1
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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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2
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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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3
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Wang R, Lan Z, Luo Y, Deng Z. The complete Chloroplast genome of Stachys geobombycis and comparative analysis with related Stachys species. Sci Rep 2024; 14:8523. [PMID: 38609472 PMCID: PMC11014926 DOI: 10.1038/s41598-024-59132-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/08/2024] [Indexed: 04/14/2024] Open
Abstract
Herb genomics, at the forefront of traditional Chinese medicine research, combines genomics with traditional practices, facilitating the scientific validation of ancient remedies. This integration enhances public understanding of traditional Chinese medicine's efficacy and broadens its scope in modern healthcare. Stachys species encompass annual or perennial herbs or small shrubs, exhibiting simple petiolate or sessile leaves. Despite their wide-ranging applications across various fields, molecular data have been lacking, hindering the precise identification and taxonomic elucidation of Stachys species. To address this gap, we assembled the complete chloroplast (CP) genome of Stachys geobombycis and conducted reannotation and comparative analysis of seven additional species within the Stachys genus. The findings demonstrate that the CP genomes of these species exhibit quadripartite structures, with lengths ranging from 14,523 to 150,599 bp. Overall, the genome structure remains relatively conserved, hosting 131 annotated genes, including 87 protein coding genes, 36 tRNA genes, and 8 rRNA genes. Additionally, 78 to 98 SSRs and long repeat sequences were detected , and notably, 6 highly variable regions were identified as potential molecular markers in the CP genome through sequence alignment. Phylogenetic analysis based on Bayesian inference and maximum likelihood methods strongly supported the phylogenetic position of the genus Stachys as a member of Stachydeae tribe. Overall, this comprehensive bioinformatics study of Stachys CP genomes lays the groundwork for phylogenetic classification, plant identification, genetic engineering, evolutionary studies, and breeding research concerning medicinal plants within the Stachys genus.
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Affiliation(s)
- Ru Wang
- Hubei Key Laboratory of Biologic Resources Protection and Utilization (Hubei Minzu University), Enshi, 445000, China
| | - Zheng Lan
- Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Yongjian Luo
- Hubei Key Laboratory of Biologic Resources Protection and Utilization (Hubei Minzu University), Enshi, 445000, China
- Central South University of Forestry and Technology, Key Laboratory of Forestry Biotechnology of Hunan Province, Changsha, 410000, China
| | - Zhijun Deng
- Hubei Key Laboratory of Biologic Resources Protection and Utilization (Hubei Minzu University), Enshi, 445000, China.
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4
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Zunino L, Cubry P, Sarah G, Mournet P, El Bakkali A, Aqbouch L, Sidibé-Bocs S, Costes E, Khadari B. Genomic evidence of genuine wild versus admixed olive populations evolving in the same natural environments in western Mediterranean Basin. PLoS One 2024; 19:e0295043. [PMID: 38232071 DOI: 10.1371/journal.pone.0295043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/14/2023] [Indexed: 01/19/2024] Open
Abstract
Crop-to-wild gene flow is a mechanism process widely documented, both in plants and animals. This can have positive or negative impacts on the evolution of admixed populations in natural environments, yet the phenomenon is still misunderstood in long-lived woody species, contrary to short-lived crops. Wild olive Olea europaea L. occurs in the same eco-geographical range as domesticated olive, i.e. the Mediterranean Basin (MB). Moreover, it is an allogamous and anemophilous species whose seeds are disseminated by birds, i.e. factors that drive gene flow between crops and their wild relatives. Here we investigated the genetic structure of western MB wild olive populations in natural environments assuming a homogenous gene pool with limited impact of cultivated alleles, as previously suggested. We used a target sequencing method based on annotated genes from the Farga reference genome to analyze 27 western MB olive tree populations sampled in natural environments in France, Spain and Morocco. We also target sequenced cultivated olive tree accessions from the Worldwide Olive Germplasm Bank of Marrakech and Porquerolles and from an eastern MB wild olive tree population. We combined PCA, sNMF, pairwise FST and TreeMix and clearly identified genuine wild olive trees throughout their natural distribution range along a north-south gradient including, for the first time, in southern France. However, contrary to our assumption, we highlighted more admixed than genuine wild olive trees. Our results raise questions regarding the admixed population evolution pattern in this environment, which might be facilitated by crop-to-wild gene flow.
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Affiliation(s)
- Lison Zunino
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- DIADE, University of Montpellier, CIRAD, IRD, Montpellier, France
| | - Philippe Cubry
- DIADE, University of Montpellier, CIRAD, IRD, Montpellier, France
| | - Gautier Sarah
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Pierre Mournet
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
| | - Ahmed El Bakkali
- INRA, UR Amélioration des Plantes et Conservation des Ressources Phytogénétiques, Meknes, Morocco
| | - Laila Aqbouch
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Stéphanie Sidibé-Bocs
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
| | - Evelyne Costes
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Bouchaib Khadari
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- Conservatoire Botanique National Méditerranéen (CBNMed), UMR AGAP Institut, Montpellier, France
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5
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Di Pietro Fernandes C, Santana LF, dos Santos JR, Fernandes DS, Hiane PA, Pott A, Freitas KDC, Bogo D, do Nascimento VA, Filiú WFDO, Asato MA, Guimarães RDCA. Nutraceutical Potential of Grape ( Vitis vinifera L.) Seed Oil in Oxidative Stress, Inflammation, Obesity and Metabolic Alterations. Molecules 2023; 28:7811. [PMID: 38067541 PMCID: PMC10708499 DOI: 10.3390/molecules28237811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/17/2023] [Accepted: 08/29/2023] [Indexed: 12/18/2023] Open
Abstract
Vitis vinifera L. (grapevine) is a perennial plant of the Vitaceae family that is widely used to produce grapes and wines. Grape seed oil is rich in fatty acids such as linoleic acid (65-75%), vitamin E (50 mg), and phytosterols in addition to phenolic compounds, such as catechins (414 mg), epicatechins (130.4 mg), and gallic acid (77 µg), shows promise as a nutritional compound and is outstanding as a therapeutic substance with active properties for health, detected mainly by in vitro studies, as well as some in vivo studies. The benefits of consuming this oil include modulating the expression of antioxidant enzymes, anti-atherosclerotic and anti-inflammatory effects, and protection against oxidative cell damage and some types of cancer. However, experimental findings confirm that therapeutic functions remain scarce; thus, more studies are needed to determine the mechanisms of action involved in the indicated therapeutic qualities.
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Affiliation(s)
- Carolina Di Pietro Fernandes
- Graduate Program in Health and Development in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, Brazil; (C.D.P.F.); (D.S.F.); (P.A.H.); (K.d.C.F.); (D.B.); (V.A.d.N.); (R.d.C.A.G.)
| | | | | | - Dayane Stéphanie Fernandes
- Graduate Program in Health and Development in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, Brazil; (C.D.P.F.); (D.S.F.); (P.A.H.); (K.d.C.F.); (D.B.); (V.A.d.N.); (R.d.C.A.G.)
| | - Priscila Aiko Hiane
- Graduate Program in Health and Development in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, Brazil; (C.D.P.F.); (D.S.F.); (P.A.H.); (K.d.C.F.); (D.B.); (V.A.d.N.); (R.d.C.A.G.)
| | - Arnildo Pott
- Laboratory of Botany, Institute of Biosciences, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, Brazil;
| | - Karine de Cássia Freitas
- Graduate Program in Health and Development in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, Brazil; (C.D.P.F.); (D.S.F.); (P.A.H.); (K.d.C.F.); (D.B.); (V.A.d.N.); (R.d.C.A.G.)
| | - Danielle Bogo
- Graduate Program in Health and Development in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, Brazil; (C.D.P.F.); (D.S.F.); (P.A.H.); (K.d.C.F.); (D.B.); (V.A.d.N.); (R.d.C.A.G.)
| | - Valter Aragão do Nascimento
- Graduate Program in Health and Development in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, Brazil; (C.D.P.F.); (D.S.F.); (P.A.H.); (K.d.C.F.); (D.B.); (V.A.d.N.); (R.d.C.A.G.)
| | | | - Marcel Arakaki Asato
- Medical School, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, Brazil;
| | - Rita de Cássia Avellaneda Guimarães
- Graduate Program in Health and Development in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, Brazil; (C.D.P.F.); (D.S.F.); (P.A.H.); (K.d.C.F.); (D.B.); (V.A.d.N.); (R.d.C.A.G.)
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6
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Breglia F, Bouby L, Wales N, Ivorra S, Fiorentino G. Disentangling the origins of viticulture in the western Mediterranean. Sci Rep 2023; 13:17284. [PMID: 37828091 PMCID: PMC10570292 DOI: 10.1038/s41598-023-44445-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 10/08/2023] [Indexed: 10/14/2023] Open
Abstract
We present direct evidence of early grape domestication in southern Italy via a multidisciplinary study of pip assemblage from one site, shedding new light on the spread of viticulture in the western Mediterranean during the Bronze Age. This consist of 55 waterlogged pips from Grotta di Pertosa, a Middle Bronze Age settlement in the south of the Italian peninsula. Direct radiocarbon dating of pips was carried out, confirming the chronological consistency of the samples with their archaeological contexts (ca. 1450-1200 BCE). The extraordinary state of conservation of the sample allowed to perform geometric morphometric (GMM) and paleogenetic analyses (aDNA) at the same time. The combination of the two methods has irrefutably shown the presence of domestic grapevines, together with wild ones, in Southern Italy during the Middle/Late Bronze Age. The results converge towards an oriental origin of the domestic grapes, most likely arriving from the Aegean area through the Mycenaeans. A parent/offspring kinship was also recognised between a domestic/wild hybrid individual and a domestic clonal group. This data point out a little known aspect of the diffusion of the first viticulture in Italy, and therefore in the western Mediterranean, which involved the hybridization between imported domestic varieties with, likely local, wild vines.
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Affiliation(s)
- Francesco Breglia
- Department of Geosciences, University of Padua, 35131, Padua, Italy.
