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Li B, Gschwend AR. Vitis labrusca genome assembly reveals diversification between wild and cultivated grapevine genomes. FRONTIERS IN PLANT SCIENCE 2023; 14:1234130. [PMID: 37719220 PMCID: PMC10501149 DOI: 10.3389/fpls.2023.1234130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 08/03/2023] [Indexed: 09/19/2023]
Abstract
Wild grapevines are important genetic resources in breeding programs to confer adaptive fitness traits and unique fruit characteristics, but the genetics underlying these traits, and their evolutionary origins, are largely unknown. To determine the factors that contributed to grapevine genome diversification, we performed comprehensive intragenomic and intergenomic analyses with three cultivated European (including the PN40024 reference genome) and two wild North American grapevine genomes, including our newly released Vitis labrusca genome. We found the heterozygosity of the cultivated grapevine genomes was twice as high as the wild grapevine genomes studied. Approximately 30% of V. labrusca and 48% of V. vinifera Chardonnay genes were heterozygous or hemizygous and a considerable number of collinear genes between Chardonnay and V. labrusca had different gene zygosity. Our study revealed evidence that supports gene gain-loss events in parental genomes resulted in the inheritance of hemizygous genes in the Chardonnay genome. Thousands of segmental duplications supplied source material for genome-specific genes, further driving diversification of the genomes studied. We found an enrichment of recently duplicated, adaptive genes in similar functional pathways, but differential retention of environment-specific adaptive genes within each genome. For example, large expansions of NLR genes were discovered in the two wild grapevine genomes studied. Our findings support variation in transposable elements contributed to unique traits in grapevines. Our work revealed gene zygosity, segmental duplications, gene gain-and-loss variations, and transposable element polymorphisms can be key driving forces for grapevine genome diversification.
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Affiliation(s)
| | - Andrea R. Gschwend
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States
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Péros JP, Launay A, Peyrière A, Berger G, Roux C, Lacombe T, Boursiquot JM. Species relationships within the genus Vitis based on molecular and morphological data. PLoS One 2023; 18:e0283324. [PMID: 37523393 PMCID: PMC10389703 DOI: 10.1371/journal.pone.0283324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/07/2023] [Indexed: 08/02/2023] Open
Abstract
The grape genus Vitis L. includes the domesticated V. vinifera, which is one of the most important fruit crop, and also close relatives recognized as valuable germplasm resources for improving cultivars. To resolve some standing problems in the species relationships within the Vitis genus we analyzed diversity in a set of 90 accessions comprising most of Vitis species and some putative hybrids. We discovered single nucleotide polymorphisms (SNPs) in SANGER sequences of twelve loci and genotyped accessions at a larger number of SNPs using a previously developed SNP array. Our phylogenic analyses consistently identified: three clades in North America, one in East Asia, and one in Europe corresponding to V. vinifera. Using heterozygosity measurement, haplotype reconstruction and chloroplast markers, we identified the hybrids existing within and between clades. The species relationships were better assessed after discarding these hybrids from analyses. We also studied the relationships between phylogeny and morphological traits and found that several traits significantly correlated with the phylogeny. The American clade that includes important species such as V. riparia and V. rupestris showed a major divergence with all other clades based on both DNA polymorphisms and morphological traits.
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Affiliation(s)
- Jean-Pierre Péros
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Amandine Launay
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - André Peyrière
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Gilles Berger
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Catherine Roux
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Thierry Lacombe
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Jean-Michel Boursiquot
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
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Talavera A, Nie ZL, Ma ZY, Johnson G, Ickert-Bond SM, Zimmer EA, Wen J. Phylogenomic analyses using a new 1013-gene Vitaceae bait-set support major groups of North American Vitis. Mol Phylogenet Evol 2023:107866. [PMID: 37354923 DOI: 10.1016/j.ympev.2023.107866] [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: 02/10/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 06/26/2023]
Abstract
A set of newly designed Vitaceae baits targeting 1013 genes was employed to explore phylogenetic relationships among North American Vitis. Eurasian Vitis taxa including Vitis vinifera were found to be nested within North American Vitis subgenus Vitis. North American Vitis subgenus Vitis can be placed into nine main groups: the Monticola group, the Occidentales group, the Californica group, the Vinifera group (introduced from Eurasia), the Mustangensis group, the Palmata group, the Aestivalis group, the Labrusca group, and the Cinerea group. Strong cytonuclear discordances were detected in North American Vitis, with many species non-monophyletic in the plastid phylogeny, while monophyletic in the nuclear phylogeny. The phylogenomic analyses support recognizing four distinct species in the Vitis cinerea complex in North America: V. cinerea, V. baileyana, V. berlandieri, and V. simpsonii. Such treatment will better serve the conservation of wild Vitis diversity in North America. Yet the evolutionary history of Vitis is highly complex, with the concordance analyses indicating conflicting signals across the phylogeny. Cytonuclear discordances and Analyses using the Species Networks applying Quartets (SNaQ) method support extensive hybridizations in North American Vitis. The results further indicate that plastid genomes alone are insufficient for resolving the evolutionary history of plant groups that have undergone rampant hybridization, like the case in North American Vitis. Nuclear gene data are essential for species delimitation, identification and reconstructing evolutionary relationships; therefore, they are imperative for plant phylogenomic studies.
