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Villano C, Corrado G, Basile B, Di Serio E, Mataffo A, Ferrara E, Aversano R. Morphological and Genetic Clonal Diversity within the 'Greco Bianco' Grapevine ( Vitis vinifera L.) Variety. PLANTS (BASEL, SWITZERLAND) 2023; 12:515. [PMID: 36771600 PMCID: PMC9921137 DOI: 10.3390/plants12030515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Grapevine (Vitis vinifera L.) has been propagated vegetatively for hundreds of years. Therefore, plants tend to accumulate somatic mutations that can result in an intra-varietal diversity capable of generating distinct clones. Although it is common that winemakers request specific clones or selections for planting new vineyards, relatively limited information is available on the extent, degree, and morphological impact of the clonal diversity in traditional, highly valued grapevine varieties within production areas protected by geographical denomination of origin. Here, we present a morphological and genetic investigation of the intra-varietal diversity in 'Greco Bianco', the grapevine variety used to produce the DOCG and PDO "Greco di Tufo" wine. Seventeen clones from different farms (all within the allowed production area) were phenotypically characterized using ampelographic and ampelometric traits. The clones were also genotyped with Simple Sequence Repeats (SSR) and retrotransposon-based DNA markers (REMAP). The morphological analysis indicated a uniformity in the qualitatively scored traits, and a limited variability for the quantitative traits of the bunch and of the berry composition. The molecular markers also depicted variability among clones, which was more evident with the use of REMAPs. The comparison of the discriminatory information of the three analyses indicated that they provided different estimates of the level of diversity. The evaluation described herein of the clonal variability has implications for the management and protection of clonal selections in 'Greco Bianco' and prompts for further multidisciplinary investigations on its possible role in winemaking.
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Affiliation(s)
- Clizia Villano
- Department of Agricultural Science, University of Naples Federico II, 80055 Portici, Italy
| | - Giandomenico Corrado
- Department of Agricultural Science, University of Naples Federico II, 80055 Portici, Italy
| | - Boris Basile
- Department of Agricultural Science, University of Naples Federico II, 80055 Portici, Italy
| | - Ermanno Di Serio
- Department of Agricultural Science, University of Naples Federico II, 80055 Portici, Italy
| | - Alessandro Mataffo
- Department of Agricultural Science, University of Naples Federico II, 80055 Portici, Italy
| | - Elvira Ferrara
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, 81100 Caserta, Italy
| | - Riccardo Aversano
- Department of Agricultural Science, University of Naples Federico II, 80055 Portici, Italy
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Analysis of Compounds with Oenological Interest in Somatic Variants of Grapevines. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae8010022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Grapevine varieties can be identified genetically by microsatellite markers. However, these molecular markers are not available to discriminate between somatic mutations that give rise to clones. Therefore, the study of compounds with oenological interest could be used to identify variability in grapevine somatic variants. In this research, sugars (glucose, fructose), acids (tartaric and malic acid) and polyphenols (22 phenolic compounds, including 13 anthocyanins) were analyzed in grape berries of two somatic variants known with different names—‘Graciano’ and ‘Tintilla de Rota’—cultivated in the same vineyard under warm climate conditions. The organic acid results show significant differences between the performance of the two accessions. Regarding phenolic compound (excluding anthocyanins) content, significant differences were observed between the two accessions. Kaempferol, caftaric acid and epicatechin were the compounds responsible for the reported differences. Differences in anthocyanin content showed opposite behavior between ‘Tintilla de Rota’ and ‘Graciano’. In this sense, ‘Graciano’ accession showed an increase in all forms of anthocyanins, with a remarkable increment of peonidin 3-O-glucoside. Principal component analysis of polyphenolic compounds revealed clearly distinguished behaviors concerning these compounds, besides showing similar tendencies between the two accessions during the ripening stage. These results could allow for the discrimination of the two accessions into somatic variants highlighting their individual identity.
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Gambino G, Moine A, Boccacci P, Perrone I, Pagliarani C. Somatic embryogenesis is an effective strategy for dissecting chimerism phenomena in Vitis vinifera cv Nebbiolo. PLANT CELL REPORTS 2021; 40:205-211. [PMID: 33089358 DOI: 10.1007/s00299-020-02626-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/08/2020] [Indexed: 06/11/2023]
Abstract
The tendency of somatic embryogenesis to regenerate plants only from the L1 layer, associated with the spread of chimerism in grapevine, must be carefully considered in the framework of biotechnological improvement programmes. Grapevine is an important fruit crop with a high economic value linked to traditional genotypes that have been multiplied for centuries by vegetative propagation. In this way, somatic variations that can spontaneously occur within the shoot apical meristem are fixed in the whole plant and represent a source of intra-varietal variability. Previously identified inconsistencies in the allelic calls of single nucleotide variants (SNVs) suggested that the Vitis vinifera 'Nebbiolo' CVT185 clone is a potential periclinal chimera. We adopted the somatic embryogenesis technique to separate the two genotypes putatively associated with the L1 and L2 layers of CVT185 into different somaclones. Despite the recalcitrance of 'Nebbiolo' to the embryogenic process, 58 somaclones were regenerated and SNV genotyping assays attested that the genotype of all them differed from that of the mother plant and was only attributable to L1. The results confirmed that L2 has low or no competence for differentiating somatic embryos. After one year in the greenhouse, the somaclones showed no phenotypic alterations in comparison with the mother plant; however further analyses are needed to identify potential endogenous sources of variation. The tendency of somatic embryogenesis to regenerate plants only from L1 must be carefully considered in the framework of biotechnological improvement programmes in this species.