- Laboratory of Archaeobotany and Palaeoecology, Cultural Heritage Department, University of Salento, 73100, Lecce, Italy.
| | - Laurent Bouby
- Institut des Sciences de l'Evolution, University of Montpellier, 34095, Montpellier, France
| | - Nathan Wales
- Department of Archaeology, University of York, York, YO1 7EP, UK
| | - Sarah Ivorra
- Institut des Sciences de l'Evolution, University of Montpellier, 34095, Montpellier, France
| | - Girolamo Fiorentino
- Laboratory of Archaeobotany and Palaeoecology, Cultural Heritage Department, University of Salento, 73100, Lecce, Italy
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7
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Lamarque LJ, Delmas CEL, Charrier G, Burlett R, Dell'Acqua N, Pouzoulet J, Gambetta GA, Delzon S. Quantifying the grapevine xylem embolism resistance spectrum to identify varieties and regions at risk in a future dry climate. Sci Rep 2023; 13:7724. [PMID: 37173393 PMCID: PMC10181993 DOI: 10.1038/s41598-023-34224-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Maintaining wine production under global warming partly relies on optimizing the choice of plant material for a given viticultural region and developing drought-resistant cultivars. However, progress in these directions is hampered by the lack of understanding of differences in drought resistance among Vitis genotypes. We investigated patterns of xylem embolism vulnerability within and among 30 Vitis species and sub-species (varieties) from different locations and climates, and assessed the risk of drought vulnerability in 329 viticultural regions worldwide. Within a variety, vulnerability to embolism decreased during summer. Among varieties, we have found wide variations in drought resistance of the vascular system in grapevines. This is particularly the case within Vitis vinifera, with varieties distributed across four clusters of embolism vulnerability. Ugni blanc and Chardonnay featured among the most vulnerable, while Pinot noir, Merlot and Cabernet Sauvignon ranked among the most resistant. Regions possibly at greater risk of being vulnerable to drought, such as Poitou-Charentes, France and Marlborough, New Zealand, do not necessarily have arid climates, but rather bear a significant proportion of vulnerable varieties. We demonstrate that grapevine varieties may not respond equally to warmer and drier conditions, and highlight that hydraulic traits are key to improve viticulture suitability under climate change.
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Affiliation(s)
- Laurent J Lamarque
- Université de Bordeaux, INRAE, BIOGECO, 33615, Pessac, France.
- Département des Sciences de l'Environnement, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada.
| | | | - Guillaume Charrier
- Université Clermont Auvergne, INRAE, PIAF, 63000, Clermont-Ferrand, France
| | - Régis Burlett
- Université de Bordeaux, INRAE, BIOGECO, 33615, Pessac, France
| | | | | | - Gregory A Gambetta
- EGFV, Bordeaux-Sciences Agro, INRAE, Université de Bordeaux, ISVV, 33882, Villenave d'Ornon, France
| | - Sylvain Delzon
- Université de Bordeaux, INRAE, BIOGECO, 33615, Pessac, France
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8
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Sharafan M, Malinowska MA, Ekiert H, Kwaśniak B, Sikora E, Szopa A. Vitis vinifera (Vine Grape) as a Valuable Cosmetic Raw Material. Pharmaceutics 2023; 15:pharmaceutics15051372. [PMID: 37242614 DOI: 10.3390/pharmaceutics15051372] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/21/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
This review refers to botanical, ecological and phytochemical characteristics of Vitis vinifera L. (vine grape)-a species, the valuable properties of which are widely exploited in the food industry and in recent times in medicine as well as in phytocosmetology. The general characteristic of V. vinifera, followed by the chemical composition and biological activities of different extracts obtained from the plant (fruit, skin, pomace, seed, leaf and stem extracts), are provided. A concise review of the extraction conditions of grape metabolites and the methods of their analysis are also presented. The biological activity of V. vinifera is determined by the presence of high contents of polyphenols, mainly flavonoids (e.g., quercetin, kaempferol), catechin derivatives, anthocyanins and stilbenoids (e.g., trans-resveratrol, trans-ε-viniferin). The review pays particular attention to the application of V. vinifera in cosmetology. It has been proven that V. vinifera possesses strong cosmetological-related properties, such as anti-ageing properties, anti-inflammatory properties and skin-whitening properties. Moreover, a review of studies on V. vinifera biological activities, which are of particular interest for dermatologic problems, are disclosed. Furthermore, the work also emphasises the importance of biotechnological studies on V. vinifera. The last part of the review is addressed to the safety of the use of V. vinifera.
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Affiliation(s)
- Marta Sharafan
- Department of Organic Chemistry and Technology, Faculty of Chemical Engineering and Technology, Cracow University of Technology, Warszawska 24, 31-155 Kraków, Poland
| | - Magdalena A Malinowska
- Department of Organic Chemistry and Technology, Faculty of Chemical Engineering and Technology, Cracow University of Technology, Warszawska 24, 31-155 Kraków, Poland
| | - Halina Ekiert
- Department of Pharmaceutical Botany, Medical College, Jagiellonian University, Medyczna 9, 30-688 Kraków, Poland
| | - Beata Kwaśniak
- Department of Pharmaceutical Botany, Medical College, Jagiellonian University, Medyczna 9, 30-688 Kraków, Poland
| | - Elżbieta Sikora
- Department of Organic Chemistry and Technology, Faculty of Chemical Engineering and Technology, Cracow University of Technology, Warszawska 24, 31-155 Kraków, Poland
| | - Agnieszka Szopa
- Department of Pharmaceutical Botany, Medical College, Jagiellonian University, Medyczna 9, 30-688 Kraków, Poland
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9
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Dong Y, Duan S, Xia Q, Liang Z, Dong X, Margaryan K, Musayev M, Goryslavets S, Zdunić G, Bert PF, Lacombe T, Maul E, Nick P, Bitskinashvili K, Bisztray GD, Drori E, De Lorenzis G, Cunha J, Popescu CF, Arroyo-Garcia R, Arnold C, Ergül A, Zhu Y, Ma C, Wang S, Liu S, Tang L, Wang C, Li D, Pan Y, Li J, Yang L, Li X, Xiang G, Yang Z, Chen B, Dai Z, Wang Y, Arakelyan A, Kuliyev V, Spotar G, Girollet N, Delrot S, Ollat N, This P, Marchal C, Sarah G, Laucou V, Bacilieri R, Röckel F, Guan P, Jung A, Riemann M, Ujmajuridze L, Zakalashvili T, Maghradze D, Höhn M, Jahnke G, Kiss E, Deák T, Rahimi O, Hübner S, Grassi F, Mercati F, Sunseri F, Eiras-Dias J, Dumitru AM, Carrasco D, Rodriguez-Izquierdo A, Muñoz G, Uysal T, Özer C, Kazan K, Xu M, Wang Y, Zhu S, Lu J, Zhao M, Wang L, Jiu S, Zhang Y, Sun L, Yang H, Weiss E, Wang S, Zhu Y, Li S, Sheng J, Chen W. Dual domestications and origin of traits in grapevine evolution. Science 2023; 379:892-901. [PMID: 36862793 DOI: 10.1126/science.add8655] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
We elucidate grapevine evolution and domestication histories with 3525 cultivated and wild accessions worldwide. In the Pleistocene, harsh climate drove the separation of wild grape ecotypes caused by continuous habitat fragmentation. Then, domestication occurred concurrently about 11,000 years ago in Western Asia and the Caucasus to yield table and wine grapevines. The Western Asia domesticates dispersed into Europe with early farmers, introgressed with ancient wild western ecotypes, and subsequently diversified along human migration trails into muscat and unique western wine grape ancestries by the late Neolithic. Analyses of domestication traits also reveal new insights into selection for berry palatability, hermaphroditism, muscat flavor, and berry skin color. These data demonstrate the role of the grapevines in the early inception of agriculture across Eurasia.
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Affiliation(s)
- Yang Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Shengchang Duan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Qiuju Xia
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Science and Oenology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Xiao Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Kristine Margaryan
- Institute of Molecular Biology, NAS RA, 0014 Yerevan, Armenia.,Yerevan State University, 0014 Yerevan, Armenia
| | - Mirza Musayev
- Genetic Resources Institute, Azerbaijan National Academy of Sciences, AZ1106 Baku, Azerbaijan
| | | | - Goran Zdunić
- Institute for Adriatic Crops and Karst Reclamation, 21000 Split, Croatia
| | - Pierre-François Bert
- Bordeaux University, Bordeaux Sciences Agro, INRAE, UMR EGFV, ISVV, 33882 Villenave d'Ornon, France
| | - Thierry Lacombe
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro Montpellier, 34398 Montpellier, France
| | - Erika Maul
- Julius Kühn Institute (JKI) - Federal Research Center for Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, 76833 Siebeldingen, Germany
| | - Peter Nick
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | | | - György Dénes Bisztray
- Hungarian University of Agriculture and Life Sciences (MATE), 1118 Budapest, Hungary
| | - Elyashiv Drori
- Department of Chemical Engineering, Ariel University, 40700 Ariel, Israel.,Eastern Regional R&D Center, 40700 Ariel, Israel
| | - Gabriella De Lorenzis
- Department of Agricultural and Environmental Sciences, University of Milano, 20133 Milano, Italy
| | - Jorge Cunha
- Instituto Nacional de Investigação Agrária e Veterinária, I.P./INIAV-Dois Portos, 2565-191 Torres Vedras, Portugal.,Green-it Unit, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Carmen Florentina Popescu
- National Research and Development Institute for Biotechnology in Horticulture, Stefanesti, 117715 Arges, Romania
| | - Rosa Arroyo-Garcia
- Center for Plant Biotechnology and Genomics, UPM-INIA/CSIC, Pozuelo de Alarcon, 28223 Madrid, Spain
| | | | - Ali Ergül
- Biotechnology Institute, Ankara University, 06135 Ankara, Turkey
| | - Yifan Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai JiaoTong University, Shanghai 200240, China
| | - Shufen Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Siqi Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Liu Tang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Chunping Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Dawei Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Yunbing Pan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Jingxian Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Ling Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Xuzhen Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Guisheng Xiang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Zijiang Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Baozheng Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Zhanwu Dai
- Beijing Key Laboratory of Grape Science and Oenology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Yi Wang
- Beijing Key Laboratory of Grape Science and Oenology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Arsen Arakelyan
- Institute of Molecular Biology, NAS RA, 0014 Yerevan, Armenia.,Armenian Bioinformatics Institute, 0014 Yerevan, Armenia.,Biomedicine and Pharmacy, RAU, 0051 Yerevan, Armenia
| | - Varis Kuliyev
- Institute of Bioresources, Nakhchivan Branch of the Azerbaijan National Academy of Sciences, AZ7000 Nakhchivan, Azerbaijan
| | - Gennady Spotar
- National Institute of Viticulture and Winemaking Magarach, Yalta 298600, Crimea
| | - Nabil Girollet
- Bordeaux University, Bordeaux Sciences Agro, INRAE, UMR EGFV, ISVV, 33882 Villenave d'Ornon, France
| | - Serge Delrot
- Bordeaux University, Bordeaux Sciences Agro, INRAE, UMR EGFV, ISVV, 33882 Villenave d'Ornon, France
| | - Nathalie Ollat
- Bordeaux University, Bordeaux Sciences Agro, INRAE, UMR EGFV, ISVV, 33882 Villenave d'Ornon, France
| | - Patrice This
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro Montpellier, 34398 Montpellier, France
| | - Cécile Marchal
- Vassal-Montpellier Grapevine Biological Resources Center, INRAE, 34340 Marseillan-Plage, France
| | - Gautier Sarah
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro Montpellier, 34398 Montpellier, France
| | - Valérie Laucou
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro Montpellier, 34398 Montpellier, France
| | - Roberto Bacilieri
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro Montpellier, 34398 Montpellier, France
| | - Franco Röckel
- Julius Kühn Institute (JKI) - Federal Research Center for Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, 76833 Siebeldingen, Germany