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Affiliation(s)
- Alicia Talavera
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013-7012, USA; Departamento de Botánica y Fisiología Vegetal, Universidad de Málaga, 29071, Málaga, Spain.
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou 416000, China
| | - Zhi-Yao Ma
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518000 China
| | - Gabriel Johnson
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Stefanie M Ickert-Bond
- UA Museum of the North Herbarium and Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK 99775-6960, USA
| | - Elizabeth A Zimmer
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013-7012, USA.
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Zhao Y, Qu D, Ma Y. Characterization of the Chloroplast Genome of Argyranthemum frutescens and a Comparison with Other Species in Anthemideae. Genes (Basel) 2022; 13:genes13101720. [PMID: 36292605 PMCID: PMC9602088 DOI: 10.3390/genes13101720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/13/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
Argyranthemum frutescens, which belongs to the Anthemideae (Asteraceae), is widely cultivated as an ornamental plant. In this study, the complete chloroplast genome of A. frutescens was obtained based on the sequences generated by Illumina HiSeq. The chloroplast genome of A. frutescens was 149,626 base pairs (bp) in length, containing a pair of inverted repeats (IR, 24,510 bp) regions separated by a small single-copy (SSC, 18,352 bp) sequence and a large single-copy (LSC, 82,254 bp) sequence. The genome contained 132 genes, consisting of 85 coding DNA sequences, 37 tRNA genes, and 8 rRNA genes, with nineteen genes duplicated in the IR region. A comparison chloroplast genome analysis among ten species from the tribe of Anthemideae revealed that the chloroplast genome size varied, but the genome structure, gene content, and oligonucleotide repeats were highly conserved. Highly divergent regions, e.g., ycf1, trnK-psbK, petN-psbM intronic, were detected. Phylogenetic analysis supported Argyranthemum as a separate genus. The findings of this study will be helpful in the exploration of the phylogenetic relationships of the tribe of Anthemideae and contribute to the breeding improvement of A. frutescens.
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Brillouet JM, Romieu C, Bacilieri R, Nick P, Trias-Blasi A, Maul E, Solymosi K, Teszlák P, Jiang JF, Sun L, Ortolani D, Londo JP, Gutierrez B, Prins B, Reynders M, Van Caekenberghe F, Maghradze D, Marchal C, Sultan A, Thomas JF, Scherberich D, Fulcrand H, Roumeas L, Billerach G, Salimov V, Musayev M, Ejaz Ul Islam Dar M, Peltier JB, Grisoni M. Tannin phenotyping of the Vitaceae reveals a phylogenetic linkage of epigallocatechin in berries and leaves. ANNALS OF BOTANY 2022; 130:159-171. [PMID: 35700109 PMCID: PMC9445598 DOI: 10.1093/aob/mcac077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS Condensed tannins, responsible for berry and wine astringency, may have been selected during grapevine domestication. This work examines the phylogenetic distribution of condensed tannins throughout the Vitaceae phylogenetic tree. METHODS Green berries and mature leaves of representative true-to-type members of the Vitaceae were collected before 'véraison', freeze-dried and pulverized, and condensed tannins were measured following depolymerization by nucleophilic addition of 2-mercaptoethanol to the C4 of the flavan-3-ol units in an organic acidic medium. Reaction products were separated and quantified by ultrahigh pressure liquid chromatography/diode array detection/mass spectrometry. KEY RESULTS AND CONCLUSIONS The original ability to incorporate epigallocatechin (EGC) into grapevine condensed tannins was lost independently in both the American and Eurasian/Asian branches of the Vitaceae, with exceptional cases of reversion to the ancestral EGC phenotype. This is particularly true in the genus Vitis, where we now find two radically distinct groups differing with respect to EGC content. While Vitis species from Asia are void of EGC, 50 % of the New World Vitis harbour EGC. Interestingly, the presence of EGC is tightly coupled with the degree of leaf margin serration. Noticeably, the rare Asian EGC-forming species are phylogenetically close to Vitis vinifera, the only remnant representative of Vitis in Eurasia. Both the wild ancestral V. vinifera subsp. sylvestris as well as the domesticated V. vinifera subsp. sativa can accumulate EGC and activate galloylation biosynthesis that compete for photoassimilates and reductive power.