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Affiliation(s)
- Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135, Torino, Italy.
| | - Amedeo Moine
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135, Torino, Italy
| | - Paolo Boccacci
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135, Torino, Italy
| | - Irene Perrone
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135, Torino, Italy
| | - Chiara Pagliarani
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135, Torino, Italy
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Álvarez Á, Yáñez J, Neira Y, Castillo-Felices R, Hinrichsen P. Simple distinction of grapevine (Vitis vinifera L.) genotypes by direct ATR-FTIR. Food Chem 2020; 328:127164. [DOI: 10.1016/j.foodchem.2020.127164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 05/14/2020] [Accepted: 05/25/2020] [Indexed: 10/24/2022]
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Assessment of genetic diversity of cultivated and wild Iranian grape germplasm using retrotransposon-microsatellite amplified polymorphism (REMAP) markers and pomological traits. Mol Biol Rep 2020; 47:7593-7606. [PMID: 32949305 DOI: 10.1007/s11033-020-05827-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/07/2020] [Indexed: 10/23/2022]
Abstract
Understanding the genetic diversity and relationships between genotypes is an effective step in designing effective breeding programs. Insertional polymorphisms of retrotransposons were studied in 75 cultivated and wild grape genotypes using retrotransposon-microsatellite amplified polymorphism (REMAP) technique. In the morphological part of work, seven pomological traits with a high breeding interest were also analyzed in the cultivated genotypes. A total of 328 markers were produced by 42 primer pairs, out of which 313 markers (95.43%) were polymorphic. Number of markers ranged from 4 in loci Tvv1Fa-873, Vine1-811, Gret1Ra-855 and Tvv1Fa-890 to 12 in locus Vine1Ra-841 with an average value of 7.45. Similarity values based on Dice's coefficient among all 75 grapevine genotypes varied from 0.41 to 0.77. Classification of genotypes using unweighted pair-group method using complete-linkage clustering led to six distinct groups. Some wild and cultivated varieties placed in the same groups. It seems there are close relationship between wild and cultivated genotypes and maybe wild genotypes are ancestor of native grapevines. Grouping of grapevine genotypes based on molecular marker data was not in agreement with clustering by agro-morphological data indicating that the most of multiplied sequences are confined to the non-coding regions of transposon elements. Results showed a substantial level of genetic diversity at molecular and pomological level and the potential of this diversity for future grape breeding programs.
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Gros‐Balthazard M, Battesti V, Ivorra S, Paradis L, Aberlenc F, Zango O, Zehdi‐Azouzi S, Moussouni S, Naqvi SA, Newton C, Terral J. On the necessity of combining ethnobotany and genetics to assess agrobiodiversity and its evolution in crops: A case study on date palms ( Phoenix dactylifera L.) in Siwa Oasis, Egypt. Evol Appl 2020; 13:1818-1840. [PMID: 32908588 PMCID: PMC7463332 DOI: 10.1111/eva.12930] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/29/2020] [Accepted: 01/31/2020] [Indexed: 11/06/2022] Open
Abstract
Crop diversity is shaped by biological and social processes interacting at different spatiotemporal scales. Here, we combined population genetics and ethnobotany to investigate date palm (Phoenix dactylifera L.) diversity in Siwa Oasis, Egypt. Based on interviews with farmers and observation of practices in the field, we collected 149 date palms from Siwa Oasis and 27 uncultivated date palms from abandoned oases in the surrounding desert. Using genotyping data from 18 nuclear and plastid microsatellite loci, we confirmed that some named types each constitute a clonal line, that is, a true-to-type cultivar. We also found that others are collections of clonal lines, that is, ethnovarieties, or even unrelated samples, that is, local categories. This alters current assessments of agrobiodiversity, which are visibly underestimated, and uncovers the impact of low-intensity, but highly effective, farming practices on biodiversity. These hardly observable practices, hypothesized by ethnographic survey and confirmed by genetic analysis, are enabled by the way Isiwans conceive and classify living beings in their oasis, which do not quite match the way biologists do: a classic disparity of etic versus. emic categorizations. In addition, we established that Siwa date palms represent a unique and highly diverse genetic cluster, rather than a subset of North African and Middle Eastern palm diversity. As previously shown, North African date palms display evidence of introgression by the wild relative Phoenix theophrasti, and we found that the uncultivated date palms from the abandoned oases share even more alleles with this species than cultivated palms in this region. The study of Siwa date palms could hence be a key to the understanding of date palm diversification in North Africa. Integration of ethnography and population genetics promoted the understanding of the interplay between diversity management in the oasis (short-time scale), and the origins and dynamic of diversity through domestication and diversification (long-time scale).