| | - Pingyin Guan
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Andreas Jung
- Historische Rebsorten-Sammlung, Rebschule (K39), 67599 Gundheim, Germany
| | - Michael Riemann
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Levan Ujmajuridze
- LEPL Scientific Research Center of Agriculture, 0159 Tbilisi, Georgia
| | | | - David Maghradze
- LEPL Scientific Research Center of Agriculture, 0159 Tbilisi, Georgia
| | - Maria Höhn
- Hungarian University of Agriculture and Life Sciences (MATE), 1118 Budapest, Hungary
| | - Gizella Jahnke
- Hungarian University of Agriculture and Life Sciences (MATE), 1118 Budapest, Hungary
| | - Erzsébet Kiss
- Hungarian University of Agriculture and Life Sciences (MATE), 1118 Budapest, Hungary
| | - Tamás Deák
- Hungarian University of Agriculture and Life Sciences (MATE), 1118 Budapest, Hungary
| | - Oshrit Rahimi
- Department of Chemical Engineering, Ariel University, 40700 Ariel, Israel
| | - Sariel Hübner
- Galilee Research Institute (Migal), Tel-Hai Academic College, 12210 Upper Galilee, Israel
| | - Fabrizio Grassi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milano, Italy.,NBFC, National Biodiversity Future Center, 90133 Palermo, Italy
| | - Francesco Mercati
- Institute of Biosciences and Bioresources, National Research Council, 90129 Palermo, Italy
| | - Francesco Sunseri
- Department AGRARIA, University Mediterranea of Reggio Calabria, Reggio 89122 Calabria, Italy
| | - José Eiras-Dias
- Instituto Nacional de Investigação Agrária e Veterinária, I.P./INIAV-Dois Portos, 2565-191 Torres Vedras, Portugal.,Green-it Unit, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Anamaria Mirabela Dumitru
- National Research and Development Institute for Biotechnology in Horticulture, Stefanesti, 117715 Arges, Romania
| | - David Carrasco
- Center for Plant Biotechnology and Genomics, UPM-INIA/CSIC, Pozuelo de Alarcon, 28223 Madrid, Spain
| | | | | | - Tamer Uysal
- Viticulture Research Institute, Ministry of Agriculture and Forestry, 59200 Tekirdağ, Turkey
| | - Cengiz Özer
- Viticulture Research Institute, Ministry of Agriculture and Forestry, 59200 Tekirdağ, Turkey
| | - Kemal Kazan
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Meilong Xu
- Institute of Horticulture, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan 750002, China
| | - Yunyue Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Shusheng Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Jiang Lu
- Center for Viticulture and Oenology, School of Agriculture and Biology, Shanghai JiaoTong University, Shanghai 200240, China
| | - Maoxiang Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai JiaoTong University, Shanghai 200240, China
| | - Lei Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai JiaoTong University, Shanghai 200240, China
| | - Songtao Jiu
- Department of Plant Science, School of Agriculture and Biology, Shanghai JiaoTong University, Shanghai 200240, China
| | - Ying Zhang
- Zhengzhou Fruit Research Institutes, CAAS, Zhengzhou 450009, China
| | - Lei Sun
- Zhengzhou Fruit Research Institutes, CAAS, Zhengzhou 450009, China
| | | | - Ehud Weiss
- The Martin (Szusz) Department of Land of Israel Studies and Archaeology, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai JiaoTong University, Shanghai 200240, China
| | - Youyong Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Science and Oenology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Jun Sheng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Wei Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
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10
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Šikuten I, Štambuk P, Tomaz I, Marchal C, Kontić JK, Lacombe T, Maletić E, Preiner D. Discrimination of genetic and geographical groups of grape varieties ( Vitis vinifera L.) based on their volatile organic compounds. FRONTIERS IN PLANT SCIENCE 2022; 13:942148. [PMID: 36340348 PMCID: PMC9634546 DOI: 10.3389/fpls.2022.942148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Grape volatile organic compounds (VOCs) play an important role in the winemaking industry due to their contribution to wine sensory characteristics. Another important role in the winemaking industry have the grapevine varieties used in specific regions or countries for wine production. Due to the high variability of grapevine germplasm, grapevine varieties are as classified based on their genetic and geographical origin into genetic-geographic groups (GEN-GEO). The aim of this research was to investigate VOCs in 50 red grapevine varieties belonging to different GEN-GEO groups. The study included varieties from groups C2 (Italy and France), C7 (Croatia), and C8 (Spain and Portugal). The analysis of VOCs was performed by SPME-Arrow-GC/MS directly from grape skins. The analyzed VOCs included aldehydes, ketones, acids, alcohols, monoterpenes, and sesquiterpenes. The most abundant VOCs were aldehydes and alcohols, while the most numerous were sesquiterpenes. The most abundant compounds, aldehydes and alcohols, were found to be (E)-2-hexenal, hexenal, (E)-2-hexen-1-ol, and 1-hexanol. Using discriminant analysis, the GEN-GEO groups were separated based on their volatile profile. Some of the individual compounds contributing to the discrimination were found in relatively small amounts, such as benzoic acid, (E,E)-2,4-hexadienal, 4-pentenal, and nonanoic acid. The groups were also discriminated by their overall volatile profile: group C2 was characterized by a higher content of aldehydes and alcohols, and group C8 was characterized by a higher content of sesquiterpenes and acids. Group C7 was characterized by all low amount of all classes of VOCs.
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Affiliation(s)
- Iva Šikuten
- Department of Viticulture and Enology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Petra Štambuk
- Department of Viticulture and Enology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Ivana Tomaz
- Department of Viticulture and Enology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Cecile Marchal
- Grapevine Biological Resources Center, INRAE, Unité Experimental Domaine de Vassal, University of Montpellier, Marseillan, France
| | - Jasminka Karoglan Kontić
- Department of Viticulture and Enology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Thierry Lacombe
- AGAP, University of Montpellier CIRAD, Institut Agro, Montpellier, France
| | - Edi Maletić
- Department of Viticulture and Enology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Darko Preiner
- Department of Viticulture and Enology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
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11
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Blanco Pastor JL. Alternative modes of introgression-mediated selection shaped crop adaptation to novel climates. Genome Biol Evol 2022; 14:6647590. [PMID: 35859297 PMCID: PMC9348624 DOI: 10.1093/gbe/evac107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
Recent plant genomic studies provide fine-grained details on the evolutionary consequences of adaptive introgression during crop domestication. Modern genomic approaches and analytical methods now make it possible to better separate the introgression signal from the demographic signal thus providing a more comprehensive and complex picture of the role of introgression in local adaptation. Adaptive introgression has been fundamental for crop expansion and has involved complex patterns of gene flow. In addition to providing new and more favorable alleles of large effect, introgression during the early stages of domestication also increased allelic diversity at adaptive loci. Previous studies have largely underestimated the effect of such increased diversity following introgression. Recent genomic studies in wheat, potato, maize, grapevine, and ryegrass show that introgression of multiple genes, of as yet unknown effect, increased the effectiveness of purifying selection, and promoted disruptive or fluctuating selection in early cultivars and landraces. Historical selection processes associated with introgression from crop wild relatives provide an instructive analog for adaptation to current climate change and offer new avenues for crop breeding research that are expected to be instrumental for strengthening food security in the coming years.
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12
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Archaeobotanical and chemical investigations on wine amphorae from San Felice Circeo (Italy) shed light on grape beverages at the Roman time. PLoS One 2022; 17:e0267129. [PMID: 35767534 PMCID: PMC9242518 DOI: 10.1371/journal.pone.0267129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 04/02/2022] [Indexed: 11/19/2022] Open
Abstract
We hereby investigate the pitch used for coating three Roman amphorae from San Felice Circeo (Italy) through a multidisciplinary study. The identification of molecular biomarkers by gas chromatography—mass spectrometry is combined with archaeobotanical evidence of pollen and plant tissues of Vitis flowers. Diterpenic chemical markers together with Pinus pollen and wood revealed Pinaceae tar coating. Aporate 3-zonocolpate pollen, identified as Vitis, together with tartaric, malic and pyruvic acids elucidate the grape-fermented nature of the content. Our conclusions open new consideration on the use of grape derivatives that cannot be supported by traditional analytical methods. Based on the finds of aporate Vitis pollen, found also in local modern and Middle Pleistocene samples, we hypothesize the use of autochthonous vines. The presence of a medicinal wine (historically reported as oenanthium) is also considered. We interrogate Vitis pollen capacity to target grapevine domestication, thereby providing innovative tools to understand such an important process. We anticipate our study to encourage a more systematic multidisciplinary approach regarding the analyses of wine amphorae.
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13
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Carolina RA, Alfredo CR. Yeast and Non-yeast Fungi: the hidden allies in Pulque Fermentation. Curr Opin Food Sci 2022. [DOI: 10.1016/j.cofs.2022.100878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Cordero-Bueso G, Vigentini I, Foschino R, Maghradze D, Ruiz-Muñoz M, Benitez-Trujillo F, Cantoral JM. Culturable Yeast Diversity of Grape Berries from Vitis vinifera ssp. sylvestris (Gmelin) Hegi. J Fungi (Basel) 2022; 8:jof8040410. [PMID: 35448641 PMCID: PMC9025944 DOI: 10.3390/jof8040410] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 02/04/2023] Open
Abstract
Vitis vinifera L. ssp. sylvestris (Gmelin) Hegi is recognized as the dioecious parental generation of today’s cultivars. Climatic change and the arrival of pathogens and pests in Europe led it to be included on the International Union for Conservation of Nature (IUCN) Red List of Threatened Species in 1997. The present work focused on the study of culturable yeast occurrence and diversity of grape berries collected from wild vines. Sampling was performed in 29 locations of Azerbaijan, Georgia, Italy, Romania, and Spain. In total, 3431 yeast colonies were isolated and identified as belonging to 49 species, including Saccharomyces cerevisiae, by 26S rDNA D1/D2 domains and ITS region sequencing. Isolates of S. cerevisiae were also analyzed by SSR–PCR obtaining 185 different genotypes. Classical ecology indices were used to obtain the richness (S), the biodiversity (H’), and the dominance (D) of the species studied. This study highlights the biodiversity potential of natural environments that still represent a fascinating source of solutions to common problems in winemaking.
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Affiliation(s)
- Gustavo Cordero-Bueso
- Department of Biomedicine, Biotechnology and Public Health, University of Cádiz, 11009 Cádiz, Spain; (M.R.-M.); (J.M.C.)
- Correspondence:
| | - Ileana Vigentini
- Department of Food, Environmental and Nutritional Sciences, University of Milan, 20122 Milan, Italy; (I.V.); (R.F.)
| | - Roberto Foschino
- Department of Food, Environmental and Nutritional Sciences, University of Milan, 20122 Milan, Italy; (I.V.); (R.F.)
| | - David Maghradze
- Department of Agriculture, Faculty of Viticulture and Winemaking, Caucasus International University, 0141 Tbilisi, Georgia;
| | - Marina Ruiz-Muñoz
- Department of Biomedicine, Biotechnology and Public Health, University of Cádiz, 11009 Cádiz, Spain; (M.R.-M.); (J.M.C.)
| | | | - Jesús M. Cantoral
- Department of Biomedicine, Biotechnology and Public Health, University of Cádiz, 11009 Cádiz, Spain; (M.R.-M.); (J.M.C.)
