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Abbasi Holasou H, Panahi B, Shahi A, Nami Y. Integration of machine learning models with microsatellite markers: New avenue in world grapevine germplasm characterization. Biochem Biophys Rep 2024; 38:101678. [PMID: 38495412 PMCID: PMC10940787 DOI: 10.1016/j.bbrep.2024.101678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/09/2024] [Accepted: 02/27/2024] [Indexed: 03/19/2024] Open
Abstract
Development of efficient analytical techniques is required for effective interpretation of biological data to take novel hypotheses and finding the critical predictive patterns. Machine Learning algorithms provide a novel opportunity for development of low-cost and practical solutions in biology. In this study, we proposed a new integrated analytical approach using supervised machine learning algorithms and microsatellites data of worldwide vitis populations. A total of 1378 wild (V. vinifera spp. sylvestris) and cultivated (V. vinifera spp. sativa) accessions of grapevine were investigated using 20 microsatellite markers. Data cleaning, feature selection, and supervised machine learning classification models vis, Naive Bayes, Support Vector Machine (SVM) and Tree Induction methods were implied to find most indicative and diagnostic alleles to represent wild/cultivated and originated geography of each population. Our combined approaches showed microsatellite markers with the highest differentiating capacity and proved efficiency for our pipeline of classification and prediction of vitis accessions. Moreover, our study proposed the best combination of markers for better distinguishing of populations, which can be exploited in future germplasm conservation and breeding programs.
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Affiliation(s)
- Hossein Abbasi Holasou
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Bahman Panahi
- Department of Genomics, Branch for Northwest and West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran
| | - Ali Shahi
- Faculty of Agriculture (Meshgin Shahr Campus), Mohaghegh Ardabili University, Ardabil, Iran
| | - Yousef Nami
- Department of Food Biotechnology, Branch for Northwest and West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran
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2
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Rodriguez-Izquierdo A, Carrasco D, Anand L, Magnani R, Catarecha P, Arroyo-Garcia R, Rodriguez Lopez CM. Epigenetic differences between wild and cultivated grapevines highlight the contribution of DNA methylation during crop domestication. BMC PLANT BIOLOGY 2024; 24:504. [PMID: 38840239 PMCID: PMC11155169 DOI: 10.1186/s12870-024-05197-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/24/2024] [Indexed: 06/07/2024]
Abstract
The domestication process in grapevines has facilitated the fixation of desired traits. Nowadays, vegetative propagation through cuttings enables easier preservation of these genotypes compared to sexual reproduction. Nonetheless, even with vegetative propagation, various phenotypes are often present within the same vineyard due to the accumulation of somatic mutations. These mutations are not the sole factors influencing phenotype. Alongside somatic variations, epigenetic variation has been proposed as a pivotal player in regulating phenotypic variability acquired during domestication. The emergence of these epialleles might have significantly influenced grapevine domestication over time. This study aims to investigate the impact of domestication on methylation patterns in cultivated grapevines. Reduced-representation bisulfite sequencing was conducted on 18 cultivated and wild accessions. Results revealed that cultivated grapevines exhibited higher methylation levels than their wild counterparts. Differential Methylation Analysis between wild and cultivated grapevines identified a total of 9955 differentially methylated cytosines, of which 78% were hypermethylated in cultivated grapevines. Functional analysis shows that core methylated genes (consistently methylated in both wild and cultivated accessions) are associated with stress response and terpenoid/isoprenoid metabolic processes. Meanwhile, genes with differential methylation are linked to protein targeting to the peroxisome, ethylene regulation, histone modifications, and defense response. Collectively, our results highlight the significant roles that epialleles may have played throughout the domestication history of grapevines.
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Affiliation(s)
- Alberto Rodriguez-Izquierdo
- Centro de Biotecnología y Genómica de Plantas (CBGP-INIA), CSIC - Universidad Politécnica de Madrid, Campus Montegancedo, Madrid, Spain
| | - David Carrasco
- Centro de Biotecnología y Genómica de Plantas (CBGP-INIA), CSIC - Universidad Politécnica de Madrid, Campus Montegancedo, Madrid, Spain
| | - Lakshay Anand
- Environmental Epigenetics and Genetics Group (EEGG), Department of Horticulture, College of Agriculture, Food and environment, University of Kentucky, Lexington, KY, USA
| | - Roberta Magnani
- Environmental Epigenetics and Genetics Group (EEGG), Department of Horticulture, College of Agriculture, Food and environment, University of Kentucky, Lexington, KY, USA
| | - Pablo Catarecha
- Centro de Biotecnología y Genómica de Plantas (CBGP-INIA), CSIC - Universidad Politécnica de Madrid, Campus Montegancedo, Madrid, Spain
| | - Rosa Arroyo-Garcia
- Centro de Biotecnología y Genómica de Plantas (CBGP-INIA), CSIC - Universidad Politécnica de Madrid, Campus Montegancedo, Madrid, Spain.
| | - Carlos M Rodriguez Lopez
- Environmental Epigenetics and Genetics Group (EEGG), Department of Horticulture, College of Agriculture, Food and environment, University of Kentucky, Lexington, KY, USA.
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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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Perko A, Trapp O, Maul E, Röckel F, Piltaver A, Vršič S. Monitoring and Genotyping of Wild Grapevine ( Vitis vinifera L. subsp. sylvestris) in Slovenia. PLANTS (BASEL, SWITZERLAND) 2024; 13:1234. [PMID: 38732448 PMCID: PMC11085864 DOI: 10.3390/plants13091234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/20/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024]
Abstract
Vitis vinifera L. subsp. sylvestris (sylvestris) is the only native wild grapevine in Eurasia (Europe and western Asia) and is the existing ancestor of the grapevine varieties (for wine and table grape production) belonging to the subsp. sativa. In Slovenia, the prevailing opinion has been that there are no Slovenian sylvestris habitats. This study describes sylvestris in Slovenia for the first time and aims to present an overview of the locations of the wild grapevine in the country. In this project, a sample set of 89 accessions were examined using 24 SSR and 2 SSR markers plus APT3 markers to determine flower sex. The accessions were found in forests on the left bank of the Sava River in Slovenia, on the border between alluvial soils and limestone and dolomite soils, five different sites, some of which are described for the first time. The proportion of female to male accessions differed between sites. At two sites, female plants dominated; at others, the ratio was balanced. The plants' genetic diversity and structure were compared with autochthonous and unique varieties of subsp. sativa from old vineyards in Slovenia and with rootstocks escaped from nature from abandoned vineyards. Sylvestris was clearly distinguishable from vinifera and the rootstocks. Based on genetic analyses, it was confirmed that Slovenian sylvestris is closest to the Balkan and German sylvestris groups. Meanwhile, a safety duplication of the wild grapevine accessions has been established at the University Centre of Viticulture and Enology Meranovo, Faculty of Agriculture and Life Sciences at the University of Maribor.