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Affiliation(s)
- Muriel Gros‐Balthazard
- Center for Genomics and Systems BiologyNew York University Abu DhabiAbu DhabiUnited Arab Emirates
- Institut des Sciences de l’ÉvolutionUMR 5554 CNRS/Université de Montpellier/IRD/EPHECC065Équipe Dynamique de la Biodiversité, Anthropo‐écologieUniversité – MontpellierMontpellier Cedex 5France
| | - Vincent Battesti
- UMR 7206 Éco‐anthropologieCNRSMuséum national d’histoire naturelleUniversite de Paris: Musée de l’HommeParisFrance
| | - Sarah Ivorra
- Institut des Sciences de l’ÉvolutionUMR 5554 CNRS/Université de Montpellier/IRD/EPHECC065Équipe Dynamique de la Biodiversité, Anthropo‐écologieUniversité – MontpellierMontpellier Cedex 5France
| | - Laure Paradis
- Institut des Sciences de l’ÉvolutionUMR 5554 CNRS/Université de Montpellier/IRD/EPHECC065Équipe Dynamique de la Biodiversité, Anthropo‐écologieUniversité – MontpellierMontpellier Cedex 5France
| | - Frédérique Aberlenc
- Institut de Recherche pour le Développement (IRD)Université de Montpellier, UMR DIADEMontpellierFrance
| | | | | | - Souhila Moussouni
- Faculté des Sciences BiologiquesLaboratoire de Recherche sur les Zones Arides (LRZA)Université des Science et de la Technologie Houari Boumediene (USTHB)AlgerAlgeria
| | - Summar Abbas Naqvi
- Institute of Horticultural SciencesUniversity of AgricultureFaisalabadPakistan
| | | | - Jean‐Frédéric Terral
- Institut des Sciences de l’ÉvolutionUMR 5554 CNRS/Université de Montpellier/IRD/EPHECC065Équipe Dynamique de la Biodiversité, Anthropo‐écologieUniversité – MontpellierMontpellier Cedex 5France
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Ferreira V, Pinto-Carnide O, Arroyo-García R, Castro I. Berry color variation in grapevine as a source of diversity. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 132:696-707. [PMID: 30146416 DOI: 10.1016/j.plaphy.2018.08.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/17/2018] [Accepted: 08/18/2018] [Indexed: 06/08/2023]
Abstract
Even though it is one of the oldest perennial domesticated fruit crops in the world, grapevine (Vitis vinifera L.) cultivation today is the result of both conventional breeding practices (i.e. hybridizations adopted during the last century) and vegetative propagation. Human-assisted asexual propagation has allowed the maintenance of desired traits but has largely impacted the frequency of spontaneous somatic mutations observed in the field. Consequently, many grapevine fruit attributes to date have been artificially selected, including: fruit yield, compactness, size and composition, the latter being greatly diversified in the pursuit of altering berry skin coloration. The present review provides an overview of various aspects related to grapevine diversity, with a special emphasis on grape berry skin color variation and will discuss the current knowledge of how grape skin color variation is affected by the synthesis of phenolic compounds, particularly anthocyanins and their underlying genetic factors. We hope this knowledge will be useful in supporting the importance of the berry color trait diversity in cultivated grapevines, which is used as basis for selection during breeding programs because of its application for vine growers, winemakers and consumers.
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Affiliation(s)
- Vanessa Ferreira
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Centre for Plant Biotechnology and Genomics (UPM-INIA, CBGP), Campus de Montegancedo, Autovía M40 km38, 28223 Pozuelo de Alarcón, Madrid, Spain.
| | - Olinda Pinto-Carnide
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
| | - Rosa Arroyo-García
- Centre for Plant Biotechnology and Genomics (UPM-INIA, CBGP), Campus de Montegancedo, Autovía M40 km38, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Isaura Castro
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
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Zequim Maia SH, de Oliveira-Collet SA, Mangolin CA, de Fátima P.S. Machado M. Differential genetic stability in vineyards of the cultivar ‘Italy’ ( Vitis vinifera L.) cultivated in different regions of Southern and Southwestern Brazil. CIÊNCIA E TÉCNICA VITIVINÍCOLA 2018. [DOI: 10.1051/ctv/20183301066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
During more than 50 years the vegetative propagation has been the form of maintaining and multiplication of the cv. ’Italy’ vineyards, a ’Bicane’ x ’Muscat Hamburg’ hybrid. In the current study, polymorphism in 17 microsatellite loci was used to evaluate the genetic stability at DNA level in vineyards of cv. ’Italy’ planted in different regions of the states of Paraná and São Paulo, Brazil. Unchanged and equal allele frequency indicating genetic stability was reported in 47% of the microsatellite loci in vineyards of six localities, while allele frequency variation has been observed in Scu15vv, Udv44, Udv74, Udv96, Udv107, Udv108, Vvmd5, Vvmd6 and Vvs3 microsatellite loci. Alleles Udv96140 and Vvs3448, detected in vines in only one of the vineyards, evidenced somatic mutations at molecular level in cv. ’Italy’. Genetic diversity, as result of changes in the allele frequencies in 53% of microsatellite loci, was detected more frequently than somatic mutations due to new alleles. Polymorphism in microsatellite loci revealed different genetic stability in vineyards of cv. ’Italy’ cultivated in six different Brazilian regions and indicated vineyards with less genetic stability as a possible source of somatic mutants, showing traits of agronomic interest with a potential to generate new cultivars.
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Gambino G, Dal Molin A, Boccacci P, Minio A, Chitarra W, Avanzato CG, Tononi P, Perrone I, Raimondi S, Schneider A, Pezzotti M, Mannini F, Gribaudo I, Delledonne M. Whole-genome sequencing and SNV genotyping of 'Nebbiolo' (Vitis vinifera L.) clones. Sci Rep 2017; 7:17294. [PMID: 29229917 PMCID: PMC5725591 DOI: 10.1038/s41598-017-17405-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 11/23/2017] [Indexed: 01/27/2023] Open
Abstract
‘Nebbiolo’ (Vitis vinifera) is among the most ancient and prestigious wine grape varieties characterised by a wide genetic variability exhibited by a high number of clones (vegetatively propagated lines of selected mother plants). However, limited information is available for this cultivar at the molecular and genomic levels. The whole-genomes of three ‘Nebbiolo’ clones (CVT 71, CVT 185 and CVT 423) were re-sequenced and a de novo transcriptome assembly was produced. Important remarks about the genetic peculiarities of ‘Nebbiolo’ and its intra-varietal variability useful for clonal identification were reported. In particular, several varietal transcripts identified for the first time in ‘Nebbiolo’ were disease resistance genes and single-nucleotide variants (SNVs) identified in ‘Nebbiolo’, but not in other cultivars, were associated with genes involved in the stress response. Ten newly discovered SNVs were successfully employed to identify some periclinal chimeras and to classify 98 ‘Nebbiolo’ clones in seven main genotypes, which resulted to be linked to the geographical origin of accessions. In addition, for the first time it was possible to discriminate some ‘Nebbiolo’ clones from the others.