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Affiliation(s)
| | | | - Roberto Bacilieri
- INRA, Equipe DAAV, UMR AGAP (Univ. Montpellier, CIRAD, INRAE, SupAgro), Montpellier, France
| | - Peter Nick
- Karlsruhe Institute of Technology, Botanical Institute, Molecular Cell Biology, Karlsruhe, Germany
| | | | - Erika Maul
- Julius Kühn-Institut (JKI), Institut für Rebenzüchtung Geilweilerhof, Siebeldingen, Germany
| | - Katalin Solymosi
- Department of Plant Anatomy, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Peter Teszlák
- Department of Viticulture and Technology Development, Research Institute of Viticulture and Oenology, University of Pécs, Pécs, Hungary
| | - Jiang-Fu Jiang
- Zhengzhou Fruit Research Institute, Zhengzhou, Henan, PR China
| | - Lei Sun
- Zhengzhou Fruit Research Institute, Zhengzhou, Henan, PR China
| | | | - Jason P Londo
- USDA, Grape Genetics Research Unit, Agricultural Research Service, Geneva, New York, NY, USA
| | - Ben Gutierrez
- USDA, Plant Genetic Resources Unit, Agricultural Research Service, Geneva, New York, NY, USA
| | - Bernard Prins
- USDA, Nat’l Clonal Germplasm Rep – Tree Fruit & Nut Crops & Grapes, University of California, Davis, California, USA
| | | | | | | | - Cecile Marchal
- INRA, Grapevine Biological Resources Center, Experimental Unit of Domaine de Vassal, Marseillan-plage, France
| | - Amir Sultan
- National Herbarium (Stewart Collection), National Agricultural Research Centre, Islamabad, Pakistan
| | | | | | | | | | | | - Vugar Salimov
- Azerbaijani Scientific Research Institute of Viticulture and Winemaking, Baku, Azerbaijan
| | - Mirza Musayev
- Genetic Resources Institute of the Azerbaijan National Academy of Sciences, Baku, Azerbaijan
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Duan Q, Liu F, Gui D, Fan W, Cui G, Jia W, Zhu A, Wang J. Phylogenetic Analysis of Wild Species and the Maternal Origin of Cultivars in the Genus Lilium Using 114 Plastid Genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:865606. [PMID: 35937320 PMCID: PMC9355515 DOI: 10.3389/fpls.2022.865606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/16/2022] [Indexed: 05/24/2023]
Abstract
Lilies are one of the most important ornamental flowers worldwide with approximately 100 wild species and numerous cultivars, but the phylogenetic relationships among wild species and their contributions to these cultivars are poorly resolved. We collected the major Lilium species and cultivars and assembled their plastome sequences. Our phylogenetic reconstruction using 114 plastid genomes, including 70 wild species representing all sections and 42 cultivars representing six hybrid divisions and two outgroups, uncovered well-supported genetic relationships within Lilium. The wild species were separated into two distinct groups (groups A and B) associated with geographical distribution, which further diversified into eight different clades that were phylogenetically well supported. Additional support was provided by the distributions of indels and single-nucleotide variants, which were consistent with the topology. The species of sections Archelirion, Sinomartagon III, and Leucolirion 6a and 6b were the maternal donors for Oriental hybrids, Asiatic hybrids, Trumpet hybrids, and Longiflorum hybrids, respectively. The maternal donors of the OT hybrids originated from the two sections Archelirion and Leucolirion 6a, and LA hybrids were derived from the two sections Leucolirion 6b and Sinomartagon. Our study provides an important basis for clarifying the infrageneric classification and the maternal origin of cultivars in Lilium.