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Affiliation(s)
- Andrej Perko
- University Centre of Viticulture and Enology Meranovo, Faculty of Agriculture and Life Sciences, University of Maribor, Pivola 10, 2311 Hoče, Slovenia;
| | - Oliver Trapp
- Julius Kühn Institute (JKI)-Federal Research Centre of Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, 76833 Siebeldingen, Germany; (O.T.); (F.R.)
| | - Erika Maul
- Julius Kühn Institute (JKI)-Federal Research Centre of Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, 76833 Siebeldingen, Germany; (O.T.); (F.R.)
| | - Franco Röckel
- Julius Kühn Institute (JKI)-Federal Research Centre of Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, 76833 Siebeldingen, Germany; (O.T.); (F.R.)
| | - Andrej Piltaver
- Institute for the Systematics of Higher Fungi, Velika vas 17, 1262 Dol pri Ljubljani, Slovenia;
| | - Stanko Vršič
- University Centre of Viticulture and Enology Meranovo, Faculty of Agriculture and Life Sciences, University of Maribor, Pivola 10, 2311 Hoče, Slovenia;
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Margaryan K, Töpfer R, Gasparyan B, Arakelyan A, Trapp O, Röckel F, Maul E. Wild grapes of Armenia: unexplored source of genetic diversity and disease resistance. FRONTIERS IN PLANT SCIENCE 2023; 14:1276764. [PMID: 38143573 PMCID: PMC10739323 DOI: 10.3389/fpls.2023.1276764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/16/2023] [Indexed: 12/26/2023]
Abstract
The present study is the first in-depth research evaluating the genetic diversity and potential resistance of Armenian wild grapes utilizing DNA-based markers to understand the genetic signature of this unexplored germplasm. In the proposed research, five geographical regions with known viticultural history were explored. A total of 148 unique wild genotypes were collected and included in the study with 48 wild individuals previously collected as seed. A total of 24 nSSR markers were utilized to establish a fingerprint database to infer information on the population genetic diversity and structure. Three nSSR markers linked to the Ren1 locus were analyzed to identify potential resistance against powdery mildew. According to molecular fingerprinting data, the Armenian V. sylvestris gene pool conserves a high genetic diversity, displaying 292 different alleles with 12.167 allele per loci. The clustering analyses and diversity parameters supported eight genetic groups with 5.6% admixed proportion. The study of genetic polymorphism at the Ren1 locus revealed that 28 wild genotypes carried three R-alleles and 34 wild genotypes carried two R-alleles associated with PM resistance among analyzed 107 wild individuals. This gene pool richness represents an immense reservoir of under-explored genetic diversity and breeding potential. Therefore, continued survey and research efforts are crucial for the conservation, sustainable management, and utilization of Armenian wild grape resources in the face of emerging challenges in viticulture.
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Affiliation(s)
- Kristine Margaryan
- Research Group of Plant Genomics, Institute of Molecular Biology of National Academy of Sciences Republic of Armenia (RA), Yerevan, Armenia
- Department of Genetics and Cytology, Yerevan State University, Yerevan, Armenia
| | - Reinhard Töpfer
- Julius Kuehn-Institute (JKI), Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Boris Gasparyan
- Institute of Archaeology and Ethnography, National Academy of Sciences Republic of Armenia (RA), Yerevan, Armenia
| | - Arsen Arakelyan
- Research Group of Plant Genomics, Institute of Molecular Biology of National Academy of Sciences Republic of Armenia (RA), Yerevan, Armenia
| | - Oliver Trapp
- Julius Kuehn-Institute (JKI), Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Franco Röckel
- Julius Kuehn-Institute (JKI), Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Erika Maul
- Julius Kuehn-Institute (JKI), Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
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Li B, Gschwend AR. Vitis labrusca genome assembly reveals diversification between wild and cultivated grapevine genomes. FRONTIERS IN PLANT SCIENCE 2023; 14:1234130. [PMID: 37719220 PMCID: PMC10501149 DOI: 10.3389/fpls.2023.1234130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 08/03/2023] [Indexed: 09/19/2023]
Abstract
Wild grapevines are important genetic resources in breeding programs to confer adaptive fitness traits and unique fruit characteristics, but the genetics underlying these traits, and their evolutionary origins, are largely unknown. To determine the factors that contributed to grapevine genome diversification, we performed comprehensive intragenomic and intergenomic analyses with three cultivated European (including the PN40024 reference genome) and two wild North American grapevine genomes, including our newly released Vitis labrusca genome. We found the heterozygosity of the cultivated grapevine genomes was twice as high as the wild grapevine genomes studied. Approximately 30% of V. labrusca and 48% of V. vinifera Chardonnay genes were heterozygous or hemizygous and a considerable number of collinear genes between Chardonnay and V. labrusca had different gene zygosity. Our study revealed evidence that supports gene gain-loss events in parental genomes resulted in the inheritance of hemizygous genes in the Chardonnay genome. Thousands of segmental duplications supplied source material for genome-specific genes, further driving diversification of the genomes studied. We found an enrichment of recently duplicated, adaptive genes in similar functional pathways, but differential retention of environment-specific adaptive genes within each genome. For example, large expansions of NLR genes were discovered in the two wild grapevine genomes studied. Our findings support variation in transposable elements contributed to unique traits in grapevines. Our work revealed gene zygosity, segmental duplications, gene gain-and-loss variations, and transposable element polymorphisms can be key driving forces for grapevine genome diversification.
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Affiliation(s)
| | - Andrea R. Gschwend
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States
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Microstructure of Croatian Wild Grapevine (Vitis vinifera subsp. sylvestris Gmel Hegi) Pollen Grains Revealed by Scanning Electron Microscopy. PLANTS 2022; 11:plants11111479. [PMID: 35684252 PMCID: PMC9182919 DOI: 10.3390/plants11111479] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 11/29/2022]
Abstract
Wild grapevine (Vitis vinifera subsp. sylvestris Gmel Hegi) is dioecious with male and female plants, whereas domesticated grapevine is mostly hermaphrodite with self-fertile hermaphrodite flowers. The pollen morphology of wild grapevine has been poorly studied. There is no detailed palynological study of V. sylvestris in Croatia and neighboring countries. Here, scanning electron microscopy (SEM) was used to analyze the pollen of V. sylvestris from male and female individuals growing at two natural sites in Croatia. The selective APT3 marker was used to confirm the flower phenotype with the genetic background. SEM analysis showed that the pollen grains of V. sylvestris were isopolar and radially symmetrical, with foveolate perforated ornamentation, regardless of the flower type of the individuals. All male flowers were 3-colporate and prolate in shape, whereas female individuals varied from subprolate to spheroidal and had inaperturate pollen grains. Pollen shape, dimensions and exine ornamentation proved very informative, and here we address the most polymorphic traits in the analyzed V. sylvestris individuals. Principal component analysis (PCA) and clustering based on pollen morphology variables clearly differentiated individuals by their flower type, and no grouping specific to population was observed, pointing to the conserved pollen structure of V. sylvestris. The results indicate the need to continue the palynological study of V. sylvestris and serve as a good phenotypic basis for functional genetic studies on genes involved in pollen morphology and function.
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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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Huang R, Liu Y, Chen J, Lu Z, Wang J, He W, Chao Z, Tian E. Limited genetic diversity and high differentiation in Angelica dahurica resulted from domestication: insights to breeding and conservation. BMC PLANT BIOLOGY 2022; 22:141. [PMID: 35331143 PMCID: PMC8953045 DOI: 10.1186/s12870-022-03545-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/21/2022] [Indexed: 05/24/2023]
Abstract
BACKGROUND Angelica dahurica belongs to the Apiaceae family, whose dry root is a famous traditional Chinese medicine named as "Bai zhi". There are two cultivars (A. dahurica cv. 'Hangbaizhi' and A. dahurica cv. 'Qibaizhi'), which have been domesticated for thousands of years. Long term artificial selection has led to great changes in root phenotypes of the two cultivars, and also decreased their adaptability to environment. We proposed hypothesis that the cultivars may have lost some of the genetic diversity found in the wild species and may be highly differentiated from the latter during the domestication process. However, few studies have been carried out on how domestication affected the genetic variation of this species. Here, we accessed the levels of genetic variation and differentiation within and between wild A. dahurica populations and two cultivars using 12 microsatellite markers. RESULTS The results revealed that the genetic diversity of the cultivars was much lower than that of wild A. dahurica, and A. dahurica cv. 'Qibaizhi' had lower genetic diversity compared to A. dahurica cv. 'Hangbaizhi'. AMOVA analysis showed significant genetic differentiation between the wild and cultivated A. dahurica populations, and between A. dahurica cv. 'Hangbaizhi' and A. dahurica cv. 'Qibaizhi'. Results from Bayesian, UPGMA, NJ and PcoA clustering analysis indicated that all 15 populations were assigned to two genetic clusters corresponding to the wild and cultivated populations. Bayesian clustering analysis further divided the cultivated populations into two sub-clusters corresponding to the two cultivars. CONCLUSIONS Our study suggests that the domestication process is likely the major factor resulting in the loss of genetic diversity in cultivated A. dahurica populations and in significant genetic differentiation from the wild populations due to founder effect and/or artificially directional selections. This large-scale analysis of population genetics could provide valuable information for genetic resources conservation and breeding programs of Angelica dahurica.