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Affiliation(s)
- Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Italy.
| | | | - Paolo Boccacci
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Italy
| | - Andrea Minio
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Walter Chitarra
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Italy
| | | | - Paola Tononi
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Irene Perrone
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Italy
| | - Stefano Raimondi
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco (TO), Italy
| | - Anna Schneider
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco (TO), Italy
| | - Mario Pezzotti
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Franco Mannini
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco (TO), Italy
| | - Ivana Gribaudo
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco (TO), Italy
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Payacan C, Moncada X, Rojas G, Clarke A, Chung KF, Allaby R, Seelenfreund D, Seelenfreund A. Phylogeography of herbarium specimens of asexually propagated paper mulberry [Broussonetia papyrifera (L.) L'Hér. ex Vent. (Moraceae)] reveals genetic diversity across the Pacific. ANNALS OF BOTANY 2017; 120:387-404. [PMID: 28633358 PMCID: PMC5591419 DOI: 10.1093/aob/mcx062] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 02/16/2017] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS Paper mulberry or Broussonetia papyrifera (L.) L'Hér. ex Vent. (Moraceae) is a dioecious species native to continental South-east Asia and East Asia, including Taiwan, that was introduced to the Pacific by pre-historic voyagers and transported intentionally and propagated asexually across the full range of Austronesian expansion from Taiwan to East Polynesia. The aim of this study was to gain insight into the dispersal of paper mulberry into Oceania through the genetic analysis of herbaria samples which represent a more complete coverage of the historical geographical range of the species in the Pacific before later introductions and local extinctions occurred. METHODS DNA from 47 herbarium specimens of B. papyrifera collected from 1882 to 2006 from different islands of the Pacific was obtained under ancient DNA protocols. Genetic characterization was based on the ribosomal internal transcribed spacer ITS-1 sequence, a sex marker, the chloroplast ndhF-rpl32 intergenic spacer and a set of ten microsatellites developed for B. papyrifera. KEY RESULTS Microsatellites allowed detection of 15 genotypes in Near and Remote Oceanian samples, in spite of the vegetative propagation of B. papyrifera in the Pacific. These genotypes are structured in two groups separating West and East Polynesia, and place Pitcairn in a pivotal position. We also detected the presence of male plants that carry the Polynesian chloroplast DNA (cpDNA) haplotype, in contrast to findings in contemporary B. papyrifera populations where only female plants bear the Polynesian cpDNA haplotype. CONCLUSIONS For the first time, genetic diversity was detected among paper mulberry accessions from Remote Oceania. A clear separation between West and East Polynesia was found that may be indicative of pulses during its dispersal history. The pattern linking the genotypes within Remote Oceania reflects the importance of central Polynesia as a dispersal hub, in agreement with archaeological evidence.
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Affiliation(s)
- Claudia Payacan
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Ximena Moncada
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), La Serena, Chile
| | - Gloria Rojas
- Museo Nacional de Historia Natural, Santiago, Chile
| | - Andrew Clarke
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Kuo-Fang Chung
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan and
| | - Robin Allaby
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Daniela Seelenfreund
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Andrea Seelenfreund
- Escuela de Antropología, Universidad Academia de Humanismo Cristiano, Santiago, Chile
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Tortosa I, Escalona JM, Bota J, Tomás M, Hernández E, Escudero EG, Medrano H. Exploring the genetic variability in water use efficiency: Evaluation of inter and intra cultivar genetic diversity in grapevines. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 251:35-43. [PMID: 27593461 DOI: 10.1016/j.plantsci.2016.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 05/21/2023]
Abstract
Genetic improvement of crop Water Use Efficiency (WUE) is a general goal because the increasing water scarcity and the trend to a more sustainable agriculture. For grapevines, this subject is relevant and need an urgent response because their wide distribution in semi-arid areas. New cultivars are difficult to introduce in viticulture due to the narrow dependency of consumer appreciation often linked to a certain particular wine taste. Clones of reputed cultivars would presumably be more accepted but little is known on the intra-cultivar genetic variability of the WUE. The present work compares, on the basis of two field assays, the variability of intrinsic water use efficiency (WUEi) in a large collection of cultivars in contrast with a collection of clones of Tempranillo cultivar. The results show that clonal variability of WUEi was around 80% of the inter-cultivar, thus providing a first assessment on the opportunity for clonal selection by WUE. Plotting the WUEi data against stem water potential or stomatal conductance it was possible to identify cultivars and clones out of the confidence intervals of this linear regression thus with significantly higher and lower WUEi values. The present results contribute to open the expectative for a genetic improvement of grapevine WUE.
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Affiliation(s)
- Ignacio Tortosa
- Research Group on Plant Biology Under Mediterranean Conditions, Department of Biology, IMEDEA (CSIC-Universitat de les Illes Balears), Carretera de Valldemossa Km 7.5, 07122 Palma de Mallorca, Spain
| | - José Mariano Escalona
- Research Group on Plant Biology Under Mediterranean Conditions, Department of Biology, IMEDEA (CSIC-Universitat de les Illes Balears), Carretera de Valldemossa Km 7.5, 07122 Palma de Mallorca, Spain
| | - Josefina Bota
- Research Group on Plant Biology Under Mediterranean Conditions, Department of Biology, IMEDEA (CSIC-Universitat de les Illes Balears), Carretera de Valldemossa Km 7.5, 07122 Palma de Mallorca, Spain
| | - Magdalena Tomás
- Research Group on Plant Biology Under Mediterranean Conditions, Department of Biology, IMEDEA (CSIC-Universitat de les Illes Balears), Carretera de Valldemossa Km 7.5, 07122 Palma de Mallorca, Spain
| | - Esther Hernández
- Research Group on Plant Biology Under Mediterranean Conditions, Department of Biology, IMEDEA (CSIC-Universitat de les Illes Balears), Carretera de Valldemossa Km 7.5, 07122 Palma de Mallorca, Spain
| | | | - Hipólito Medrano
- Research Group on Plant Biology Under Mediterranean Conditions, Department of Biology, IMEDEA (CSIC-Universitat de les Illes Balears), Carretera de Valldemossa Km 7.5, 07122 Palma de Mallorca, Spain.