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15
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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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16
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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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17
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Fournier P, Pellan L, Barroso-Bergadà D, Bohan DA, Candresse T, Delmotte F, Dufour MC, Lauvergeat V, Le Marrec C, Marais A, Martins G, Masneuf-Pomarède I, Rey P, Sherman D, This P, Frioux C, Labarthe S, Vacher C. The functional microbiome of grapevine throughout plant evolutionary history and lifetime. ADV ECOL RES 2022. [DOI: 10.1016/bs.aecr.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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18
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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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19
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The genomes of 204 Vitis vinifera accessions reveal the origin of European wine grapes. Nat Commun 2021; 12:7240. [PMID: 34934047 PMCID: PMC8692429 DOI: 10.1038/s41467-021-27487-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 11/18/2021] [Indexed: 01/29/2023] Open
Abstract
In order to elucidate the still controversial processes that originated European wine grapes from its wild progenitor, here we analyse 204 genomes of Vitis vinifera and show that all analyses support a single domestication event that occurred in Western Asia and was followed by numerous and pervasive introgressions from European wild populations. This admixture generated the so-called international wine grapes that have diffused from Alpine countries worldwide. Across Europe, marked differences in genomic diversity are observed in local varieties that are traditionally cultivated in different wine producing countries, with Italy and France showing the largest diversity. Three genomic regions of reduced genetic diversity are observed, presumably as a consequence of artificial selection. In the lowest diversity region, two candidate genes that gained berry–specific expression in domesticated varieties may contribute to the change in berry size and morphology that makes the fruit attractive for human consumption and adapted for winemaking. Reports on the origin of European wine grapes are controversial. Here, the authors perform population genetics analyses on a large set of representative wine-making varieties and reveal a single domestication event at the origin of the entire germplasm followed by repeated introgression from wild populations.
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Augusto D, Ibáñez J, Pinto-Sintra AL, Falco V, Leal F, Martínez-Zapater JM, Oliveira AA, Castro I. Grapevine Diversity and Genetic Relationships in Northeast Portugal Old Vineyards. PLANTS 2021; 10:plants10122755. [PMID: 34961228 PMCID: PMC8705298 DOI: 10.3390/plants10122755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 11/16/2022]
Abstract
More than 100 grapevine varieties are registered as suitable for wine production in “Douro” and “Trás-os-Montes” Protected Designations of Origin regions; however, only a few are actually used for winemaking. The identification of varieties cultivated in past times can be an important step to take advantage of all the potential of these regions grape biodiversity. The conservation of the vanishing genetic resources boosts greater product diversification, and it can be considered strategic in the valorisation of these wine regions. Hence, one goal of the present study was to prospect and characterise, through molecular markers, 310 plants of 11 old vineyards that constitute a broad representation of the grape genetic patrimony of “Douro” and “Trás-os-Montes” wine regions; 280 samples, grouped into 52 distinct known varieties, were identified through comparison of their genetic profiles generated via 6 nuclear SSR and 43 informative SNP loci amplification; the remaining 30 samples, accounting for 13 different genotypes, did not match with any profile in the consulted databases and were considered as new genotypes. This study also aimed at evaluating the population structure among the 65 non-redundant genotypes identified, which were grouped into two ancestral genetic groups. The mean probability of identity values of 0.072 and 0.510 (for the 6 SSR and 226 SNP sets, respectively) were determined. Minor differences were observed between frequencies of chlorotypes A and D within the non-redundant genotypes studied. Twenty-seven pedigrees were confirmed and nine new trios were established. Ancestors of eight genotypes remain unknown.
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Affiliation(s)
- Diana Augusto
- Department of Genetics and Biotechnology, University of Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal;
| | - Javier Ibáñez
- Institute of Grapevine and Wine Sciences (ICVV), Spanish National Research Council (CSIC), University of La Rioja and Government of La Rioja, 26007 Logroño, Spain; (J.I.); (J.M.M.-Z.)
| | - Ana Lúcia Pinto-Sintra
- Centre for Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), University of Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal; (A.L.P.-S.); (F.L.); (A.A.O.)
| | - Virgílio Falco
- Chemistry Research Centre, Vila Real (CQ-VR), University of Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal;
| | - Fernanda Leal
- Centre for Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), University of Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal; (A.L.P.-S.); (F.L.); (A.A.O.)
| | - José Miguel Martínez-Zapater
- Institute of Grapevine and Wine Sciences (ICVV), Spanish National Research Council (CSIC), University of La Rioja and Government of La Rioja, 26007 Logroño, Spain; (J.I.); (J.M.M.-Z.)
| | - Ana Alexandra Oliveira
- Centre for Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), University of Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal; (A.L.P.-S.); (F.L.); (A.A.O.)
| | - Isaura Castro
- Centre for Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), University of Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal; (A.L.P.-S.); (F.L.); (A.A.O.)
- Correspondence:
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Fedosov DY, Korzhenkov AA, Petrova KO, Sapsay AO, Sharko FS, Toshchakov SV, Kolosova AA, Bakhmutova ED, Patrushev MV. SNP-Based Analysis Reveals Authenticity and Genetic Similarity of Russian Indigenous V. vinifera Grape Cultivars. PLANTS 2021; 10:plants10122696. [PMID: 34961167 PMCID: PMC8706836 DOI: 10.3390/plants10122696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/15/2021] [Accepted: 12/03/2021] [Indexed: 11/23/2022]
Abstract
9 Russian Vitis vinifera grape varieties and the European variety Muscat Hamburg were sequenced and genotyped using 527 SNPs (single nucleotide polymorphisms) with high minor allele frequency for the first time. The data were coupled with previously identified genotypes of 783 varieties and subjected to parentage and population analysis. As a result, contrary to the historical and ampelographic data published in many sources from 1800 to 2012, only two of the nine Russian varieties (Pukhlyakovskiy Belyi and Sibirkovyi) were related to foreign ones and were obviously imported from Europe to the Russian Empire. The remaining seven varieties, led by Krasnostop Zolotovskiy, are not directly related either in the Caucasus or in Europe, they form separate clusters on the genetic distance-based dendrogram and the world parentage network of V. vinifera. The resulting pedigree of Muscat Hamburg and its descendants is in accordance with SSR-based (simple sequence repeats) studies and the described pedigree of this variety which confirms the use of the reduced SNP set for further studies.
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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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Abstract
The pip, as the most common grapevine archaeological remain, is extensively used to document past viticulture dynamics. This paper uses state of the art morphological analyses to analyse the largest reference collection of modern pips to date, representative of the present-day diversity of the domesticated grapevine from Western Eurasia. We tested for a costructure between the form of the modern pips and the: destination use (table/wine), geographical origins, and populational labels obtained through two molecular approaches. Significant structuring is demonstrated for each of these cofactors and for the first time it is possible to infer properties of varieties without going through the parallel with modern varieties. These results provide a unique tool that can be applied to archaeological pips in order to reconstruct the spatio-temporal dynamics of grape diversity on a large scale and to better understand viticulture history. The models obtained were then used to infer the affiliations with archaeobotanical remains recovered in Mas de Vignoles XIV (Nîmes, France). The results show a twofold shift between the Late Iron Age and the Middle Ages, from table to wine grape varieties and from eastern to western origins which correlates with previous palaeogenomic results.
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Discrimination of genetic and geographical groups of grape varieties (Vitis vinifera L.) based on their polyphenolic profiles. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.104062] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Biodiversity in a Cool-Climate Vineyard: A Case Study from Quebec. INSECTS 2021; 12:insects12080750. [PMID: 34442316 PMCID: PMC8396841 DOI: 10.3390/insects12080750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/13/2021] [Accepted: 08/16/2021] [Indexed: 11/26/2022]
Abstract
Simple Summary This paper documents research activities related to the biodiversity of the l’Orpailleur vineyard located in Dunham (Quebec, Canada) from 1997 to 2021. In a first phase starting in 1997, the biodiversity of insecticide-free and insecticide-treated parts of the vineyard was determined for several taxa. In a second phase starting 2004, entomological problems were addressed on an ad hoc basis as they unfolded. For example, at the request of viticulturists, research was conducted on the tarnished plant bug (Lygus lineolaris-Miridae) and on the system phytoplasmas/cicadellids/grapevines. In a third phase starting in 2014, management of plants between grapevine rows and areas adjacent to the vineyard was carried out to increase biodiversity with the aim to achieve arthropod control with minimal insecticide and acaricide use. To address the advent of a new pest, such as the Japanese beetle (Popillia japonica-Scarabaeidae), a biocontrol program based on the parasite Istocheta aldrichi (Tachinidae) was initiated. Abstract In Quebec (Canada), viticulture has experienced steady growth in the last 35 years in terms of surfaces cultivated and value, although it is practiced in climatic conditions at the edge of what is considered a cool-climate area. This case study documents biodiversity studies conducted at the l’Orpailleur vineyard (Dunham, QC, Canada) from 1997 to 2021. In a first phase starting in 1997, the biodiversity of insecticide-free and insecticide-treated plots was determined for the taxa Scarabaeidae, Curculionidae, Chrysomelidae, Cicadellidae, Acari and Aranae. This step provided a baseline allowing to identify key arthropods. In a second phase starting in 2004, entomological issues were addressed on an ad hoc basis. In 2014, a third phase began with a perspective of sustainability and management of plant diversity in the vineyard to conserve natural enemies. Because of increased Japanese beetle (Popillia japonica-Scarabaeidae) populations and threats to vineyards, a biocontrol program based on the parasitoid Istocheta aldrichi (Tachinidae) was initiated. The unusually fast development of grapevines during the growing season, selection of flowering species, as well as selected arthropods associated with these flowering species, will be illustrated. Periodic update of protection programs will be required to address future challenges associated with climate change scenarios and world trade.
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Enological properties of red wine produced from native Kösetevek grapes (Vitis vinifera L.) cultivated in Eastern Anatolia. Eur Food Res Technol 2021. [DOI: 10.1007/s00217-021-03774-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Miliordos DE, Merkouropoulos G, Kogkou C, Arseniou S, Alatzas A, Proxenia N, Hatzopoulos P, Kotseridis Y. Explore the Rare—Molecular Identification and Wine Evaluation of Two Autochthonous Greek Varieties: “Karnachalades” and “Bogialamades”. PLANTS 2021; 10:plants10081556. [PMID: 34451601 PMCID: PMC8398411 DOI: 10.3390/plants10081556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 11/29/2022]
Abstract
Wines produced from autochthonous Vitis vinifera varieties have an essential financial impact on the national economy of Greece. However, scientific data regarding characteristics and quality aspects of these wines is extremely limited. The aim of the current study is to define the molecular profile and to describe chemical and sensory characteristics of the wines produced by two autochthonous red grapevine varieties—“Karnachalades” and “Bogialamades”—grown in the wider area of Soufli (Thrace, Greece). We used seven microsatellites to define the molecular profile of the two varieties, and then we compared their profile to similar molecular data from other autochthonous as well as international varieties. Grape berries were harvested at optimum technological maturity from a commercial vineyard for two consecutive vintages (2017–2018) and vilification was performed using a common vinification protocol: the 2017 vintage provided wines, from both varieties, with greater rates of phenolics and anthocyanins than 2018, whereas regarding the sensory analysis, “Bogialamades” wine provided a richer profile than “Karnachalades”. To our knowledge, this is the first study that couples both molecular profiling and exploration of the enological potential of the rare Greek varieties “Karnachalades” and “Bogialamades”; they represent two promising varieties for the production of red wines in the historic region of Thrace.
