closely linked to the gene and second to search for possible signatures of domestication. RESULTS In total, 62 regions (17 SSR, 3 SNP, 1 CAPS and 41 re-sequenced gene fragments) were scanned for polymorphism along a 3.4 Mb interval (85,127-3,506,060 bp) at the top of the chromosome 18, in both V. vinifera cv. Chardonnay and a genotype carrying the flb mutation, V. vinifera cv. Ugni Blanc mutant. A nearly complete homozygosity in Ugni Blanc (wild and mutant forms) and an expected high level of heterozygosity in Chardonnay were revealed. Experiments using qPCR and BAC FISH confirmed the observed homozygosity. Under the assumption that flb could be one of the genes involved into the domestication syndrome of grapevine, we sequenced 69 gene fragments, spread over the flb region, representing 48,874 bp in a highly diverse set of cultivated and wild V. vinifera genotypes, to identify possible signatures of domestication in the cultivated V. vinifera compartment. We identified eight gene fragments presenting a significant deviation from neutrality of the Tajima's D parameter in the cultivated pool. One of these also showed higher nucleotide diversity in the wild compartments than in the cultivated compartments. In addition, SNPs significantly associated to berry weight variation were identified in the flb region. CONCLUSIONS We observed the occurrence of a large homozygous region in a non-repetitive region of the grapevine otherwise highly-heterozygous genome and propose a hypothesis for its formation. We demonstrated the feasibility to apply BAC FISH on the very small grapevine chromosomes and provided a specific probe for the identification of chromosome 18 on a cytogenetic map. We evidenced genes showing putative signatures of selection and SNPs significantly associated with berry weight variation in the flb region. In addition, we provided to the community 554 SNPs at the top of chromosome 18 for the development of a genotyping chip for future fine mapping of the flb gene in a F2 population when available.
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Affiliation(s)
- Cléa Houel
- Unité mixte de Recherche en Génomique Végétale (URGV), INRA UEVE ERL CNRS, 2 rue Gaston Crémieux, 91 057 Evry cedex, France
| | - Rémi Bounon
- Unité mixte de Recherche en Génomique Végétale (URGV), INRA UEVE ERL CNRS, 2 rue Gaston Crémieux, 91 057 Evry cedex, France
- Unité INRA Etude du Polymorphisme des Végétaux (EPGV), 2 rue Gaston Crémieux, 91 057 Evry cedex, France
| | - Jamila Chaïb
- CSIRO Plant Industry, PO BOX 350, Glen Osmond SA 5064, Australia
| | - Cécile Guichard
- Unité mixte de Recherche en Génomique Végétale (URGV), INRA UEVE ERL CNRS, 2 rue Gaston Crémieux, 91 057 Evry cedex, France
| | - Jean-Pierre Péros
- Unité mixte de Recherche Diversité et Adaptation des Plantes Cultivées (DiaPC), INRA SupAgro, 2 place Pierre Viala, 34 060 Montpellier Cedex, France
| | - Roberto Bacilieri
- Unité mixte de Recherche Diversité et Adaptation des Plantes Cultivées (DiaPC), INRA SupAgro, 2 place Pierre Viala, 34 060 Montpellier Cedex, France
| | - Alexis Dereeper
- Unité mixte de Recherche Diversité et Adaptation des Plantes Cultivées (DiaPC), INRA SupAgro, 2 place Pierre Viala, 34 060 Montpellier Cedex, France
| | - Aurélie Canaguier
- Unité mixte de Recherche en Génomique Végétale (URGV), INRA UEVE ERL CNRS, 2 rue Gaston Crémieux, 91 057 Evry cedex, France
| | - Thierry Lacombe
- Unité mixte de Recherche Diversité et Adaptation des Plantes Cultivées (DiaPC), INRA SupAgro, 2 place Pierre Viala, 34 060 Montpellier Cedex, France
| | - Amidou N'Diaye
- Unité mixte de Recherche Diversité et Adaptation des Plantes Cultivées (DiaPC), INRA SupAgro, 2 place Pierre Viala, 34 060 Montpellier Cedex, France
| | | | - Marie-Stéphanie Vernerey
- Unité mixte de Recherche Amélioration des Plantes et Biotechnologies Végétales (APBV), INRA Agrocampus Rennes, Plate-forme cytologique moléculaire, 35 653 Le Rheu Cedex, France
- Unité mixte de Recherche Biologie et Génétique des Interactions Plantes-Agents Pathogènes (BGPI), INRA SupAgro CIRAD, 2 place Pierre Viala, 34 060 Montpellier Cedex, France
| | - Olivier Coriton
- Unité mixte de Recherche Amélioration des Plantes et Biotechnologies Végétales (APBV), INRA Agrocampus Rennes, Plate-forme cytologique moléculaire, 35 653 Le Rheu Cedex, France
| | - Dominique Brunel