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12
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Fang J, Zhu X, Wang C, Shangguan L. Applications of DNA Technologies in Agriculture. Curr Genomics 2016; 17:379-86. [PMID: 27499686 PMCID: PMC4955036 DOI: 10.2174/1389202917666160331203224] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 09/22/2015] [Accepted: 09/29/2015] [Indexed: 11/22/2022] Open
Abstract
With the development of molecular biology, some DNA-based technologies have showed great potentiality in promoting the efficiency of crop breeding program, protecting germplasm resources, improving the quality and outputs of agricultural products, and protecting the eco-environment etc., making their roles in modern agriculture more and more important. To better understand the application of DNA technologies in agriculture, and achieve the goals to promote their utilities in modern agriculture, this paper describes, in some different way, the applications of molecular markers, transgenic engineering and gene's information in agriculture. Some corresponding anticipations for their development prospects are also made.
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Affiliation(s)
- Jinggui Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing,P.R. China
| | - Xudong Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing,P.R. China
| | - Chen Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing,P.R. China
| | - Lingfei Shangguan
- College of Horticulture, Nanjing Agricultural University, Nanjing,P.R. China
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13
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Santos S, Oliveira M, Amorim A, van Asch B. A forensic perspective on the genetic identification of grapevine (Vitis vinifera L.) varieties using STR markers. Electrophoresis 2014; 35:3201-7. [PMID: 25146979 DOI: 10.1002/elps.201400107] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 08/10/2014] [Accepted: 08/12/2014] [Indexed: 11/07/2022]
Abstract
The grapevine (Vitis vinifera subsp. vinifera) is one of the most important agricultural crops worldwide. A long interest in the historical origins of ancient and cultivated current grapevines, as well as the need to establish phylogenetic relationships and parentage, solve homonymies and synonymies, fingerprint cultivars and clones, and assess the authenticity of plants and wines has encouraged the development of genetic identification methods. STR analysis is currently the most commonly used method for these purposes. A large dataset of grapevines genotypes for many cultivars worldwide has been produced in the last decade using a common set of recommended dinucleotide nuclear STRs. This type of marker has been replaced by long core-repeat loci in standardized state-of-the-art human forensic genotyping. The first steps toward harmonized grapevine genotyping have already been taken to bring the genetic identification methods closer to human forensic STR standards by previous authors. In this context, we bring forward a set of basic suggestions that reinforce the need to (i) guarantee trueness-to-type of the sample; (ii) use the long core-repeat markers; (iii) verify the specificity and amplification consistency of PCR primers; (iv) sequence frequent alleles and use these standardized allele ladders; (v) consider mutation rates when evaluating results of STR-based parentage and pedigree analysis; (vi) genotype large and representative samples in order to obtain allele frequency databases; (vii) standardize genotype data by establishing allele nomenclature based on repeat number to facilitate information exchange and data compilation.
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Affiliation(s)
- Sara Santos
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal; Faculdade de Ciências da Universidade do Porto, Porto, Portugal
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14
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Muñoz C, Gomez-Talquenca S, Chialva C, Ibáñez J, Martinez-Zapater JM, Peña-Neira Á, Lijavetzky D. Relationships among gene expression and anthocyanin composition of Malbec grapevine clones. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:6716-6725. [PMID: 24983916 DOI: 10.1021/jf501575m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Anthocyanin profiles are commonly used for grapevine cultivar identification because it is currently accepted that this trait is closely related to their genetic characteristics. Nevertheless, the extent of the variation for the anthocyanin profiles among clones of the same cultivar has not yet been studied in depth. The relative concentration of anthocyanins of 131 Malbec clones grown in the same vineyard was investigated by HPLC-DAD and the use of comprehensive statistic procedures. Complementarily, the expression level of structural and regulatory genes was studied via real time polymerase chain reaction. Significant variation was identified among the profiles of the clones, mainly due to variations in the amounts of malvidin derivatives. Finally, the differential expression in F3'5'H, OMT1 and AM2 genes seems to be related to the malvidin content variation. This work shows the existence of variation for the anthocyanin profiles among clones from the same grapevine cultivar and the putative involvement of genes related to hydroxylation, methylation, and transport of anthocyanins on the basis of such variation.
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Affiliation(s)
- Claudio Muñoz
- Instituto de Biologı́a Agrícola de Mendoza (IBAM), Consejo Nacional de Investigaciones Cientı́ficas y Técnicas (CONICET), Universidad Nacional de Cuyo (FCA-UNCuyo) , Almirante Brown 500, M5528AHB Chacras de Coria, Mendoza, Argentina
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15
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Gismondi A, Impei S, Di Marco G, Crespan M, Leonardi D, Canini A. Detection of new genetic profiles and allelic variants in improperly classified grapevine accessions. Genome 2014; 57:111-8. [DOI: 10.1139/gen-2013-0218] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Thirty-seven grapevine accessions, collected in Central Italy, were characterized by morphological and genetic analysis, according to guidelines developed by European Union programs of grapevine research and standardization. Traditional denominations of some sampled varieties were revealed to be incorrect; moreover, 10 synonymies and 12 homonymies were recognized. Ampelographic and ampelometric measurements of leaf characters were performed. These data generated a phenotypic similarity matrix and a relative diagram showing morphological differences between specimens. Many samples presented different morphology even in the presence of the same genotype, probably as a result of various environmental pressures. Grapevines were typed by 12 microsatellite loci and then compared with the CRA-VIT genetic resource database. Twenty-five SSR profiles were clearly identified as well-known cultivars, while nine genotypes did not find a direct correspondence: these samples could represent putative new autochthonous Latial Vitis vinifera cultivars or hybrid varieties. The genetic approach also detected three new (169 and 173 in VVMD27 locus; 179 in ISV2 locus) and seven rare allelic variants. Plant sample classification by oral history, morphological observations, and molecular results were compared and discussed. Scions of samples were planted in the Botanic Garden of the University of Rome “Tor Vergata”, to preserve grapevine biodiversity and to protect possible new autochthonous varieties.