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Affiliation(s)
- Rong Huang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Yinrong Liu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Jianling Chen
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Zuyu Lu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Jiajia Wang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Wei He
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Zhi Chao
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China.
- Department of Pharmacy, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China.
- Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou, 510515, China.
| | - Enwei Tian
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China.
- Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou, 510515, China.
- Guangdong Provincial Engineering Laboratory of Chinese Medicine Preparation Technology, Guangzhou, 510515, China.
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Milovanov A, Savenkova D, Elisyutikova A, Khachumov V, Troshin L. Chloroplast genomes of Vitis sylvestris Gmel. samples from Damanskaya population of the Krasnodar region. BIO WEB OF CONFERENCES 2022. [DOI: 10.1051/bioconf/20225302001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This article presents the structures of chloroplast genomes of three Vitis sylvestris Gmel. samples from Damanskaya population of the Krasnodar Territory. An expedition to the place where wild forest grapevine grows was made. After that, the selected leaves served as a source of chloroplasts. DNA was isolated from them and DNA libraries were prepared and sequenced. Genome assembly was carried out after selection of the most suitable reference sample at coverage of 35.0x. The genomes ranged in size from 159,900 to 160,887. Aligned chloroplast genomes were annotated with GeSeq and GeneMark.hmm. OGDRAW was used to visualize the structure of the genomes. GenBank search allowed to determine their belonging to V. sylvestris species. At the same time, a comparison of the genomes with each other showed the presence of minor differences in their structure.
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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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Rahimi O, Ohana‐Levi N, Brauner H, Inbar N, Hübner S, Drori E. Demographic and ecogeographic factors limit wild grapevine spread at the southern edge of its distribution range. Ecol Evol 2021; 11:6657-6671. [PMID: 34141248 PMCID: PMC8207413 DOI: 10.1002/ece3.7519] [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] [Revised: 03/03/2021] [Accepted: 03/15/2021] [Indexed: 11/13/2022] Open
Abstract
The spatial distribution of plants is constrained by demographic and ecogeographic factors that determine the range and abundance of the species. Wild grapevine (Vitis vinifera ssp. sylvestris) is distributed from Switzerland in the north to Israel in the south. However, little is known about the ecogeographic constraints of this species and its genetic and phenotypic characteristics, especially at the southern edge of its distribution range in the Levant region. In this study, we explore the population structure of southern Levantine wild grapevines and the correlation between demographic and ecogeographic characteristics. Based on our genetic analysis, the wild grapevine populations in this region can be divided into two major subgroups in accordance with a multivariate spatial and ecogeographical clustering model. The identified subpopulations also differ in morphological traits, mainly leaf hairiness which may imply adaptation to environmental stress. The findings suggest that the Upper Jordan River population was spread to the Sea of Galilee area and that a third smaller subpopulation at the south of the Golan Heights may represent a distinguished gene pool or a recent establishment of a new population. A spatial distribution model indicated that distance to water sources, Normalized difference vegetation index, and precipitation are the main environmental factors constraining V. v. sylvestris distribution at its southern distribution range. These factors in addition to limited gene flow between populations prevent further spread of wild grapevines southwards to semi-arid regions.
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Affiliation(s)
- Oshrit Rahimi
- Department of Chemical EngineeringAriel UniversityArielIsrael
| | | | - Hodaya Brauner
- The Samson Family Grape and Wine Research CenterEastern Regional R&D CenterArielIsrael
| | - Nimrod Inbar
- Department of Civil EngineeringAriel UniversityArielIsrael
- The Department of Geophysics and Space ScienceEastern Regional R&D CenterArielIsrael
| | - Sariel Hübner
- Galilee Research Institute (Migal)Tel‐Hai Academic CollegeUpper GalileeIsrael
| | - Elyashiv Drori
- Department of Chemical EngineeringAriel UniversityArielIsrael
- The Samson Family Grape and Wine Research CenterEastern Regional R&D CenterArielIsrael
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14
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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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15
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Genetic structure analysis of cultivated and wild chestnut populations reveals gene flow from cultivars to natural stands. Sci Rep 2021; 11:240. [PMID: 33420378 PMCID: PMC7794426 DOI: 10.1038/s41598-020-80696-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 12/21/2020] [Indexed: 02/04/2023] Open
Abstract
Japanese chestnut (Castanea crenata Sieb. et Zucc.), the only fruit tree species domesticated in Japan, has been cultivated alongside natural stands since prehistorical times. Understanding the genetic diversity of this species and the relationships between cultivated and wild chestnut is important for clarifying its breeding history and determining conservation strategies. We assessed 3 chestnut cultivar populations and 29 wild chestnut populations (618 accessions). Genetic distance analysis revealed that wild populations in the Kyushu region are genetically distant from other populations, whereas other wild and cultivar populations are comparatively similar. Assignment tests suggested that cultivars were relatively similar to populations from central to western Honshu. Bayesian structure analyses showed that wild individuals were roughly classified according to geographical distribution along the Japanese archipelago, except that some wild individuals carried the genetic cluster prevalent in cultivars. Parentage analyses between cultivars and wild individuals identified 26 wild individuals presumed to have a parent–offspring relationship with a cultivar. These results suggested that the genetic structure of some wild individuals in natural stands was influenced by gene flow from cultivars. To conserve wild individuals carrying true “wild” genetic clusters, these individuals should be collected and preserved by ex situ conservation programs.
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16
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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: 15] [Impact Index Per Article: 5.0] [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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17
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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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18
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Genetic Structure and Relationships among Wild and Cultivated Grapevines from Central Europe and Part of the Western Balkan Peninsula. Genes (Basel) 2020; 11:genes11090962. [PMID: 32825336 PMCID: PMC7563143 DOI: 10.3390/genes11090962] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/07/2020] [Accepted: 08/17/2020] [Indexed: 11/16/2022] Open
Abstract
The genetic diversity and relationship between wild (Vitis vinifera L. subsp. sylvestris (Gmel.) Hegi and cultivated (V. vinifera L. subsp. vinifera) grapevine in the western Balkan region and Central Europe have not been studied together previously, although this area has a rich viticultural past. Here, we studied wild grapevine populations sampled from their natural habitats in several countries of the western Balkan region and Central Europe. Their genetic diversity and structure were compared to cultivars that are traditionally in use in this region. A sample set of 243 accessions was genotyped at 20 nuclear microsatellite loci, including 167 sylvestris and 76 diverse vinifera cultivars. The genetic diversity of the wild grapevines was lower than that of cultivars by all genetic parameters. Both hierarchical and nonhierarchical clustering methods differentiated two main groups, indicating clear separation between wild and cultivated vines but also revealed clear gene flow between the cultivated and wild gene pools through overlaps and admixed ancestry values in the graphs. There was greater affinity to the wild grapes in Central European cultivars than in Balkan cultivars. Fine arrangement of the structure among cultivated grapevines showed differentiation among Central European and Balkan cultivars. These results confirm the divergence of wild grapes from vinifera and highlight the "crossroad" role of the western Balkan peninsula in the broader context of European viticulture.