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Affiliation(s)
- Dimitrios Evangelos Miliordos
- Laboratory of Enology and Alcoholic Drinks, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece; (C.K.); (S.A.); (N.P.); (Y.K.)
- Correspondence:
| | - Georgios Merkouropoulos
- Department of Vitis, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organisation—DIMITRA, Leoforos Sofokli Venizelou 1, Lykovrysi, 14123 Attiki, Greece;
| | - Charikleia Kogkou
- Laboratory of Enology and Alcoholic Drinks, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece; (C.K.); (S.A.); (N.P.); (Y.K.)
| | - Spyridon Arseniou
- Laboratory of Enology and Alcoholic Drinks, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece; (C.K.); (S.A.); (N.P.); (Y.K.)
| | - Anastasios Alatzas
- Molecular Biology Laboratory, Department of Biotechnology, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece; (A.A.); (P.H.)
| | - Niki Proxenia
- Laboratory of Enology and Alcoholic Drinks, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece; (C.K.); (S.A.); (N.P.); (Y.K.)
| | - Polydefkis Hatzopoulos
- Molecular Biology Laboratory, Department of Biotechnology, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece; (A.A.); (P.H.)
| | - Yorgos Kotseridis
- Laboratory of Enology and Alcoholic Drinks, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece; (C.K.); (S.A.); (N.P.); (Y.K.)
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Raimondeau P, Manzi S, Brucato N, Kinipi C, Leavesley M, Ricaut FX, Besnard G. Genome skims analysis of betel palms (Areca spp., Arecaceae) and development of a profiling method to assess their plastome diversity. Gene 2021; 800:145845. [PMID: 34274465 DOI: 10.1016/j.gene.2021.145845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/13/2021] [Indexed: 11/30/2022]
Abstract
The betel nut (Areca catechu L., Arecaceae) is a monoecious cultivated palm tree that is widespread in tropical regions. It is mainly cultivated for producing areca nuts, from which seeds are extracted and chewed by local populations principally in the Indo-Pacific region. Seeds contain alkaloids which are central nervous system stimulants and are highly addictive. Wild relatives of the betel nut are distributed in South Asia and Australasia, with ca. 40-50 Areca species currently recognized. The geographic origin(s) of the betel nut and its subsequent diffusion and diversification remains poorly documented. Here, a genome skimming approach was applied to screen nucleotidic variation in the most abundant genomic regions. Low coverage sequencing data allowed us to assemble full plastomes, mitochondrial regions (either full mitogenomes or the full set of mitochondrial genes) and the nuclear ribosomal DNA cluster for nine representatives of the Areca genus collected in the field and herbarium collections (including a 182-years old specimen collected during the Dumont d'Urville's expedition). These three genomic compartments provided similar phylogenetic signals, and revealed very low genomic diversity in our sample of cultivated betel nut. We finally developed a genotyping method targeting 34 plastid DNA microsatellites. This plastome profiling approach is useful for tracing the spread of matrilineages, and in combination with nuclear genomic data, can resolve the history of the betel nut. Our method also proves to be efficient for analyzing herbarium specimens, even those collected >100 years ago.
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Affiliation(s)
- Pauline Raimondeau
- Laboratoire Évolution & Diversité Biologique (EDB, UMR 5174), Université de Toulouse, CNRS-IRD-UPS, 118 route de Narbonne, Bât. 4R1, 31062 Toulouse, France
| | - Sophie Manzi
- Laboratoire Évolution & Diversité Biologique (EDB, UMR 5174), Université de Toulouse, CNRS-IRD-UPS, 118 route de Narbonne, Bât. 4R1, 31062 Toulouse, France
| | - Nicolas Brucato
- Laboratoire Évolution & Diversité Biologique (EDB, UMR 5174), Université de Toulouse, CNRS-IRD-UPS, 118 route de Narbonne, Bât. 4R1, 31062 Toulouse, France
| | - Christopher Kinipi
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea
| | - Matthew Leavesley
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea; CABAH & College of Arts, Society and Education, James Cook University, PO Box 6811, Cairns, QLD 4870, Australia
| | - François-Xavier Ricaut
- Laboratoire Évolution & Diversité Biologique (EDB, UMR 5174), Université de Toulouse, CNRS-IRD-UPS, 118 route de Narbonne, Bât. 4R1, 31062 Toulouse, France
| | - Guillaume Besnard
- Laboratoire Évolution & Diversité Biologique (EDB, UMR 5174), Université de Toulouse, CNRS-IRD-UPS, 118 route de Narbonne, Bât. 4R1, 31062 Toulouse, France.
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Phylogeographic and demographic modeling analyses of the multiple origins of the rheophytic goldenrod Solidago yokusaiana Makino. Heredity (Edinb) 2021; 126:831-845. [PMID: 33510467 PMCID: PMC8102582 DOI: 10.1038/s41437-021-00408-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 01/11/2021] [Accepted: 01/11/2021] [Indexed: 01/30/2023] Open
Abstract
Understanding adaptation mechanisms is important in evolutionary biology. Parallel adaptation provides good opportunities to investigate adaptive evolution. To confirm parallel adaptation, it is effective to examine whether the phenotypic similarity has one or multiple origins and to use demographic modeling to consider the gene flow between ecotypes. Solidago yokusaiana is a rheophyte endemic to the Japanese Archipelago that diverged from Solidago virgaurea. This study examined the parallel origins of S. yokusaiana by distinguishing between multiple and single origins and subsequent gene flow. The haplotypes of noncoding chloroplast DNA and genotypes at 14 nuclear simple sequence repeat (nSSR) loci and single-nucleotide polymorphisms (SNPs) revealed by double-digest restriction-associated DNA sequencing (ddRADseq) were used for phylogeographic analysis; the SNPs were also used to model population demographics. Some chloroplast haplotypes were common to S. yokusaiana and its ancestor S. virgaurea. Also, the population genetic structures revealed by nSSR and SNPs did not correspond to the taxonomic species. The demographic modeling supported the multiple origins of S. yokusaiana in at least four districts and rejected a single origin with ongoing gene flow between the two species, implying that S. yokusaiana independently and repeatedly adapted to frequently flooding riversides.
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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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Abstract
We studied the grape sex-determining region (SDR) in 12 Vitis genomes and demonstrated its conservation across 556 genotypes including 193 accessions from 47 world-wide wild grapevine species and 363 accessions of cultivated grapevine. Although the grape SDR is recombination free in all wild species, we found two distinct hermaphrodite (H) haplotypes (H1 and H2) among the cultivated grapevines, both chimeras of male (M) and female (f) haplotypes. The two independent recombinations carry different genetic signatures which long predate the domestication of grapevine, suggesting independent evolutions of this trait in wild European grapevine gene pools prior to human domestication. Hermaphroditic (perfect) flowers were a key trait in grapevine domestication, enabling a drastic increase in yields due to the efficiency of self-pollination in the domesticated grapevine (Vitis vinifera L. ssp. vinifera). In contrast, all extant wild Vitis species are dioecious, each plant having only male or female flowers. In this study, we identified the male (M) and female (f) haplotypes of the sex-determining region (SDR) in the wild grapevine species V. cinerea and confirmed the boundaries of the SDR. We also demonstrated that the SDR and its boundaries are precisely conserved across the Vitis genus using shotgun resequencing data of 556 wild and domesticated accessions from North America, East Asia, and Europe. A high linkage disequilibrium was found at the SDR in all wild grape species, while different recombination signatures were observed along the hermaphrodite (H) haplotype of 363 cultivated accessions, revealing two distinct H haplotypes, named H1 and H2. To further examine the H2 haplotype, we sequenced the genome of two grapevine cultivars, 'Riesling' and 'Chardonnay'. By reconstructing the first two H2 haplotypes, we estimated the divergence time between H1 and H2 haplotypes at ∼6 million years ago, which predates the domestication of grapevine (∼8,000 y ago). Our findings emphasize the important role of recombination suppression in maintaining dioecy in wild grape species and lend additional support to the hypothesis that at least two independent recombination events led to the reversion to hermaphroditism in grapevine.
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Péros JP, Cousins P, Launay A, Cubry P, Walker A, Prado E, Peressotti E, Wiedemann-Merdinoglu S, Laucou V, Merdinoglu D, This P, Boursiquot JM, Doligez A. Genetic diversity and population structure in Vitis species illustrate phylogeographic patterns in eastern North America. Mol Ecol 2021; 30:2333-2348. [PMID: 33710711 DOI: 10.1111/mec.15881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 02/22/2021] [Accepted: 03/02/2021] [Indexed: 12/21/2022]
Abstract
Geographical distribution and diversity of current plant species have been strongly shaped by climatic oscillations during the Quaternary. Analysing the resulting divergence among species and differentiation within species is crucial to understand the evolution of taxa like the Vitis genus, which provides very useful genetic resources for grapevine improvement and might reveal original recolonization patterns due to growth habit and dispersal mode. Here, we studied the genetic structure in natural populations of three species from eastern North America: Vitis aestivalis, V. cinerea and V. riparia using different marker types. Vitis aestivalis and V. cinerea showed higher diversity than V. riparia. The two former species are less differentiated, confirming an earlier divergence of V. riparia. V. aestivalis and V. riparia exhibited different genetic groups on both sides of the Appalachian Mountains that could mirror different recolonization routes from southern refugia. Genetic structure was stronger in V. cinerea, for which two varieties (var. berlandieri and var. cinerea) are morphologically recognized. Our results confirm this distinction and suggest the existence of three other lineages within var. cinerea. These discontinuities appear linked to adaptation of var. berlandieri to dry and limy areas of Texas and partially to the Mississippi River Valley. Rapid range expansions from refugia upon climate warming are also suggested by the low linkage disequilibrium values observed. Furthermore, large variation for downy mildew resistance was observed in the three species. Our findings appeared consistent with the vegetation history of eastern North America.