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Affiliation(s)
- A. Gismondi
- Department of Biology, University of Rome “Tor Vergata”, via della Ricerca Scientifica 1, Rome 00133, Italy
| | - S. Impei
- Department of Biology, University of Rome “Tor Vergata”, via della Ricerca Scientifica 1, Rome 00133, Italy
| | - G. Di Marco
- Department of Biology, University of Rome “Tor Vergata”, via della Ricerca Scientifica 1, Rome 00133, Italy
| | - M. Crespan
- Consiglio per la ricerca e la sperimentazione in agricoltura, Centro di ricerca per la viticoltura (CRA-VIT), viale XXVIII Aprile 26, Conegliano (TV) 31015, Italy
| | - D. Leonardi
- Department of Biology, University of Rome “Tor Vergata”, via della Ricerca Scientifica 1, Rome 00133, Italy
| | - A. Canini
- Department of Biology, University of Rome “Tor Vergata”, via della Ricerca Scientifica 1, Rome 00133, Italy
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16
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Scarcelli N, Couderc M, Baco MN, Egah J, Vigouroux Y. Clonal diversity and estimation of relative clone age: application to agrobiodiversity of yam (Dioscorea rotundata). BMC PLANT BIOLOGY 2013; 13:178. [PMID: 24219837 PMCID: PMC3832681 DOI: 10.1186/1471-2229-13-178] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 11/06/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Clonal propagation is a particular reproductive system found in both the plant and animal kingdoms, from human parasites to clonally propagated crops. Clonal diversity provides information about plant and animal evolutionary history, i.e. how clones spread, or the age of a particular clone. In plants, this could provide valuable information about agrobiodiversity dynamics and more broadly about the evolutionary history of a particular crop. We studied the evolutionary history of yam, Dioscorea rotundata. In Africa, Yam is cultivated by tuber clonal propagation. RESULTS We used 12 microsatellite markers to identify intra-clonal diversity in yam varieties. We then used this diversity to assess the relative ages of clones. Using simulations, we assessed how Approximate Bayesian Computation could use clonal diversity to estimate the age of a clone depending on the size of the sample, the number of independent samples and the number of markers. We then applied this approach to our particular dataset and showed that the relative ages of varieties could be estimated, and that each variety could be ranked by age. CONCLUSIONS We give a first estimation of clone age in an approximate Bayesian framework. However the precise estimation of clone age depends on the precision of the mutation rate. We provide useful information on agrobiodiversity dynamics and suggest recurrent creation of varietal diversity in a clonally propagated crop.
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Affiliation(s)
- Nora Scarcelli
- UMR DIADE, Team DYNADIV, Institut de Recherche pour le Développement (IRD), 911 Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Marie Couderc
- UMR DIADE, Team DYNADIV, Institut de Recherche pour le Développement (IRD), 911 Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Mohamed N Baco
- Faculté d’Agronomie, Université de Parakou, BP 123 Parakou, Bénin
| | - Janvier Egah
- Faculté d’Agronomie, Université de Parakou, BP 123 Parakou, Bénin
| | - Yves Vigouroux
- UMR DIADE, Team DYNADIV, Institut de Recherche pour le Développement (IRD), 911 Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
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17
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Chiang YC, Huang BH, Chang CW, Wan YT, Lai SJ, Huang S, Liao PC. Asymmetric introgression in the horticultural living fossil cycas sect. Asiorientales using a genome-wide scanning approach. Int J Mol Sci 2013; 14:8228-51. [PMID: 23591840 PMCID: PMC3645740 DOI: 10.3390/ijms14048228] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Revised: 03/25/2013] [Accepted: 03/26/2013] [Indexed: 11/29/2022] Open
Abstract
The Asian cycads are mostly allopatric, distributed in small population sizes. Hybridization between allopatric species provides clues in determining the mechanism of species divergence. Horticultural introduction provides the chance of interspecific gene flow between allopatric species. Two allopatrically eastern Asian Cycas sect. Asiorientales species, C. revoluta and C. taitungensis, which are widely distributed in Ryukyus and Fujian Province and endemic to Taiwan, respectively, were planted in eastern Taiwan for horticultural reason. Higher degrees of genetic admixture in cultivated samples than wild populations in both cycad species were detected based on multilocus scans by neutral AFLP markers. Furthermore, bidirectional but asymmetric introgression by horticultural introduction of C. revoluta is evidenced by the reanalyses of species associated loci, which are assumed to be diverged after species divergence. Partial loci introgressed from native cycad to the invaders were also detected at the loci of strong species association. Consistent results tested by all neutral loci, and the species-associated loci, specify the recent introgression from the paradox of sharing of ancestral polymorphisms. Phenomenon of introgression of cultivated cycads implies niche conservation among two geographic-isolated cycads, even though the habitats of the extant wild populations of two species are distinct.
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Affiliation(s)
- Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 80424, Taiwan; E-Mail:
| | - Bing-Hong Huang
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan; E-Mails: (B.-H.H.); (Y.-T.W.); (S.-J.L.)
| | - Chun-Wen Chang
- Department of Life Science, National Taiwan Normal University, Taipei 116, Taiwan; E-Mail: (C.-W.C); (S.H.)