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Tello J, Torres-Pérez R, Flutre T, Grimplet J, Ibáñez J. VviUCC1 Nucleotide Diversity, Linkage Disequilibrium and Association with Rachis Architecture Traits in Grapevine. Genes (Basel) 2020; 11:E598. [PMID: 32485819 PMCID: PMC7348735 DOI: 10.3390/genes11060598] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 11/25/2022] Open
Abstract
Cluster compactness is a trait with high agronomic relevance, affecting crop yield and grape composition. Rachis architecture is a major component of cluster compactness determinism, and is a target trait toward the breeding of grapevine varieties less susceptible to pests and diseases. Although its genetic basis is scarcely understood, a preliminary result indicated a possible involvement of the VviUCC1 gene. The aim of this study was to characterize the VviUCC1 gene in grapevine and to test the association between the natural variation observed for a series of rachis architecture traits and the polymorphisms detected in the VviUCC1 sequence. This gene encodes an uclacyanin plant-specific cell-wall protein involved in fiber formation and/or lignification processes. A high nucleotide diversity in the VviUCC1 gene promoter and coding regions was observed, but no critical effects were predicted in the protein domains, indicating a high level of conservation of its function in the cultivated grapevine. After correcting statistical models for genetic stratification and linkage disequilibrium effects, marker-trait association results revealed a series of single nucleotide polymorphisms (SNPs) significantly associated with cluster compactness and rachis traits variation. Two of them (Y-984 and K-88) affected two common cis-transcriptional regulatory elements, suggesting an effect on phenotype via gene expression regulation. This work reinforces the interest of further studies aiming to reveal the functional effect of the detected VviUCC1 variants on grapevine rachis architecture.
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Affiliation(s)
- Javier Tello
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), 26080 Logroño, Spain; (R.T.-P.); (J.G.); (J.I.)
| | - Rafael Torres-Pérez
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), 26080 Logroño, Spain; (R.T.-P.); (J.G.); (J.I.)
- Servicio de Bioinformática para Genómica y Proteómica (BioinfoGP), Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
| | - Timothée Flutre
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190 Gif-sur-Yvette, France;
| | - Jérôme Grimplet
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), 26080 Logroño, Spain; (R.T.-P.); (J.G.); (J.I.)
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), 50059 Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2 (CITA-Universidad de Zaragoza), 50059 Zaragoza, Spain
| | - Javier Ibáñez
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), 26080 Logroño, Spain; (R.T.-P.); (J.G.); (J.I.)
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20
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D’Onofrio C. Introgression Among Cultivated and Wild Grapevine in Tuscany. FRONTIERS IN PLANT SCIENCE 2020; 11:202. [PMID: 32184799 PMCID: PMC7058638 DOI: 10.3389/fpls.2020.00202] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/11/2020] [Indexed: 05/06/2023]
Abstract
Wild grapevine, Vitis vinifera L. subsp. sylvestris (Gmelin, Hegi) is spontaneous to Europe and common in Tuscany. In this study, wild grapevines were identified in 22 populations from eight locations in Tuscan Maremma (Grosseto and Siena province). The plants were propagated by cuttings, collected in a vineyard, genotyped by nuclear simple sequence repeats (SSRs), chloroplast SSRs and single nucleotide polymorphisms (SNPs), and compared to locally cultivated varieties (Vitis vinifera L. subsp. sativa) and to non-vinifera and non-vitis genotypes. The identity analysis revealed that some individuals were redundant genotypes, suggesting natural vegetative propagation. In addition, four of the supposed V.v. sylvestris were in fact naturalized V.v. sativa. The majority of putative sylvestris genotypes had chlorotype A, while the remainder had chlorotype D, as the majority of Vitis vinifera subsp. sativa cultivated in Italy. Some of the recovered sylvestris genotypes appeared to be natural crosses with cultivated grapevine varieties in Tuscany, and their chlorotype suggests a higher pollen flow from sativa to the sylvestris genotypes than in the opposite direction. In addition, other genotypes appeared to be crosses within sylvestris, sylvestris-sativa or sylvestris-sylvestris siblings, or equivalent relationships. These relationships suggest a noticeably level of sexual reproductive activities among sylvestris and sylvestris-sativa genotypes. A cluster and structure analysis clearly differentiated the true sylvestris from the sativa, and the non-vinifera or non-vitis genotypes, and also highlighted a possible introgression of sylvestris into some Italian and French cultivated varieties. The results therefore suggest that, in addition to the primary ancient center of domestication from the Near East to Central Asia, the introgression among cultivated and wild grapevine occurred in other centers of diversification along the migration routes, contributing to the domestication processes, and suggesting that these processes are still ongoing despite the reduction in populations of sylvestris. The results also highlight that the GrapeReSeq 18K Vitis genotyping chip are suitable for non-vitis genotyping and that the range of SNPs heterozygosity in sylvestris appears to be up to 6% less and does not overlap the heterozygosity range of sativa genotypes.
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Affiliation(s)
- Claudio D’Onofrio
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
- Nutraceuticals and Food for Health – Nutrafood, University of Pisa, Pisa, Italy
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21
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Cronin D, Kron P, Husband BC. The origins and evolutionary history of feral apples in southern Canada. Mol Ecol 2019; 29:1776-1790. [PMID: 31622503 DOI: 10.1111/mec.15277] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 09/30/2019] [Accepted: 10/03/2019] [Indexed: 12/11/2022]
Abstract
Feral populations of domesticated crops can establish through two nonmutually exclusive pathways: hybridization with native relatives and recruitment of and recombination between known cultivars. The extent and relative importance of these pathways is not known, especially for woody fruit crops. Here, we examined the evolutionary origins of feral populations of Malus domestica (domestic apple) in southern Canada using a population genetic analysis. We characterized genotypes of 578 putative feral apple trees and evaluated them in relation to genotypes of 156 commercial cultivars, 28 non-native, ornamental crabapples and 47 native Malus coronaria trees using 14 microsatellite markers. No feral trees were genetic admixtures between domestic and native Malus; however, a minority of trees were admixed with introduced ornamental Malus. Feral trees and commercial cultivars both occurred in two major genetic groups and seven subgroups distributed throughout all commercial growing regions. A total of 42 cultivars, both heritage and currently grown, occurred in probable parental pairs for feral trees, with nine heritage varieties accounting for 72% of parental assignments. We conclude that feral apples in southern Canada are not products of hybridization with native M. coronaria but we cannot exclude ornamental apple species as contributing to the naturalization process. Nonhybrid feral domestic apples have multiple origins, with a prominent signature of early heritage cultivars. These lineages have spread and coexist throughout Ontario, rather than being derived strictly from local sources.