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Affiliation(s)
- Jean-Pierre Péros
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | | | - Amandine Launay
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Philippe Cubry
- UMR DIADE, University of Montpellier, IRD, Montpellier, France
| | - Andy Walker
- Department of Viticulture and Enology, University of Davis, Davis, CA, USA
| | | | | | | | - Valérie Laucou
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | | | - Patrice This
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Jean-Michel Boursiquot
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Agnès Doligez
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
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Methodological Approaches to DNA Authentication of Foods, Wines and Raw Materials for Their Production. Foods 2021; 10:foods10030595. [PMID: 33799888 PMCID: PMC8002015 DOI: 10.3390/foods10030595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/25/2021] [Accepted: 03/03/2021] [Indexed: 11/16/2022] Open
Abstract
DNA authentication of wines is a process of verifying their authenticity by genetic identification of the main plant component. The sample preparation of experimental and commercial wines was carried out by precipitation of wine debris by centrifugation with preliminary exposure with precipitators and co-precipitators, including developed macro- and micro-volume methods applicable to white or red wines, using polyvinylpyrrolidone as a co-precipitator. Addition of 2-mercaptoethanol and proteinase K to the lysing solution made it possible to adapt the technology for DNA extraction from the precipitated wine debris. The additionally tested technique of DNA extraction from wine debris by dimethyl sulfoxide (DMSO) lysis had fewer stages and, consequently, a lower risk of contamination. The results of further testing of one of the designed primer pairs (UFGT-F1 and UFGT-R1) in conjunction with the tested methods of wine material sample preparation and nucleic acid extraction, showed the advantage in the given set of oligonucleotides over previously used ones in terms of sensitivity, specificity and reproducibility. The developing strategy for genetic identification of grape varieties and DNA authentication of wines produced from them based on direct sequencing of polymerase chain reaction (PCR) products is implemented by interpreting the detected polymorphic positions of variable Vitis vinifera L. UFGT gene locus with distribution and split into 13 UFGT gene-associated groups.
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Sharing the Agrarian Knowledge with Archaeology: First Evidence of the Dimorphism of Vitis Pollen from the Middle Bronze Age of N Italy (Terramara Santa Rosa di Poviglio). SUSTAINABILITY 2021. [DOI: 10.3390/su13042287] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The recovery of inaperturate pollen from functionally female flowers in archaeological layers opens the question of a possible pollen-based discrimination between wild and domesticated Vitis vinifera in prehistoric times. Pollen analysis applied to archaeology has not routinely considered the existence of pollen dimorphism in Vitis, a well-known trait in the field of agrarian studies. Therefore, the inaperturate shape of grapevine pollen is ignored by studies on the archaeobotanical history of viticulture. In this paper we investigate pollen morphology of the domesticated and wild subspecies of V. vinifera, and report the first evidence of inaperturate Vitis pollen from an archaeological site. We studied exemplar cases of plants with hermaphroditic flowers, belonging to the subspecies vinifera with fully developed male and female organs, cases of dioecious plants with male or female flowers, belonging to the wild subspecies sylvestris and cases of V. vinifera subsp. vinifera with morphologically hermaphroditic but functionally female flowers. The pollen produced by hermaphroditic and male flowers is usually trizonocolporate; the pollen produced by female flowers is inaperturate. This paper reports on the inaperturate pollen of Vitis found in an archeological site of the Po Plain, Northern Italy. The site dated to the Bronze Age, which is known to have been a critical age for the use of this plant with a transition from wild to domesticated Vitis in central Mediterranean. Can the inaperturate Vitis pollen be a marker of wild Vitis vinifera in prehistoric times? Palynology suggests a possible new investigation strategy on the ancient history of the wild and cultivated grapevine. The pollen dimorphism also implies a different production and dispersal of pollen of the wild and the domesticated subspecies. Grapevine plants are palynologically different from the other Mediterranean “cultural trees”. In fact, Olea, Juglans and Castanea, which are included in the OJC index, have the same pollen morphology and the same pollen dispersal, in wild and domesticated plants. In contrast, the signal of Vitis pollen in past records may be different depending on the hermaphroditic or dioecious subspecies.
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Sargolzaei M, Rustioni L, Cola G, Ricciardi V, Bianco PA, Maghradze D, Failla O, Quaglino F, Toffolatti SL, De Lorenzis G. Georgian Grapevine Cultivars: Ancient Biodiversity for Future Viticulture. FRONTIERS IN PLANT SCIENCE 2021; 12:630122. [PMID: 33613611 PMCID: PMC7892605 DOI: 10.3389/fpls.2021.630122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/13/2021] [Indexed: 05/14/2023]
Abstract
Grapevine (Vitis vinifera) is one of the most widely cultivated plant species of agricultural interest, and is extensively appreciated for its fruits and the wines made from its fruits. Considering the high socio-economic impact of the wine sector all over the world, in recent years, there has been an increase in work aiming to investigate the biodiversity of grapevine germplasm available for breeding programs. Various studies have shed light on the genetic diversity characterizing the germplasm from the cradle of V. vinifera domestication in Georgia (South Caucasus). Georgian germplasm is placed in a distinct cluster from the European one and possesses a rich diversity for many different traits, including eno-carpological and phenological traits; resistance to pathogens, such as oomycetes and phytoplasmas; resistance to abiotic stresses, such as sunburn. The aim of this review is to assess the potential of Georgian cultivars as a source of useful traits for breeding programs. The unique genetic and phenotypic aspects of Georgian germplasm were unraveled, to better understand the diversity and quality of the genetic resources available to viticulturists, as valuable resources for the coming climate change scenario.
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Affiliation(s)
- Maryam Sargolzaei
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milan, Italy
| | - Laura Rustioni
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento – Centro Ecotekne, Lecce, Italy
| | - Gabriele Cola
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milan, Italy
| | - Valentina Ricciardi
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milan, Italy
| | - Piero A. Bianco
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milan, Italy
| | - David Maghradze
- Faculty of Viticulture and Winemaking, Caucasus International University, Tbilisi, Georgia
- National Wine Agency of Georgia, Tbilisi, Georgia
| | - Osvaldo Failla
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milan, Italy
| | - Fabio Quaglino
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milan, Italy
| | - Silvia L. Toffolatti
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milan, Italy
- *Correspondence: Silvia L. Toffolatti,
| | - Gabriella De Lorenzis
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milan, Italy
- Gabriella De Lorenzis,
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Khattab IM, Sahi VP, Baltenweck R, Maia-Grondard A, Hugueney P, Bieler E, Dürrenberger M, Riemann M, Nick P. Ancestral chemotypes of cultivated grapevine with resistance to Botryosphaeriaceae-related dieback allocate metabolism towards bioactive stilbenes. THE NEW PHYTOLOGIST 2021; 229:1133-1146. [PMID: 32896925 DOI: 10.1111/nph.16919] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/24/2020] [Indexed: 06/11/2023]
Abstract
Grapevine trunk diseases have devastating consequences on vineyards worldwide. European wild grapevines (Vitis vinifera subs. sylvestris) from the last viable population in Germany along the Rhine river showed variable degrees of resistance against Neofusicoccum parvum (strain Bt-67), a fungus associated with Botryosphaeriaceae-related dieback. Representative genotypes from different subclades of this population were mapped with respect to their ability to induce wood necrosis, as well as their defence responses in a controlled inoculation system. The difference in colonization patterns could be confirmed by cryo-scanning electron microscopy, while there was no relationship between vessel diameter and infection success. Resistant lines accumulated more stilbenes, that were in addition significantly partitioned to nonglycosylated viniferin trimers. By contrast, the susceptible genotypes accumulated less stilbenes with a significantly higher proportion of glycosylated piceid. We suggest a model in which in the resistant genotypes phenylpropanoid metabolism is channelled rapidly and specifically to the bioactive stilbenes. Our study specifies a resistant chemotype against grapevines trunk diseases and paves a way to breed for resistance against grapevine Botryosphaeriaceae-related dieback.
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Affiliation(s)
- Islam M Khattab
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
- Department of Horticulture, Faculty of Agriculture, Damanhour University, PO Box 59, Damanhour, Egypt
| | - Vaidurya P Sahi
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | | | | | - Philippe Hugueney
- INRAE, SVQV UMR-A 1131, Université de Strasbourg, Colmar, F-68000, France
| | - Eva Bieler
- Swiss Nanoscience Institute - Nano Imaging Lab, University of Basel, Klingelbergstrasse 50/70, Basel, CH-4056, Switzerland
| | - Markus Dürrenberger
- Swiss Nanoscience Institute - Nano Imaging Lab, University of Basel, Klingelbergstrasse 50/70, Basel, CH-4056, Switzerland
| | - Michael Riemann
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Peter Nick
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
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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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Ruzicka J, Hacek M, Novak J. Mitochondrial relationships between various chamomile accessions. J Appl Genet 2020; 62:73-84. [PMID: 33294951 PMCID: PMC7822786 DOI: 10.1007/s13353-020-00602-3] [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] [Received: 08/12/2020] [Revised: 11/21/2020] [Accepted: 11/26/2020] [Indexed: 11/29/2022]
Abstract
Matricaria chamomilla L. (GRIN; The Plant List 2013) is an important medicinal plant and one of the most frequently consumed tea plants. In order to assess mitochondrial genome variation of different cultivated chamomile accessions, 36 mitochondrial SNP markers were used in a HRM (high resolution melting) approach. In thirteen accessions of chamomile (n = 155), twenty mitochondrial haplotypes (genetic distances 0.028–0.693) were identified. Three of the accessions (‘Camoflora’, ‘Mat19’ and ‘Manzana’) were monomorphic. The highest genotypic variability was found for the Croatian accession ‘PG029’ with nine mitochondrial haplotypes (mitotypes) and the Argentinian ‘Argenmilla’ with seven mitotypes. However, most of the mitotypes detected in these accessions were infrequent in our sample set, thus disclosing an unusual high amount of substitutions within the mitochondrial genome of these accessions. The mitotypes with the highest frequency in the examined dataset were MT1 (n = 27), MT9 (n = 23) and MT17 (n = 20). All of the frequent mitochondrial lines are distributed not only over several accessions but also over several geographical origins. The origins often build a triplet with on average two to three concurrent lines. The most distantly related accessions were ‘Mat19’ and ‘Camoflora’ (0.539), while ‘PNOS’ and ‘Margaritar’ (0.007) showed the lowest genetic distance.
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Affiliation(s)
- Joana Ruzicka
- Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Veterinaerplatz 1, A-1210, Vienna, Austria.
| | - Marion Hacek
- Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Veterinaerplatz 1, A-1210, Vienna, Austria
| | - Johannes Novak
- Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Veterinaerplatz 1, A-1210, Vienna, Austria
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Bonhomme V, Picq S, Ivorra S, Evin A, Pastor T, Bacilieri R, Lacombe T, Figueiral I, Terral JF, Bouby L. Eco-evo-devo implications and archaeobiological perspectives of trait covariance in fruits of wild and domesticated grapevines. PLoS One 2020; 15:e0239863. [PMID: 33156832 PMCID: PMC7647109 DOI: 10.1371/journal.pone.0239863] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 09/15/2020] [Indexed: 11/19/2022] Open
Abstract
The phenotypic changes that occurred during the domestication and diversification of grapevine are well known, particularly changes in seed morphology, but the functional causes and consequences behind these variations are poorly understood. Wild and domesticate grapes differ, among others, in the form of their pips: wild grapes produce roundish pips with short stalks and cultivated varieties have more elongated pips with longer stalks. Such variations of form are of first importance for archaeobotany since the pip form is, most often, the only remaining information in archaeological settings. This study aims to enlighten archaeobotanical record and grapevine pip development by better understanding how size and shape (co)variates between pip and berry in both wild and domesticated Vitis vinifera. The covariation of berry size, number of seeds per berry (“piposity”), pip size and pip shape were explored on 49 grapevine accessions sampled among Euro-Mediterranean traditional cultivars and wild grapevines. We show that for wild grapevine, the higher the piposity, the bigger the berry and the more elongated the pip. For both wild and domesticated grapevine, the longer is the pip, the more it has a “domesticated” shape. Consequences for archaeobotanical studies are tested and discussed, and these covariations allowed the inference of berry dimensions from archaeological pips from a Southern France Roman site. This systematic exploration sheds light on new aspects of pip-berry relationship, in both size and shape, on grapevine eco-evo-devo changes during domestication, and invites to explore further the functional ecology of grapevine pip and berry and notably the impact of cultivation practices and human selection on grapevine morphology.