- Taiwan Forestry Research Institute, Technical Service Division, Taipei 10066, Taiwan
| | - Yu-Ting Wan
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan; E-Mails: (B.-H.H.); (Y.-T.W.); (S.-J.L.)
| | - Shih-Jie Lai
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan; E-Mails: (B.-H.H.); (Y.-T.W.); (S.-J.L.)
| | - Shong Huang
- Department of Life Science, National Taiwan Normal University, Taipei 116, Taiwan; E-Mail: (C.-W.C); (S.H.)
| | - Pei-Chun Liao
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan; E-Mails: (B.-H.H.); (Y.-T.W.); (S.-J.L.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +886-8-7-703-202 (ext. 6364); Fax: +886-8-7-740-584
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18
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Abstract
In the present study, we analyze the genetic structure and diversity among accessions of popcorn obtained from the CIMMYT International Maize and Wheat Improvement Center that represent the diversity available for current use by breeding programs. The main objectives were to identify SSR loci that were the best indicators of genetic diversity, to measure the genetic diversity within popcorn genotypes, and to analyze the genetic structure of the promising populations destined for use in breeding programs. The mean gene diversity of all SSR loci was 0.6352. An extremely high population differentiation level was detected (F(st) = 0.3152) with F(st) for each locus ranging from 0.1125 (Umc1229) to 0.4870 (Umc1755). Analyzing the genetic structure of eight popcorn accessions was especially important for identifying both SSR loci with high levels of heterozygosity and genotypes showing high heterozygosity (BOYA462 and ARZM13 050). This analysis should be the medium and long-term selection goal for the generation of inbred lines and the future production of new cultivars. Plant accessions ARZM05 083, ARZM13 050, and URUG298 may also be useful varieties that exhibit important agronomic characteristics that can be used through crosses to broaden the genetic basis of popcorn.
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19
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Carrier G, Le Cunff L, Dereeper A, Legrand D, Sabot F, Bouchez O, Audeguin L, Boursiquot JM, This P. Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L. PLoS One 2012; 7:e32973. [PMID: 22427919 PMCID: PMC3299709 DOI: 10.1371/journal.pone.0032973] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 02/06/2012] [Indexed: 12/22/2022] Open
Abstract
Through multiple vegetative propagation cycles, clones accumulate mutations in somatic cells that are at the origin of clonal phenotypic diversity in grape. Clonal diversity provided clones such as Cabernet-Sauvignon N°470, Chardonnay N° 548 and Pinot noir N° 777 which all produce wines of superior quality. The economic impact of clonal selection is therefore very high: since approx. 95% of the grapevines produced in French nurseries originate from the French clonal selection. In this study we provide the first broad description of polymorphism in different clones of a single grapevine cultivar, Pinot noir, in the context of vegetative propagation. Genome sequencing was performed using 454 GS-FLX methodology without a priori, in order to identify and quantify for the first time molecular polymorphisms responsible for clonal variability in grapevine. New generation sequencing (NGS) was used to compare a large portion of the genome of three Pinot noir clones selected for their phenotypic differences. Reads obtained with NGS and the sequence of Pinot noir ENTAV-INRA® 115 sequenced by Velasco et al., were aligned on the PN40024 reference sequence. We then searched for molecular polymorphism between clones. Three types of polymorphism (SNPs, Indels, mobile elements) were found but insertion polymorphism generated by mobile elements of many families displayed the highest mutational event with respect to clonal variation. Mobile elements inducing insertion polymorphism in the genome of Pinot noir were identified and classified and a list is presented in this study as potential markers for the study of clonal variation. Among these, the dynamic of four mobile elements with a high polymorphism level were analyzed and insertion polymorphism was confirmed in all the Pinot clones registered in France.
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Affiliation(s)
- Grégory Carrier
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France.
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20
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Wang XC, Guo L, Shangguan LF, Wang C, Yang G, Qu SC, Fang JG. Analysis of expressed sequence tags from grapevine flower and fruit and development of simple sequence repeat markers. Mol Biol Rep 2012; 39:6825-34. [DOI: 10.1007/s11033-012-1507-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 01/24/2012] [Indexed: 10/14/2022]
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21
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Lima-Brito J, Castro L, Coutinho J, Morais F, Gomes L, Guedes-Pinto H, Carvalho A. Genetic variability in Sambucus nigra L. clones: a preliminary molecular approach. J Genet 2011; 90:e47-52. [PMID: 21873774 DOI: 10.1007/s12041-011-0066-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- J Lima-Brito
- Institute for Biotechnology and Bioengineering (IBB), Centre of Genomics and Biotechnology (CGB), University of Tras-os-Montes and Alto Douro (UTAD), P.O. Box 1013, 5001-801, Vila Real, Portugal.
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22
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Raj S, Bräutigam K, Hamanishi ET, Wilkins O, Thomas BR, Schroeder W, Mansfield SD, Plant AL, Campbell MM. Clone history shapes Populus drought responses. Proc Natl Acad Sci U S A 2011; 108:12521-6. [PMID: 21746919 PMCID: PMC3145742 DOI: 10.1073/pnas.1103341108] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Just as animal monozygotic twins can experience different environmental conditions by being reared apart, individual genetically identical trees of the genus Populus can also be exposed to contrasting environmental conditions by being grown in different locations. As such, clonally propagated Populus trees provide an opportunity to interrogate the impact of individual environmental history on current response to environmental stimuli. To test the hypothesis that current responses to an environmental stimulus, drought, are contingent on environmental history, the transcriptome- level drought responses of three economically important hybrid genotypes-DN34 (Populus deltoides × Populus nigra), Walker [P. deltoides var. occidentalis × (Populus laurifolia × P. nigra)], and Okanese [Walker × (P. laurifolia × P. nigra)]-derived from two different locations were compared. Strikingly, differences in transcript abundance patterns in response to drought were based on differences in geographic origin of clones for two of the three genotypes. This observation was most pronounced for the genotypes with the longest time since establishment and last common propagation. Differences in genome-wide DNA methylation paralleled the transcriptome level trends, whereby the clones with the most divergent transcriptomes and clone history had the most marked differences in the extent of total DNA methylation, suggesting an epigenomic basis for the clone history-dependent transcriptome divergence. The data provide insights into the interplay between genotype and environment in the ecologically and economically important Populus genus, with implications for the industrial application of Populus trees and the evolution and persistence of these important tree species and their associated hybrids.