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Affiliation(s)
- Dane Cronin
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Paul Kron
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Brian C Husband
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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22
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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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24
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Işçi B. Genetic relationships of some local and introduced grapes ( Vitis vinifera L.) by microsatellite markers. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1664320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Burçak Işçi
- Department of Horticulture, Agriculture Faculty, Ege University, Izmir, Turkey
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25
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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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26
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Macková L, Vít P, Urfus T. Crop-to-wild hybridization in cherries-Empirical evidence from Prunus fruticosa. Evol Appl 2018; 11:1748-1759. [PMID: 30344640 PMCID: PMC6183504 DOI: 10.1111/eva.12677] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 06/14/2018] [Accepted: 06/19/2018] [Indexed: 12/25/2022] Open
Abstract
Crop cultivation can lead to genetic swamping of indigenous species and thus pose a serious threat for biodiversity. The rare Eurasian tetraploid shrub Prunus fruticosa (ground cherry) is suspected of hybridizing with cultivated allochthonous tetraploid P. cerasus and autochthonous diploid P. avium. Three Prunus taxa (447 individuals of P. fruticosa, 43 of P. cerasus and 73 of P. avium) and their hybrids (198 individuals) were evaluated using analysis of absolute genome size/ploidy level and multivariate morphometrics. Flow cytometry revealed considerable differentiation in absolute genome size at the tetraploid level (average 2C of P. fruticosa = 1.30 pg, average 2C of P. cerasus = 1.42 pg, i.e., a 9.2% difference). The combination of methods used allowed us to ascertain the frequency of hybrids occurring under natural conditions in Central Europe. The morphological evaluation of leaves was based upon distance-based morphometrics supplemented by elliptic Fourier analysis. The results provided substantial evidence for ongoing hybridization (hybrids occurred in 39.5% of P. fruticosa populations). We detected homoploid introgressive hybridization with alien P. cerasus at the tetraploid level. We also found previously overlooked but frequent triploid hybrids resulting from heteroploid hybridization with indigenous P. avium, which, however, probably represent only the F1 generation. Although both hybrids differ in ploidy, they cannot be distinguished using morphometrics. Hybrids are frequent and may endanger wild populations of genuine P. fruticosa via direct niche competition or, alternatively or in addition, via introgression at the homoploid level (i.e., genetic swamping). The cultivation of cherries thus substantially threatens the existence of genuine P. fruticosa.
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Affiliation(s)
- Lenka Macková
- Department of BotanyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Petr Vít
- Institute of BotanyThe Czech Academy of SciencesPrůhoniceCzech Republic
- Faculty of Environmental SciencesCzech University of Life Sciences PraguePragueCzech Republic
| | - Tomáš Urfus
- Department of BotanyFaculty of ScienceCharles UniversityPragueCzech Republic
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27
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Marrano A, Micheletti D, Lorenzi S, Neale D, Grando MS. Genomic signatures of different adaptations to environmental stimuli between wild and cultivated Vitis vinifera L. HORTICULTURE RESEARCH 2018; 5:34. [PMID: 29977570 PMCID: PMC6026492 DOI: 10.1038/s41438-018-0041-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 03/23/2018] [Accepted: 04/06/2018] [Indexed: 05/03/2023]
Abstract
The application of population genetic methods in combination with gene mapping strategies can help to identify genes and mutations selected during the evolution from wild plants to crops and to explore the considerable genetic variation still maintained in natural populations. We genotyped a grapevine germplasm collection of 44 wild (Vitis vinifera subsp. sylvestris) and 48 cultivated (V. vinifera subsp. sativa) accessions at 54 K single-nucleotide polymorphisms (SNPs) to perform a whole-genome comparison of the main population genetic statistics. The analysis of Wright Fixation Index (FST) along the whole genome allowed us to identify several putative "signatures of selection" spanning over two thousand SNPs significantly differentiated between sativa and sylvestris. Many of these genomic regions included genes involved in the adaptation to environmental changes. An overall reduction of nucleotide diversity was observed across the whole genome within sylvestris, supporting a small effective population size of the wild grapevine. Tajima's D resulted positive in both wild and cultivated subgroups, which may indicate an ongoing balancing selection. Association mapping for six domestication-related traits was performed in combination with population genetics, providing further evidence of different perception and response to environmental stresses between sativa and sylvestris.
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Affiliation(s)
- Annarita Marrano
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all ‘Adige (TN), Italy
| | - Diego Micheletti
- Computational Biology Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all ‘Adige (TN), Italy
| | - Silvia Lorenzi
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all ‘Adige (TN), Italy
| | - David Neale
- Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - M. Stella Grando
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all ‘Adige (TN), Italy
- Center Agriculture Food Environment (C3A), University of Trento, San Michele all ‘Adige (TN), Italy
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28
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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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29
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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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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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Rebaa F, Abid G, Aouida M, Abdelkarim S, Aroua I, Muhovski Y, Baudoin JP, M’hamdi M, Sassi K, Jebara M. Genetic variability in Tunisian populations of faba bean ( Vicia faba L. var. major) assessed by morphological and SSR markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:397-409. [PMID: 28461727 PMCID: PMC5391353 DOI: 10.1007/s12298-017-0419-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 01/09/2017] [Accepted: 01/17/2017] [Indexed: 06/07/2023]
Abstract
The genetic diversity of 21 faba bean populations was examined using morphological and molecular markers. DNA was extracted from 189 individuals and 8 microsatellite markers were genotyped individually in these 21 populations. A total of 53 alleles were obtained in all populations, with an average of 6.62 alleles per locus. The expected and observed heterozygosity was 0.38 and 0.62 respectively. The average polymorphism index content of SSR markers was 0.61, ranging from 0.31 to 0.81. The unweighted pair group method with arithmetic mean dendrogram clustered all the populations into two groups, each for them subdivided into 3 sub-groups according to geographical origin. Morphological variation showed that the populations were not grouped according to their geographical origin. Therefore, patterns of differentiation of morphological traits did not coincide with molecular differentiation, indicating that morphological variation does not reflect genetic subdivision in studied faba bean populations. Analysis of molecular variance revealed high levels of genetic variation (83%) within population and provides a good base for designing genetic improvement programs. The result of Principal Component Analysis (PCA) revealed that three dimensional principal components (PC1, PC2 and PC3) contributed 40.56% of the total variability and accounted with values of 20.64, 11.22 and 8.70%, respectively. Cluster analysis based on PCA indicated three separate groups of populations. The genetic relationships found between the 21 populations samples were the same in both the PCA and STRUCTURE analysis which support the results observed. These data may serve as a foundation for the development of faba bean breeding programs.