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Affiliation(s)
- Qing Duan
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming, China
- Joint Lab of Yunnan Seed Industry, Kunming, China
| | - Fang Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Daping Gui
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Weishu Fan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Guangfen Cui
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming, China
- Joint Lab of Yunnan Seed Industry, Kunming, China
| | - Wenjie Jia
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming, China
- Joint Lab of Yunnan Seed Industry, Kunming, China
| | - Andan Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jihua Wang
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming, China
- Joint Lab of Yunnan Seed Industry, Kunming, China
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Chung SW, Huang WJ, Chen ZH, Liu SH. Blumea chishangensis sp. nov. (Asteraceae: Inuleae) from Taiwan and new insights into the phylogeny of Blumea. BOTANICAL STUDIES 2022; 63:21. [PMID: 35821129 PMCID: PMC9276887 DOI: 10.1186/s40529-022-00350-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/25/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Blumea plants are widely distributed in the tropical areas of Asia, Africa, and Australia, especially tropical Asia. Limited studies left the taxonomy and infrageneric phylogeny of Blumea insubstantial. Here, a new species, Blumea chishangensis S. W. Chung, Z. H. Chen, S. H. Liu & W. J. Huang, from Taiwan is described, and an extended phylogeny is reconstructed to provide new perceptions of Blumea evolution. RESULTS The new species is distinguished from B. hieraciifolia by the following features: leaf blade sparsely pilose or glabrescent (vs. silky villous), the leaves margins regularly remote mucronulate (vs. double serrate or dentate), capitula pedicelled (vs. capitula sessile or subsessile), and leaves basal rosette or sub-basal rosette and a few cauline (vs. mostly cauline). Phylogenetic analysis based on the ITS, trnL-trnF, and trnH-psbA regions places the new species in the subclade II in B. lacera clade and shows a close relationship with B. axillaris and B. oxyodonta. A key to Blumea species in Taiwan and the studied species in the subclade II is provided. Moreover, the evolutionary inferences of B. conspicua, B. linearis, and B. sinuata are first reported here. The paraphyly of B. formosana and B. sinuata are also revealed for the first time. CONCLUSIONS Both morphological and molecular data support that B. chishangensis is a new species. Our phylogeny highlights the need for further taxonomic and evolutionary studies on Blumea.
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Affiliation(s)
- Shih-Wen Chung
- Botanical Garden Division, Taiwan Forestry Research Institute, Taipei, 100, Taiwan
- Forestry Research Institute Herbarium (TAIF), Taiwan Forestry Research Institute, Taipei, 100, Taiwan
| | - Wei-Jie Huang
- Botanical Garden Division, Taiwan Forestry Research Institute, Taipei, 100, Taiwan
| | - Zhi-Hao Chen
- Observer Ecological Consultant Co., Ltd., Taipei, 103, Taiwan
| | - Shih-Hui Liu
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 804, Taiwan.
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Foria S, Magris G, Jurman I, Schwope R, De Candido M, De Luca E, Ivanišević D, Morgante M, Di Gaspero G. Extent of wild-to-crop interspecific introgression in grapevine (Vitis vinifera) as a consequence of resistance breeding and implications for the crop species definition. HORTICULTURE RESEARCH 2022; 9:uhab010. [PMID: 35039824 PMCID: PMC8801725 DOI: 10.1093/hr/uhab010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 01/18/2022] [Accepted: 09/25/2021] [Indexed: 05/31/2023]
Abstract
Over the past two centuries, introgression through repeated backcrossing has introduced disease resistance from wild grape species into the domesticated lineage Vitis vinifera subsp. sativa. Introgression lines are being cultivated over increasing vineyard surface areas, as their wines now rival in quality those obtained from preexisting varieties. There is, however, a lot of debate about whether and how wine laws defining commercial product categories, which are based on the classification of V. vinifera and interspecific hybrid grapes, should be revised to accommodate novel varieties that do not fit either category. Here, we developed a method of multilocus genotype analysis using short-read resequencing to identify haplotypic blocks of wild ancestry in introgression lines and quantify the physical length of chromosome segments free-of-introgression or with monoallelic and biallelic introgression. We used this genomic data to characterize species, hybrids and introgression lines and show that newly released resistant varieties contain 76.5-94.8% of V. vinifera DNA. We found that varietal wine ratings are not always commensurate with the percentage of V. vinifera ancestry and linkage drag of wild alleles around known resistance genes persists over at least 7.1-11.5 Mb, slowing down the recovery of the recurrent parental genome. This method also allowed us to identify the donor species of known resistance haplotypes, define the ancestry of wild genetic background in introgression lines with complex pedigrees, validate the ancestry of the historic varieties Concord and Norton, and unravel sample curation errors in public databases.