- Unité INRA Etude du Polymorphisme des Végétaux (EPGV), 2 rue Gaston Crémieux, 91 057 Evry cedex, France
| | - Patrice This
- Unité mixte de Recherche Diversité et Adaptation des Plantes Cultivées (DiaPC), INRA SupAgro, 2 place Pierre Viala, 34 060 Montpellier Cedex, France
| | - Laurent Torregrosa
- Unité mixte de Recherche Diversité et Adaptation des Plantes Cultivées (DiaPC), INRA SupAgro, 2 place Pierre Viala, 34 060 Montpellier Cedex, France
| | - Anne-Françoise Adam-Blondon
- Unité mixte de Recherche en Génomique Végétale (URGV), INRA UEVE ERL CNRS, 2 rue Gaston Crémieux, 91 057 Evry cedex, France
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Zecca G, De Mattia F, Lovicu G, Labra M, Sala F, Grassi F. Wild grapevine: silvestris, hybrids or cultivars that escaped from vineyards? Molecular evidence in Sardinia. PLANT BIOLOGY (STUTTGART, GERMANY) 2010; 12:558-62. [PMID: 20522194 DOI: 10.1111/j.1438-8677.2009.00226.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Vitis vinifera ssp. silvestris, the spontaneous subspecies of V. vinifera L., is believed to be the ancestor of present grapevine cultivars. In this work, polymorphism at 13 SSR loci was investigated to answer the following key question: are wild plants (i) true silvestris, (ii) hybrids between wild and cultivated plants or (iii) or 'escapes' from vineyards? In particular, the objective of the present study was to identify truly wild individuals and to search for possible hybridization events. The study was performed in Sardinia, the second largest island in the Mediterranean Sea, which is characterized by a large and well-described number of both grape cultivars and wild populations. This region was ideal for the study because of its spatial isolation and, consequently, limited contamination from outside material. The results of this study show that domesticated and wild grapevine germplasms are genetically divergent and thus are real silvestris. Pure lineages (both domesticated and wild) show very high average posterior probabilities of assignment to their own clusters, with a low level of introgression.
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Affiliation(s)
- G Zecca
- Botanical Garden, Department of Biology, University of Milan, Milano, Italy.
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Grassi F, Minuto L, Casazza G, Labra M, Sala F. Haplotype richness in refugial areas: phylogeographical structure of Saxifraga callosa. JOURNAL OF PLANT RESEARCH 2009; 122:377-387. [PMID: 19363647 DOI: 10.1007/s10265-009-0230-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Accepted: 03/01/2009] [Indexed: 05/27/2023]
Abstract
This paper illustrates the phylogeographical structure of Saxifraga callosa in order to describe its genetic richness in refugial areas and to reconstruct its glacial history. S. callosa is a species spread throughout south-east France and Italy with a high distribution in the Maritime Alps. Four chloroplast microsatellite and AFLP markers were analyzed in populations of S. callosa. The size variants of all tested loci amount to 11 different haplotypes. Intrapopulational haplotype variation was found in two of the populations analyzed: on the Mt. Toraggio in the Maritime Alps, and in the Apuan Alps. On the other hand, no intrapopulational variation was found in 25 populations, most of which were sampled from isolated areas. Analysis of the haplotype distribution showed that population subdivision across all populations was high (G (ST) = 0.899). Moreover, its genetic structure was studied using AMOVA and STRUCTURE analysis. The study legitimated inferred conclusions about the phylogeographical structure of the species and identified centers of diversity. Considerations concerning genetic structure and divergence among three major clades (Maritime Alps, Apuan Alps and Apennines), the patchy distribution of haplotypes, and the high number of private haplotypes support the proposal that S. callosa survived in some refugia within the Italian Peninsula refugium, and that mainly northern populations of refugia were involved in postglacial recolonization.
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Affiliation(s)
- F Grassi
- Botanical Garden, Department of Biology, University of Milan, 20133 Milan, Italy.
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