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Affiliation(s)
- Feten Rebaa
- Laboratory of Legumes, Center of Biotechnology of Borj Cedria, University of Tunis El Manar, 901, 2050 Hammam-Lif, Tunisia
| | - Ghassen Abid
- Laboratory of Legumes, Center of Biotechnology of Borj Cedria, University of Tunis El Manar, 901, 2050 Hammam-Lif, Tunisia
| | - Marwa Aouida
- Laboratory of Legumes, Center of Biotechnology of Borj Cedria, University of Tunis El Manar, 901, 2050 Hammam-Lif, Tunisia
| | - Souhir Abdelkarim
- Laboratory of Legumes, Center of Biotechnology of Borj Cedria, University of Tunis El Manar, 901, 2050 Hammam-Lif, Tunisia
| | - Ibtissem Aroua
- Laboratory of Legumes, Center of Biotechnology of Borj Cedria, University of Tunis El Manar, 901, 2050 Hammam-Lif, Tunisia
| | - Yordan Muhovski
- Department of Life Sciences, Unit of Biological Engineering, Walloon Agricultural Research Centre, Chaussée de Charleroi, 234, 5030 Gembloux, Belgium
| | - Jean-Pierre Baudoin
- Laboratory of Tropical Agroecology, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, 5030 Gembloux, Belgium
| | - Mahmoud M’hamdi
- Laboratory of Vegetable Crops, Higher Agronomic Institute of Chott Mariem (ISA-CM), 47, 4042 Chott-Mariem, Tunisia
| | - Khaled Sassi
- Department of Agronomy and Plant Biotechnology, National Agronomy Institute of Tunisia (INAT), University of Carthage, Avenue Charles Nicolle, 43, 1082 Tunis-Mahrajène, Tunisia
| | - Moez Jebara
- Laboratory of Legumes, Center of Biotechnology of Borj Cedria, University of Tunis El Manar, 901, 2050 Hammam-Lif, Tunisia
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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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Marrano A, Birolo G, Prazzoli ML, Lorenzi S, Valle G, Grando MS. SNP-Discovery by RAD-Sequencing in a Germplasm Collection of Wild and Cultivated Grapevines (V. vinifera L.). PLoS One 2017; 12:e0170655. [PMID: 28125640 PMCID: PMC5268455 DOI: 10.1371/journal.pone.0170655] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 01/09/2017] [Indexed: 01/27/2023] Open
Abstract
Whole-genome comparisons of Vitis vinifera subsp. sativa and V. vinifera subsp. sylvestris are expected to provide a better estimate of the valuable genetic diversity still present in grapevine, and help to reconstruct the evolutionary history of a major crop worldwide. To this aim, the increase of molecular marker density across the grapevine genome is fundamental. Here we describe the SNP discovery in a grapevine germplasm collection of 51 cultivars and 44 wild accessions through a novel protocol of restriction-site associated DNA (RAD) sequencing. By resequencing 1.1% of the grapevine genome at a high coverage, we recovered 34K BamHI unique restriction sites, of which 6.8% were absent in the ‘PN40024’ reference genome. Moreover, we identified 37,748 single nucleotide polymorphisms (SNPs), 93% of which belonged to the 19 assembled chromosomes with an average of 1.8K SNPs per chromosome. Nearly half of the SNPs fell in genic regions mostly assigned to the functional categories of metabolism and regulation, whereas some nonsynonymous variants were identified in genes related with the detection and response to environmental stimuli. SNP validation was carried-out, showing the ability of RAD-seq to accurately determine genotypes in a highly heterozygous species. To test the usefulness of our SNP panel, the main diversity statistics were evaluated, highlighting how the wild grapevine retained less genetic variability than the cultivated form. Furthermore, the analysis of Linkage Disequilibrium (LD) in the two subspecies separately revealed how the LD decays faster within the domesticated grapevine compared to its wild relative. Being the first application of RAD-seq in a diverse grapevine germplasm collection, our approach holds great promise for exploiting the genetic resources available in one of the most economically important fruit crops.
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Affiliation(s)
- Annarita Marrano
- Department of Genomics and Biology of Fruit Crops, Grapevine Genetics and Breeding, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trentino, Italy
- * E-mail:
| | - Giovanni Birolo
- CRIBI Biotechnology Centre, University of Padua, Padua, Italy
| | - Maria Lucia Prazzoli
- Department of Genomics and Biology of Fruit Crops, Grapevine Genetics and Breeding, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trentino, Italy
| | - Silvia Lorenzi
- Department of Genomics and Biology of Fruit Crops, Grapevine Genetics and Breeding, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trentino, Italy
| | - Giorgio Valle
- CRIBI Biotechnology Centre, University of Padua, Padua, Italy
- Department of Biology, University of Padua, Padua, Italy
| | - Maria Stella Grando
- Department of Genomics and Biology of Fruit Crops, Grapevine Genetics and Breeding, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trentino, Italy
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Barazani O, Keren-Keiserman A, Westberg E, Hanin N, Dag A, Ben-Ari G, Fragman-Sapir O, Tugendhaft Y, Kerem Z, Kadereit JW. Genetic variation of naturally growing olive trees in Israel: from abandoned groves to feral and wild? BMC PLANT BIOLOGY 2016; 16:261. [PMID: 27964727 PMCID: PMC5154132 DOI: 10.1186/s12870-016-0947-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 12/05/2016] [Indexed: 05/29/2023]
Abstract
BACKGROUND Naturally growing populations of olive trees are found in the Mediterranean garrigue and maquis in Israel. Here, we used the Simple Sequence Repeat (SSR) genetic marker technique to investigate whether these represent wild var. sylvestris. Leaf samples were collected from a total of 205 trees at six sites of naturally growing olive populations in Israel. The genetic analysis included a multi-locus lineage (MLL) analysis, Rousset's genetic distances, Fst values, private alleles, other diversity values and a Structure analysis. The analyses also included scions and suckers of old cultivated olive trees, for which the dominance of one clone in scions (MLL1) and a second in suckers (MLL7) had been shown earlier. RESULTS The majority of trees from a Judean Mts. population and from one population from the Galilee showed close genetic similarity to scions of old cultivated trees. Different from that, site-specific and a high number of single occurrence MLLs were found in four olive populations from the Galilee and Carmel which also were genetically more distant from old cultivated trees, had relatively high genetic diversity values and higher numbers of private alleles. Whereas in two of these populations MLL7 (and partly MLL1) were found in low frequency, the two other populations did not contain these MLLs and were very similar in their genetic structure to suckers of old cultivated olive trees that originated from sexual reproduction. CONCLUSIONS The genetic distinctness from old cultivated olive trees, particularly of one population from Galilee and one from Carmel, suggests that trees at these sites might represent wild var. sylvestris. The similarity in genetic structure of these two populations with the suckers of old cultivated trees implies that wild trees were used as rootstocks. Alternatively, trees at these two sites may be remnants of old cultivated trees in which the scion-derived trunk died and was replaced by suckers. However, considering landscape and topographic environment at the two sites this second interpretation is less likely.
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Affiliation(s)
- Oz Barazani
- Institute of Plant Sciences, the Israel Plant Gene Bank, Agricultural Research Organization, Rishon LeZion, 75359 Israel
| | - Alexandra Keren-Keiserman
- Institute of Plant Sciences, the Israel Plant Gene Bank, Agricultural Research Organization, Rishon LeZion, 75359 Israel
- Herbarium, the National Natural History Collections, the Hebrew University of Jerusalem, Jerusalem, 91904 Israel
| | - Erik Westberg
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität Mainz, D-55099 Mainz, Germany
| | - Nir Hanin
- Institute of Plant Sciences, the Israel Plant Gene Bank, Agricultural Research Organization, Rishon LeZion, 75359 Israel
| | - Arnon Dag
- Institute of Plant Sciences, Department of Fruit Tree Sciences, Agricultural Research Organization, Gilat Research Center, Gilat, 85280 Israel
| | - Giora Ben-Ari
- Institute of Plant Sciences, Department of Fruit Trees Sciences, Agricultural Research Organization, Rishon LeZion, 75359 Israel
| | - Ori Fragman-Sapir
- Jerusalem Botanical Gardens, the Hebrew University, Giv’at Ram, Jerusalem, 9021904 Israel
| | - Yizhar Tugendhaft
- Institute of Plant Sciences, Department of Fruit Tree Sciences, Agricultural Research Organization, Gilat Research Center, Gilat, 85280 Israel
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, the Hebrew University of Jerusalem, Rehovot, 76100 Israel
| | - Zohar Kerem
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, the Hebrew University of Jerusalem, Rehovot, 76100 Israel
| | - Joachim W. Kadereit
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität Mainz, D-55099 Mainz, Germany
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Puig-Pujol A, Ferrando N, Capdevila F, Ocete R, Revilla E. Yeast biodiversity from Vitis viniferaL., subsp. sylvestris (Gmelin) Hegi to face up the oenological consequences of climate change. BIO WEB OF CONFERENCES 2016. [DOI: 10.1051/bioconf/20160702026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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37
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Revilla E, Bellido A, Yus J, Ortiz P, Carrasco D, Arroyo RA. Flavonols in skins of wild grapes ( Vitis viniferaL., subsp. sylvestris (Gmelin) Hegi). BIO WEB OF CONFERENCES 2016. [DOI: 10.1051/bioconf/20160701018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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38
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Katayama H, Amo H, Wuyun T, Uematsu C, Iketani H. Genetic structure and diversity of the wild Ussurian pear in East Asia. BREEDING SCIENCE 2016; 66:90-99. [PMID: 27069394 PMCID: PMC4780806 DOI: 10.1270/jsbbs.66.90] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/25/2016] [Indexed: 06/05/2023]
Abstract
The Ussurian pear is the most important cultivated pear in the northern part of China. Cultivated Ussurian pears are considered to have derived from Pyrus ussuriensis Maxim. which is native to the northeast of China. In Japan, two varieties of P. ussuriensis, P. ussuriensis var. aromatica and var. hondoensis are native to the northern area and the central area of the main island respectively. In order to reveal the origin of Pyrus ussuriensis var. aromatica distributed in the northern area of main island of Japan, more than 40 explorations have been performed in Japan and in China, and more than 30 natural habitats were recognized. These natural habitats are at risk of extinction because of human development and forest degradation caused by climate change. Population structure and genetic diversity of P. ussuriensis in China and P. ussuriensis var. aromatica in Japan have been investigated using both morphological and molecular markers in order to define appropriate conservation units, and to provide a good focus for conservation management. Distant evolutionary relationships between P. ussuriensis Maxim. in China and P. ussuriensis var. aromatica in Japan inferred from population genetic structure and phylogenetic analysis are also discussed.