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Affiliation(s)
- Vincent Bonhomme
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Équipe « Dynamique de la biodiversité, anthropo-écologie », CC065 Montpellier Cedex 5, France
- * E-mail:
| | - Sandrine Picq
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Équipe « Dynamique de la biodiversité, anthropo-écologie », CC065 Montpellier Cedex 5, France
- Laurentian Forestry Centre, Natural Resources Canada, Québec, Canada
| | - Sarah Ivorra
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Équipe « Dynamique de la biodiversité, anthropo-écologie », CC065 Montpellier Cedex 5, France
| | - Allowen Evin
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Équipe « Dynamique de la biodiversité, anthropo-écologie », CC065 Montpellier Cedex 5, France
| | - Thierry Pastor
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Équipe « Dynamique de la biodiversité, anthropo-écologie », CC065 Montpellier Cedex 5, France
| | - Roberto Bacilieri
- UMR AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Equipe « Diversité, Adaptation et Amélioration de la Vigne », Montpellier, France
| | - Thierry Lacombe
- UMR AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Equipe « Diversité, Adaptation et Amélioration de la Vigne », Montpellier, France
| | - Isabel Figueiral
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Équipe « Dynamique de la biodiversité, anthropo-écologie », CC065 Montpellier Cedex 5, France
| | - Jean-Frédéric Terral
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Équipe « Dynamique de la biodiversité, anthropo-écologie », CC065 Montpellier Cedex 5, France
| | - Laurent Bouby
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Équipe « Dynamique de la biodiversité, anthropo-écologie », CC065 Montpellier Cedex 5, France
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Raimondi S, Tumino G, Ruffa P, Boccacci P, Gambino G, Schneider A. DNA-based genealogy reconstruction of Nebbiolo, Barbera and other ancient grapevine cultivars from northwestern Italy. Sci Rep 2020; 10:15782. [PMID: 32978486 PMCID: PMC7519648 DOI: 10.1038/s41598-020-72799-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/01/2020] [Indexed: 01/08/2023] Open
Abstract
Northwestern Italy is a wine region of the world with the highest of reputations, where top quality wines of remarkable economic value are produced from traditional, long-cultivated varieties. Kinship analyses were performed using 32 microsatellite loci and more than 10 K single-nucleotide polymorphism markers on 227 traditional grapes mostly from Northwestern Italy—including those that have been neglected or are threatened. This was done to better understand the genetic grapevine origins and history of this reputable wine producing area, thus enhancing its cultural value and the marketing appeal of its wines. The work revealed a complex network of genetic relationships among varieties, with little contribution of genotypes from other areas. It revealed the major role played by a few ancient grape varieties as parents of numerous offspring, including some that are endangered today. The ancestry of many cultivars is proposed. Among these are Dolcetto, Barbera and Riesling italico. Through the inference of parent–offspring and sibling relations, marker profiles of ungenotyped putative parents were reconstructed, suggesting kinship relations and a possible parentage for Nebbiolo, one of the most ancient wine grapes worldwide. Historic and geographic implications from the resulting kinships are discussed.
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Affiliation(s)
- Stefano Raimondi
- National Research Council of Italy-Institute for Sustainable Plant Protection (CNR-IPSP), Strada delle Cacce 73, 10135, Turin, Italy
| | - Giorgio Tumino
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Paola Ruffa
- National Research Council of Italy-Institute for Sustainable Plant Protection (CNR-IPSP), Strada delle Cacce 73, 10135, Turin, Italy.,University of Turin-Department of Agricultural, Forest and Food Sciences (UNITO-DiSAFA), L. Braccini 2, 10095, Grugliasco, Turin, Italy
| | - Paolo Boccacci
- National Research Council of Italy-Institute for Sustainable Plant Protection (CNR-IPSP), Strada delle Cacce 73, 10135, Turin, Italy
| | - Giorgio Gambino
- National Research Council of Italy-Institute for Sustainable Plant Protection (CNR-IPSP), Strada delle Cacce 73, 10135, Turin, Italy
| | - Anna Schneider
- National Research Council of Italy-Institute for Sustainable Plant Protection (CNR-IPSP), Strada delle Cacce 73, 10135, Turin, Italy.
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Population genetic analysis in old Montenegrin vineyards reveals ancient ways currently active to generate diversity in Vitis vinifera. Sci Rep 2020; 10:15000. [PMID: 32929127 PMCID: PMC7490262 DOI: 10.1038/s41598-020-71918-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 08/20/2020] [Indexed: 11/08/2022] Open
Abstract
Global viticulture has evolved following market trends, causing loss of cultivar diversity and traditional practices. In Montenegro, modern viticulture co-exists with a traditional viticulture that still maintains ancient practices and exploits local cultivars. As a result, this region provides a unique opportunity to explore processes increasing genetic diversity. To evaluate the diversity of Montenegrin grapevines and the processes involved in their diversification, we collected and analyzed 419 samples in situ across the country (cultivated plants from old orchards and vines growing in the wild), and 57 local varieties preserved in a grapevine collection. We obtained 144 different genetic profiles, more than 100 corresponding to cultivated grapevines, representing a surprising diversity for one of the smallest European countries. Part of this high diversity reflects historical records indicating multiple and intense introduction events from diverse viticultural regions at different times. Another important gene pool includes many autochthonous varieties, some on the edge of extinction, linked in a complex parentage network where two varieties (Razaklija and Kratošija) played a leading role on the generation of indigenous varieties. Finally, analyses of genetic structure unveiled several putative proto-varieties, likely representing the first steps involved in the generation of new cultivars or even secondary domestication events.
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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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Grigoriou A, Tsaniklidis G, Hagidimitriou M, Nikoloudakis N. The Cypriot Indigenous Grapevine Germplasm Is a Multi-Clonal Varietal Mixture. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1034. [PMID: 32824004 PMCID: PMC7463456 DOI: 10.3390/plants9081034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/07/2020] [Accepted: 08/13/2020] [Indexed: 12/21/2022]
Abstract
Cypriot vineyards are considered as one among the earliest niches of viticulture and a pivotal hub for the domestication and dissemination of grapevine. The millennial presence of Vitis spp. in this Eastern Mediterranean island has given rise to a plethora of biotypes that have not been adequately characterized, despite their unique attributes and stress tolerance. This ancient germplasm also has an additional value since it survived the phylloxera outbreak; hence, it possesses a large amount of genetic diversity that has been unnoticed. In order to provide useful insights to the lineage of Cypriot vineyards, a two-year-spanning collection of centennial grapevine cultivars mostly regarded to belong to four indigenous variety clusters ("Mavro", "Xynisteri", "Maratheftiko", and "Veriko") was initiated. There were 164 accessions across the broader Commandaria wine zone sampled and characterized using a universal microsatellite primer set. Genetic analysis indicated that considered indigenous Cypriot germplasm has a polyclonal structure with a high level of heterozygosity. Moreover, several lineages or unexplored varieties may exist, since a larger than considered number of discrete genotypes was discovered. Furthermore, it was established that grapevine lineages in Cyprus were shaped across eras via clonal, as well as, sexual propagation. The special attributes of the Cypriot landscape are discussed.
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Affiliation(s)
- Apostolis Grigoriou
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol CY-3603, Cyprus;
| | - Georgios Tsaniklidis
- Institute of Olive Tree, Subtropical Plants and Viticulture, Hellenic Agricultural Organization ‘Demeter’ (NAGREF), 71003 Heraklio, Greece;
| | | | - Nikolaos Nikoloudakis
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol CY-3603, Cyprus;
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Grassi F, Arroyo-Garcia R. Editorial: Origins and Domestication of the Grape. FRONTIERS IN PLANT SCIENCE 2020; 11:1176. [PMID: 32903797 PMCID: PMC7438903 DOI: 10.3389/fpls.2020.01176] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Affiliation(s)
| | - Rosa Arroyo-Garcia
- CBGP-INIA (Center for Plant Biotechnology and Genomics-National Institute of Agricultural and Food Research and Technology), Madrid, Spain
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Nikoghosyan M, Schmidt M, Margaryan K, Loeffler-Wirth H, Arakelyan A, Binder H. SOMmelier-Intuitive Visualization of the Topology of Grapevine Genome Landscapes Using Artificial Neural Networks. Genes (Basel) 2020; 11:genes11070817. [PMID: 32709105 PMCID: PMC7397337 DOI: 10.3390/genes11070817] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/26/2020] [Accepted: 07/15/2020] [Indexed: 01/02/2023] Open
Abstract
Background: Whole-genome studies of vine cultivars have brought novel knowledge about the diversity, geographical relatedness, historical origin and dissemination, phenotype associations and genetic markers. Method: We applied SOM (self-organizing maps) portrayal, a neural network-based machine learning method, to re-analyze the genome-wide Single Nucleotide Polymorphism (SNP) data of nearly eight hundred grapevine cultivars. The method generates genome-specific data landscapes. Their topology reflects the geographical distribution of cultivars, indicates paths of cultivar dissemination in history and genome-phenotype associations about grape utilization. Results: The landscape of vine genomes resembles the geographic map of the Mediterranean world, reflecting two major dissemination paths from South Caucasus along a northern route via Balkan towards Western Europe and along a southern route via Palestine and Maghreb towards Iberian Peninsula. The Mediterranean and Black Sea, as well as the Pyrenees, constitute barriers for genetic exchange. On the coarsest level of stratification, cultivars divide into three major groups: Western Europe and Italian grapes, Iberian grapes and vine cultivars from Near East and Maghreb regions. Genetic landmarks were associated with agronomic traits, referring to their utilization as table and wine grapes. Pseudotime analysis describes the dissemination of grapevines in an East to West direction in different waves of cultivation. Conclusion: In analogy to the tasks of the wine waiter in gastronomy, the sommelier, our ‘SOMmelier’-approach supports understanding the diversity of grapevine genomes in the context of their geographic and historical background, using SOM portrayal. It offers an option to supplement vine cultivar passports by genome fingerprint portraits.
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Affiliation(s)
- Maria Nikoghosyan
- Research Group of Bioinformatics, Institute of Molecular Biology of National Academy of Sciences RA, Yerevan 0014, Armenia; (M.N.); (A.A.)