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Affiliation(s)
- Serena Foria
- Istituto di Genomica Applicata,
via Jacopo Linussio, 51, 33100 Udine, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
- Dr. Schär R&D Centre, Padriciano 99, 34149 Trieste, Italy
| | - Gabriele Magris
- Istituto di Genomica Applicata,
via Jacopo Linussio, 51, 33100 Udine, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
| | - Irena Jurman
- Istituto di Genomica Applicata,
via Jacopo Linussio, 51, 33100 Udine, Italy
| | - Rachel Schwope
- Istituto di Genomica Applicata,
via Jacopo Linussio, 51, 33100 Udine, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
| | - Massimo De Candido
- VCR Research Center, Vivai Cooperativi Rauscedo, Via Ruggero Forti 4, 33095 San Giorgio della Richinvelda, Italy
| | - Elisa De Luca
- VCR Research Center, Vivai Cooperativi Rauscedo, Via Ruggero Forti 4, 33095 San Giorgio della Richinvelda, Italy
| | - Dragoslav Ivanišević
- Faculty of Agriculture, University of Novi Sad, Trg Dositeja Obradovića 8, 21102 Novi Sad, Serbia
| | - Michele Morgante
- Istituto di Genomica Applicata,
via Jacopo Linussio, 51, 33100 Udine, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
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Phenolic compounds are dependent on cultivation conditions in face of UV-C radiation in ‘Concord’ grape juices (Vitis labrusca). Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112681] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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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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Liu BB, Wang YB, Hong DY, Wen J. A synopsis of the expanded Rhaphiolepis (Maleae, Rosaceae). PHYTOKEYS 2020; 154:19-55. [PMID: 32848498 PMCID: PMC7419340 DOI: 10.3897/phytokeys.154.52790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/06/2020] [Indexed: 06/11/2023]
Abstract
As part of the integrative systematic studies on the tribe Maleae, a synopsis of the expanded Rhaphiolepis is presented, recognizing 45 species. Three new forms were validated: R. bengalensis f. contracta B.B.Liu & J.Wen, R. bengalensis f. intermedia B.B.Liu & J.Wen, and R. bengalensis f. multinervata B.B.Liu & J.Wen, and four new combinations are made here: R. bengalensis f. angustifolia (Cardot) B.B.Liu & J.Wen, R. bengalensis f. gigantea (J.E.Vidal) B.B.Liu & J.Wen, R. laoshanica (W.B.Liao, Q.Fan & S.F.Chen) B.B.Liu & J.Wen, and R. latifolia (Hook.f.) B.B.Liu & J.Wen. Furthermore, one new name, Rhaphiolepis yui B.B.Liu & J.Wen is proposed here, and three taxa were reduced as new synonyms. We also provide lectotypification for 13 names: Crataegus bibas, Eriobotrya philippinensis, Mespilus spiralis, Opa integerrima, Photinia luzonensis, Rhaphiolepis brevipetiolata, R. ferruginea var. serrata, R. fragrans, R. gracilis, R. hainanensis, R. kerrii, R. indica subsp. umbellata var. liukiuensis, and R. parvibracteolata.
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Affiliation(s)
- Bin-Bin Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, ChinaChinese Academy of SciencesBeijingChina
- Department of Botany, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USANational Museum of Natural HistoryWashingtonUnited States of America
| | - Yu-Bing Wang
- Department of Botany, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USANational Museum of Natural HistoryWashingtonUnited States of America
| | - De-Yuan Hong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, ChinaChinese Academy of SciencesBeijingChina
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USANational Museum of Natural HistoryWashingtonUnited States of America
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