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Affiliation(s)
- Hironori Katayama
- Food Resources Education and Research Center, Faculty of Agriculture, Kobe University,
1348 Uzurano, Kasai, Hyogo 675-2103,
Japan
| | - Hitomi Amo
- Food Resources Education and Research Center, Faculty of Agriculture, Kobe University,
1348 Uzurano, Kasai, Hyogo 675-2103,
Japan
| | - Tana Wuyun
- Paulownia Research and Development Center of China, Non-timber Forestry Research and Development of CAF,
Weiwu Road, Zhengzhou City 450003,
China
| | - Chiyomi Uematsu
- Botanical Gardens, Graduate School of Science, Osaka City University,
2000 Kisaichi, Katano, Osaka 576-0004,
Japan
| | - Hiroyuki Iketani
- NARO Institute of Fruit Tree Science,
2-1 Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
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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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Population Structure of and Conservation Strategies for Wild Pyrus ussuriensis Maxim. in China. PLoS One 2015; 10:e0133686. [PMID: 26252516 PMCID: PMC4529180 DOI: 10.1371/journal.pone.0133686] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 06/30/2015] [Indexed: 11/19/2022] Open
Abstract
Pyrus ussriensis Maxim. is native to the northern part of China, but whose habitats are currently being destroyed by environmental changes and human deforestation. An investigation of population structure and genetic diversity of wild Ussurian pear is a priority in order to acquire fundamental knowledge for conservation. A total of 153 individuals of wild Ussurian pear from the main habitats, Heilongjiang, Jilin, and Inner Mongolia in China, possessed low genetic diversity as a result of habitat fragmentation. The genetic diversity of the populations in Inner Mongolia and north east of Heilongjiang was especially low and there was the possibility of inbreeding. Wild Ussurian pears were divided into 5 groups based on the Bayesian clustering method using 20 nuclear SSRs (nSSRs) and 5 groups by haplotype distributions using 16 chloroplast SSRs (cpSSRs), and the populations in Inner Mongolia and north east of Heilongjiang represented unique genotypes. AMOVA indicated there was a 20.05% variation in nSSRs and a 44.40% variation in cpSSRs among populations. These values are relatively high when compared to those of other tree species. Haplotype E, positioned in the center of the cpSSR analysis network and showed the largest number of connections with other haplotypes, represented the most important haplotype. Inner Mongolia and the north east of Heilongjiang are two areas that need urgent conservation because of their genetic vulnerability and peculiarity. We determined 4 conservation units based on the clustering by nSSRs and cpSSRs, and geographic factor. This information is helpful in deciding the conservation strategies for wild Ussurian pear in China.
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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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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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Fu N, Wang PY, Liu XD, Shen HL. Use of EST-SSR markers for evaluating genetic diversity and fingerprinting celery (Apium graveolens L.) cultivars. Molecules 2014; 19:1939-55. [PMID: 24518809 PMCID: PMC6270925 DOI: 10.3390/molecules19021939] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/05/2014] [Accepted: 02/07/2014] [Indexed: 11/26/2022] Open
Abstract
Celery (Apium graveolens L.) is one of the most economically important vegetables worldwide, but genetic and genomic resources supporting celery molecular breeding are quite limited, thus few studies on celery have been conducted so far. In this study we made use of simple sequence repeat (SSR) markers generated from previous celery transcriptome sequencing and attempted to detect the genetic diversity and relationships of commonly used celery accessions and explore the efficiency of the primers used for cultivars identification. Analysis of molecular variance (AMOVA) of Apium graveolens L. var. dulce showed that approximately 43% of genetic diversity was within accessions, 45% among accessions, and 22% among horticultural types. The neighbor-joining tree generated by unweighted pair group method with arithmetic mean (UPGMA), and population structure analysis, as well as principal components analysis (PCA), separated the cultivars into clusters corresponding to the geographical areas where they originated. Genetic distance analysis suggested that genetic variation within Apium graveolens was quite limited. Genotypic diversity showed any combinations of 55 genic SSRs were able to distinguish the genotypes of all 30 accessions.
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Affiliation(s)
- Nan Fu
- College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China.
| | - Ping-Yong Wang
- College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China.
| | - Xiao-Dan Liu
- College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China.
| | - Huo-Lin Shen
- College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China.
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Wang Z, Kang M, Liu H, Gao J, Zhang Z, Li Y, Wu R, Pang X. High-level genetic diversity and complex population structure of Siberian apricot (Prunus sibirica L.) in China as revealed by nuclear SSR markers. PLoS One 2014; 9:e87381. [PMID: 24516551 PMCID: PMC3917850 DOI: 10.1371/journal.pone.0087381] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 12/20/2013] [Indexed: 12/24/2022] Open
Abstract
Siberian apricot (Prunus sibirica L.), an ecologically and economically important tree species with a high degree of tolerance to a variety of extreme environmental conditions, is widely distributed across the mountains of northeastern and northern China, eastern and southeastern regions of Mongolia, Eastern Siberia, and the Maritime Territory of Russia. However, few studies have examined the genetic diversity and population structure of this species. Using 31 nuclear microsatellites, we investigated the level of genetic diversity and population structure of Siberian apricot sampled from 22 populations across China. The number of alleles per locus ranged from 5 to 33, with an average of 19.323 alleles. The observed heterozygosity and expected heterozygosity ranged from 0.037 to 0.874 and 0.040 to 0.924 with average values of 0.639 and 0.774, respectively. A STRUCTURE-based analysis clustered all of the populations into four genetic clusters. Significant genetic differentiation was observed between all population pairs. A hierarchical analysis of molecular variance attributed about 94% of the variation to within populations. No significant difference was detected between the wild and semi-wild groups, indicating that recent cultivation practices have had little impact on the genetic diversity of Siberian apricot. The Mantel test showed that the genetic distance among the populations was not significantly correlated with geographic distance (r = 0.4651, p = 0.9940). Our study represents the most comprehensive investigation of the genetic diversity and population structure of Siberian apricot in China to date, and it provides valuable information for the collection of genetic resources for the breeding of Siberian apricot and related species.