- Institute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan 0051, Armenia
| | - Maria Schmidt
- Interdisciplinary Centre for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany; (M.S.); (H.L.-W.)
| | - Kristina Margaryan
- Research Group of Plant Genetics and Immunology, Institute of Molecular Biology of National Academy of Sciences RA, Yerevan 0014, Armenia;
- Department of Genetics and Cytology, Yerevan State University, Yerevan 0025, Armenia
| | - Henry Loeffler-Wirth
- Interdisciplinary Centre for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany; (M.S.); (H.L.-W.)
| | - Arsen Arakelyan
- Research Group of Bioinformatics, Institute of Molecular Biology of National Academy of Sciences RA, Yerevan 0014, Armenia; (M.N.); (A.A.)
- Institute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan 0051, Armenia
| | - Hans Binder
- Interdisciplinary Centre for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany; (M.S.); (H.L.-W.)
- Correspondence:
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Genetic Diversity, Population Structure, and Parentage Analysis of Croatian Grapevine Germplasm. Genes (Basel) 2020; 11:genes11070737. [PMID: 32630730 PMCID: PMC7397172 DOI: 10.3390/genes11070737] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/25/2020] [Accepted: 06/25/2020] [Indexed: 12/29/2022] Open
Abstract
Croatian viticulture was most extensive at the beginning of the 20th century, when about 400 varieties were in use. Autochthonous varieties are the result of spontaneous hybridization from the pre-phylloxera era and are still cultivated today on about 35 % of vineyard area, while some exist only in repositories. We present what is the most comprehensive genetic analysis of all major Croatian national repositories, with a large number of microsatellite, or simple sequence repeat (SSR) markers, and it is also the first study to apply single nucleotide polymorphism (SNP) markers. After 212 accessions were fingerprinted, 95 were classified as unique to Croatian germplasm. Genetic diversity of Croatian germplasm is rather high considering its size. SNP markers proved useful for fingerprinting but less informative and practical than SSRs. Analysis of the genetic structure showed that Croatian germplasm is predominantly part of the Balkan grape gene pool. A high number of admixed varieties and synonyms is a consequence of complex pedigrees and migrations. Parentage analysis confirmed 24 full parentages, as well as 113 half-kinships. Unexpectedly, several key genitors could not be detected within the present Croatian germplasm. The low number of reconstructed parentages (19%) points to severe genetic erosion and stresses the importance of germplasm repositories.
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Unraveling the genetic origin of 'Glera', 'Ribolla Gialla' and other autochthonous grapevine varieties from Friuli Venezia Giulia (northeastern Italy). Sci Rep 2020; 10:7206. [PMID: 32350312 PMCID: PMC7190720 DOI: 10.1038/s41598-020-64061-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 04/01/2020] [Indexed: 12/20/2022] Open
Abstract
'Glera' and 'Ribolla Gialla' are the most economically relevant local grapevine cultivars of Friuli Venezia Giulia region (north-eastern Italy). 'Glera' is used to produce the world-renowned Prosecco wine. 'Ribolla Gialla' cultivation is constantly increasing due to the strong demand for sparkling wine and is the most important variety in Brda (Slovenia). Knowledge of local varieties history in terms of migration and pedigree relationships has scientific and marketing appeal. Following prospections, genotyping and ampelographic characterization of minor germplasm in Friuli Venezia Giulia, a further research was developed to understand the parentage relationships among the grapevine varieties grown in this region. An integrated strategy was followed combining the analysis of nuclear and chloroplast microsatellites with the Vitis 18k SNP chip. Two main recurrent parents were found, which can be regarded as "founders": 'Vulpea', an Austrian variety parent-offspring related with at least ten Friuli Venezia Giulia cultivars, among them 'Glera', and 'Refosco Nostrano', first degree related with other six Friuli Venezia Giulia varieties. 'Ribolla Gialla' was shown to be another member of the impressively long list of offspring derived from the prolific 'Heunisch Weiss'. Combining molecular markers and historical references was a high-performance strategy for retracing and adjusting the history of cultivars.
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Haddad B, Gristina AS, Mercati F, Saadi AE, Aiter N, Martorana A, Sharaf A, Carimi F. Molecular Analysis of the Official Algerian Olive Collection Highlighted a Hotspot of Biodiversity in the Central Mediterranean Basin. Genes (Basel) 2020; 11:E303. [PMID: 32183122 PMCID: PMC7140851 DOI: 10.3390/genes11030303] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/04/2020] [Accepted: 03/09/2020] [Indexed: 12/20/2022] Open
Abstract
Genetic diversity and population structure studies of local olive germplasm are important to safeguard biodiversity, for genetic resources management and to improve the knowledge on the distribution and evolution patterns of this species. In the present study Algerian olive germplasm was characterized using 16 nuclear (nuSSR) and six chloroplast (cpSSR) microsatellites. Algerian varieties, collected from the National Olive Germplasm Repository (ITAFV), 10 of which had never been genotyped before, were analyzed. Our results highlighted the presence of an exclusive genetic core represented by 13 cultivars located in a mountainous area in the North-East of Algeria, named Little Kabylie. Comparison with published datasets, representative of the Mediterranean genetic background, revealed that the most Algerian varieties showed affinity with Central and Eastern Mediterranean cultivars. Interestingly, cpSSR phylogenetic analysis supported results from nuSSRs, highlighting similarities between Algerian germplasm and wild olives from Greece, Italy, Spain and Morocco. This study sheds light on the genetic relationship of Algerian and Mediterranean olive germplasm suggesting possible events of secondary domestication and/or crossing and hybridization across the Mediterranean area. Our findings revealed a distinctive genetic background for cultivars from Little Kabylie and support the increasing awareness that North Africa represents a hotspot of diversity for crop varieties and crop wild relative species.
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Affiliation(s)
- Benalia Haddad
- Département de Productions Végétales, Laboratoire Amélioration Intégrative Des Productions Végétales (AIPV, C2711100), Ecole Nationale Supérieure Agronomique (ENSA), Hassan Badi, El Harrach, Algiers 16000, Algeria;
| | - Alessandro Silvestre Gristina
- Institute of Biosciences and BioResources, National Research Council (CNR), Research Division of Palermo, Corso Calatafimi 414, 90129 Palermo, Italy; (F.M.); (A.M.); (A.S.); (F.C.)
| | - Francesco Mercati
- Institute of Biosciences and BioResources, National Research Council (CNR), Research Division of Palermo, Corso Calatafimi 414, 90129 Palermo, Italy; (F.M.); (A.M.); (A.S.); (F.C.)
| | - Abd Elkader Saadi
- University Hassiba Benbouali, Faculty of Science of Nature and Life, Plant Biotechnology Laboratory, BP 151, Chlef 02000, Algeria;
| | - Nassima Aiter
- Université Saad Dahleb-Blida 1, Faculté des Sciences de la Nature et de la Vie, Laboratoire de Biotechnologie des Productions Végétales, Département de Biotechnologies, Blida 09000, Algeria
- Laboratoire de culture in vitro, Département central, Institut Technique de l’Arboriculture Fruitière et de la Vigne, ITAFV, Algiers 16000, Algeria
| | - Adriana Martorana
- Institute of Biosciences and BioResources, National Research Council (CNR), Research Division of Palermo, Corso Calatafimi 414, 90129 Palermo, Italy; (F.M.); (A.M.); (A.S.); (F.C.)
| | - Abdoallah Sharaf
- Institute of Biosciences and BioResources, National Research Council (CNR), Research Division of Palermo, Corso Calatafimi 414, 90129 Palermo, Italy; (F.M.); (A.M.); (A.S.); (F.C.)
- Institute of Molecular Biology of Plants, Biology Centre, CAS, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Francesco Carimi
- Institute of Biosciences and BioResources, National Research Council (CNR), Research Division of Palermo, Corso Calatafimi 414, 90129 Palermo, Italy; (F.M.); (A.M.); (A.S.); (F.C.)
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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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Cunha J, Ibáñez J, Teixeira-Santos M, Brazão J, Fevereiro P, Martínez-Zapater JM, Eiras‐Dias JE. Genetic Relationships Among Portuguese Cultivated and Wild Vitis vinifera L. Germplasm. FRONTIERS IN PLANT SCIENCE 2020; 11:127. [PMID: 32194583 PMCID: PMC7066319 DOI: 10.3389/fpls.2020.00127] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/28/2020] [Indexed: 05/04/2023]
Abstract
The domesticated grapevine spread along the Mediterranean basin from the primary Near East domestication area, where the greatest genetic diversity is found in its ancestor, the wild vine populations. Portuguese wild populations are on the southwestern fringe of the distribution of the Vitis vinifera L. ssp. sylvestris (C.C. Gmel.) Hegi in Europe. During the last Glacial Period they became isolated from the previous continuum that had been the territory of wild vine populations. Archaeological remains of domesticated vinifera grapevines in Portugal date back from 795 Before Common Era (BCE) in the lower Tagus river basin. In this work, 258 Portuguese vinifera varieties and sylvestris plants were characterized using 261 single nucleotide polymorphism (SNP) markers. The study of the genetic diversity of this local germplasm, its population structure and kinship, all framed in their historical and geographical backgrounds, revealed a complex network of first-degree relationships, where only Iberian varieties are involved. Some Iberian genotypes, like Alfrocheiro (Bruñal, in Spain), Sarigo (Cayetana Blanca), Mourisco Branco (Hebén), Amaral (Caiño Bravo), and Marufo (Moravia Dulce) are ancestors of a considerable fraction of all the autochthonous analyzed varieties. A part of the diversity developed was mostly local in some cases as shown by the closeness of several varieties (Vinhos Verdes) to the wild cluster in different analyses. Besides, several evidences of introgression of domesticated germplasm into wild vines was found, substantiating the high risk of genetic contamination of the sylvestris subspecies. All these findings together to the known matching between the wild maternal lineage of the Iberian Peninsula and an important number of Portuguese grapevine varieties (chlorotype A), point out that some of these varieties derive, directly or indirectly, from originally local wild populations, supporting the possible occurrence of secondary events of local domestication, or, at least, of an introgression process of wild into cultivated grapevines.
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Affiliation(s)
- Jorge Cunha
- Instituto Nacional de Investigação Agrária e Veterinária, Dois Portos, Portugal
- Green-it Unit, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- *Correspondence: Jorge Cunha,
| | - Javier Ibáñez
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino, (Consejo Superior de Investigaciones Científicas, Universidad de La Rioja, Gobierno de La Rioja), Logroño, Spain
| | | | - João Brazão
- Instituto Nacional de Investigação Agrária e Veterinária, Dois Portos, Portugal
- Green-it Unit, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Pedro Fevereiro
- Green-it Unit, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Departamento de Biologia Vegetal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - José M. Martínez-Zapater
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino, (Consejo Superior de Investigaciones Científicas, Universidad de La Rioja, Gobierno de La Rioja), Logroño, Spain
| | - José E. Eiras‐Dias
- Instituto Nacional de Investigação Agrária e Veterinária, Dois Portos, Portugal
- Green-it Unit, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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