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Affiliation(s)
- Zhe Wang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Ming Kang
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Huabo Liu
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Jiao Gao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Zhengdong Zhang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yingyue Li
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Rongling Wu
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xiaoming Pang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
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Battilana J, Lorenzi S, Moreira FM, Moreno-Sanz P, Failla O, Emanuelli F, Grando MS. Linkage mapping and molecular diversity at the flower sex locus in wild and cultivated grapevine reveal a prominent SSR haplotype in hermaphrodite plants. Mol Biotechnol 2013; 54:1031-7. [PMID: 23532385 PMCID: PMC3641292 DOI: 10.1007/s12033-013-9657-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cultivars used for wine and table grape have self-fertile hermaphrodite flowers whereas wild European vines and American and Asian species are dioecious, having either male or female flowers. Consistent with previous studies, the flower sex trait was mapped as a single major locus on chromosome 2 based on a pure Vitis vinifera population segregating for hermaphrodite and female progeny, and a hybrid population producing all three flower sex types. The sex locus was placed between the same SSR and SNP markers on both genetic maps, although abnormal segregation hampered to fine map the genomic region. From a total of 55 possible haplotypes inferred for three SSR markers around the sex locus, in a population of 132 V. sylvestris accessions and 171 V. vinifera cultivars, one of them accounted for 66 % of the hermaphrodite individuals and may be the result of domestication. Specific size variants of the VVIB23 microsatellite sequence within the 3'-UTR of a putative YABBY1 gene were found to be statistically significantly associated with the sex alleles M, H and f; these markers can provide assistance in defining the status of wild grapevine germplasm.
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Affiliation(s)
- Juri Battilana
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach Via E. Mach 1, 38010 San Michele all’Adige, TN Italy
| | - Silvia Lorenzi
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach Via E. Mach 1, 38010 San Michele all’Adige, TN Italy
| | - Flavia M. Moreira
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach Via E. Mach 1, 38010 San Michele all’Adige, TN Italy
- Present Address: Instituto Federal de Santa Catarina, Rua José Lino Kretzer 608–Praia Comprida, São José, Santa Catarina 88130-310 Brazil
| | - Paula Moreno-Sanz
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach Via E. Mach 1, 38010 San Michele all’Adige, TN Italy
| | - Osvaldo Failla
- Department of Crop Production, Faculty of Agriculture, University of Milano, Via Celoria 2, 20133 Milan, Italy
| | - Francesco Emanuelli
- Department of Crop Production, Faculty of Agriculture, University of Milano, Via Celoria 2, 20133 Milan, Italy
| | - M. Stella Grando
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach Via E. Mach 1, 38010 San Michele all’Adige, TN Italy
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Riaz S, Boursiquot JM, Dangl GS, Lacombe T, Laucou V, Tenscher AC, Walker MA. Identification of mildew resistance in wild and cultivated Central Asian grape germplasm. BMC PLANT BIOLOGY 2013; 13:149. [PMID: 24093598 PMCID: PMC3851849 DOI: 10.1186/1471-2229-13-149] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 09/30/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND Cultivated grapevines, Vitis vinifera subsp. sativa, evolved from their wild relative, V. vinifera subsp. sylvestris. They were domesticated in Central Asia in the absence of the powdery mildew fungus, Erysiphe necator, which is thought to have originated in North America. However, powdery mildew resistance has previously been discovered in two Central Asian cultivars and in Chinese Vitis species. RESULTS A set of 380 unique genotypes were evaluated with data generated from 34 simple sequence repeat (SSR) markers. The set included 306 V. vinifera cultivars, 40 accessions of V. vinifera subsp. sylvestris, and 34 accessions of Vitis species from northern Pakistan, Afghanistan and China. Based on the presence of four SSR alleles previously identified as linked to the powdery mildew resistance locus, Ren1, 10 new mildew resistant genotypes were identified in the test set: eight were V. vinifera cultivars and two were V. vinifera subsp. sylvestris based on flower and seed morphology. Sequence comparison of a 620 bp region that includes the Ren1-linked allele (143 bp) of the co-segregating SSR marker SC8-0071-014, revealed that the ten newly identified genotypes have sequences that are essentially identical to the previously identified mildew resistant V. vinifera cultivars: 'Kishmish vatkana' and 'Karadzhandal'. Kinship analysis determined that three of the newly identified powdery mildew resistant accessions had a relationship with 'Kishmish vatkana' and 'Karadzhandal', and that six were not related to any other accession in this study set. Clustering procedures assigned accessions into three groups: 1) Chinese species; 2) a mixed group of cultivated and wild V. vinifera; and 3) table grape cultivars, including nine of the powdery mildew resistant accessions. Gene flow was detected among the groups. CONCLUSIONS This study provides evidence that powdery mildew resistance is present in V. vinifera subsp. sylvestris, the dioecious wild progenitor of the cultivated grape. Four first-degree parent progeny relationships were discovered among the hermaphroditic powdery mildew resistant cultivars, supporting the existence of intentional grape breeding efforts. Although several Chinese grape species are resistant to powdery mildew, no direct genetic link to the resistance found in V. vinifera could be established.
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Affiliation(s)
- Summaira Riaz
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA
| | - Jean-Michel Boursiquot
- UMR AGAP, Equipe Diversité et Adaptation de la Vigne et des Espèces Méditerranéennes, Montpellier SupAgro, 2 Place Viala, Montpellier 34060, France
| | - Gerald S Dangl
- Foundation Plant Services, University of California, Davis, CA 95616, USA
| | - Thierry Lacombe
- UMR AGAP, Equipe Diversité et Adaptation de la Vigne et des Espèces Méditerranéennes, INRA, 2 Place Viala, Montpellier 34060, France
| | - Valerie Laucou
- UMR AGAP, Equipe Diversité et Adaptation de la Vigne et des Espèces Méditerranéennes, INRA, 2 Place Viala, Montpellier 34060, France
| | - Alan C Tenscher
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA
| | - M Andrew Walker
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA
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Cambrollé J, García JL, Ocete R, Figueroa ME, Cantos M. Growth and photosynthetic responses to copper in wild grapevine. CHEMOSPHERE 2013; 93:294-301. [PMID: 23746388 DOI: 10.1016/j.chemosphere.2013.04.080] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 02/20/2013] [Accepted: 04/27/2013] [Indexed: 06/02/2023]
Abstract
The present study evaluates the tolerance and accumulation potential of Vitis vinifera ssp. sylvestris under moderate and high external Cu levels. A greenhouse experiment was conducted in order to investigate the effects of a range of external Cu concentrations (0-23mmolL(-1)) on growth and photosynthetic performance by measuring gas exchange, chlorophyll fluorescence parameters and photosynthetic pigments. We also measured the total copper, nitrogen, phosphorus, sulphur, calcium, magnesium, iron, potassium and sodium concentrations in the plant tissues. All the experimental plants survived even with external Cu concentrations as high as 23mmolL(-1) (1500mg Cu L(-1)), although the excess of metal resulted in a biomass reduction of 35%. The effects of Cu on growth were linked to a reduction in net photosynthesis, which may be related to the effect of the high concentration of the metal on photosynthetic electron transport. V. vinifera ssp. sylvestris survived with leaf Cu concentrations as high as 80mgkg(-1) DW and growth parameters were unaffected by leaf tissue concentrations of 35mg Cu kg(-1) DW. The results of our study indicate that plants of V. vinifera ssp. sylvestris from the studied population are more tolerant to Cu than the commercial varieties of grapevine that have been studied in the literature, and could constitute a basis for the genetic improvement of Cu tolerance in grapevine.
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Affiliation(s)
- J Cambrollé
- Instituto de Recursos Naturales y Agrobiología de Sevilla (C.S.I.C.), P.O. Box 1052, 41080 Sevilla, Spain.
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Lu L, Wang W, Chen Z, Wen J. Phylogeny of the non-monophyletic Cayratia Juss. (Vitaceae) and implications for character evolution and biogeography. Mol Phylogenet Evol 2013; 68:502-15. [DOI: 10.1016/j.ympev.2013.04.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 01/15/2013] [Accepted: 04/19/2013] [Indexed: 11/26/2022]
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