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Affiliation(s)
- Sherosha Raj
- Department of Cell & Systems Biology
- Centre for the Analysis of Genome Evolution & Function, and
| | - Katharina Bräutigam
- Department of Cell & Systems Biology
- Centre for the Analysis of Genome Evolution & Function, and
| | - Erin T. Hamanishi
- Centre for the Analysis of Genome Evolution & Function, and
- Faculty of Forestry, University of Toronto, Toronto, ON, Canada M5S 3B2
| | - Olivia Wilkins
- Department of Cell & Systems Biology
- Centre for the Analysis of Genome Evolution & Function, and
| | - Barb R. Thomas
- Alberta-Pacific Forest Industries, Boyle, AB, Canada T0A 0M0
- Department of Renewable Resources, University of Alberta, Edmonton, AB, Canada T6G 2H1
| | - William Schroeder
- Agroforestry Development Centre, Agriculture and Agri-Food Canada, Indian Head, SK, Canada S0G 2K0
| | - Shawn D. Mansfield
- Department of Wood Science, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Aine L. Plant
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; and
| | - Malcolm M. Campbell
- Department of Cell & Systems Biology
- Centre for the Analysis of Genome Evolution & Function, and
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada M1C 1A4
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23
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Pereira-Lorenzo S, Costa RML, Ramos-Cabrer AM, Ciordia-Ara M, Ribeiro CAM, Borges O, Barreneche T. Chestnut cultivar diversification process in the Iberian Peninsula, Canary Islands, and Azores. Genome 2011; 54:301-15. [DOI: 10.1139/g10-122] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This is a large-scale molecular study based on simple sequence repeat (SSR) loci of the diversification process in chestnut cultivars from Portugal and Spain, from the northern Iberian Peninsula to the Canary Islands and the Azores. A total of 593 grafted chestnut trees (Castanea sativa Mill.) were analysed with 10 SSRs: 292 from Portugal and 301 from Spain. Some of the trees studied were more than 300 years old. Accessions were analysed using a model-based Bayesian procedure to assess the geographical structure and to assign individuals to reconstructed populations based on the SSR genotypes. We found 356 different genotypes with a mean value of clonality of 33% owing to grafting. Mutations accounted for 6%, with hybridization being the main diversification process that can explain the great diversity found. Ten main cultivar groups were detected: four in northern Spain, five in the centre of the Iberian Peninsula, and one in southern Spain related to the centre of the Iberian Peninsula. This work demonstrated that cultivar origin and the diversification process was a combination of clonal propagation of selected seedlings, hybridization, and mutations, which allowed high levels of diversity to be maintained with respect to selected clones for fruit production. Furthermore, seedlings and graft sticks facilitated the transport to new destinations in the colonization process, transporting sometimes more than 3000 km if we consider the Azores and the Canary Islands.
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Affiliation(s)
- Santiago Pereira-Lorenzo
- Escola Politécnica Superior, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain
| | - Rita Maria Lourenço Costa
- Instituto Nacional de Recursos Biológicos, I.P. Instituto Nacional de Investigação Agrária, Quinta do Marquês, Av. da República 2780-159 Oeiras, Portugal
| | - Ana María Ramos-Cabrer
- Escola Politécnica Superior, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain
| | - Marta Ciordia-Ara
- Servicio Regional de Investigación y Desarrollo Agroalimentario, Consejería de Medio Rural y Pesca, Principado de Asturias. Apt. 13. 33300 Villaviciosa, Asturias, Spain
| | - Carla Alexandra Marques Ribeiro
- Instituto Nacional de Recursos Biológicos, I.P. Instituto Nacional de Investigação Agrária, Quinta do Marquês, Av. da República 2780-159 Oeiras, Portugal
| | - Olga Borges
- Direcção Regional de Agricultura e Pescas do Norte, Quinta do Valongo Mirandela 5110-062 Carvalhal, Portugal
| | - Teresa Barreneche
- Institut National de la Recherche Agronomique , UR419 Unité de Recherches sur les Espèces Fruitières, F-33883 Villenave d'Ornon, France
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24
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Pelsy F, Hocquigny S, Moncada X, Barbeau G, Forget D, Hinrichsen P, Merdinoglu D. An extensive study of the genetic diversity within seven French wine grape variety collections. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:1219-31. [PMID: 20062965 DOI: 10.1007/s00122-009-1250-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Accepted: 12/14/2009] [Indexed: 05/21/2023]
Abstract
The process of vegetative propagation used to multiply grapevine varieties produces, in most cases, clones genetically identical to the parental plant. Nevertheless, spontaneous somatic mutations can occur in the regenerative cells that give rise to the clones, leading to consider varieties as populations of clones that conform to a panel of phenotypic traits. Using two sets of nuclear microsatellite markers, the present work aimed at evaluating and comparing the intravarietal genetic diversity within seven wine grape varieties: Cabernet franc, Cabernet Sauvignon, Chenin blanc, Grolleau, Pinot noir, Riesling, Savagnin, comprising a total number of 344 accessions of certified clones and introductions preserved in French repositories. Ten accessions resulted in being either self-progeny, possible offspring of the expected variety or misclassified varieties. Out of the 334 remaining accessions, 83 displayed genotypes different from the varietal reference, i.e., the microsatellite profile shared by the larger number of accessions. They showed a similarity value ranging from 0.923 to 0.992, and thus were considered as polymorphic monozygotic clones. The fraction of polymorphic clones ranged from 2 to 75% depending on the variety and the set of markers, the widest clonal diversity being observed within the Savagnin. Among the 83 polymorphic clones, 29 had unique genotype making them distinguishable; others were classified in 21 groups sharing the same genotype. All microsatellite markers were not equally efficient to show diversity within clone collections and a standard set of five microsatellite markers (VMC3a9, VMC5g7, VVS2, VVMD30, and VVMD 32) relevant to reveal clonal polymorphism is proposed.
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25
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Bocharova BR, Kovaliova IA, Mazurenko LS. Identification of grapevine clone genotypes by use of microsatellite markers. CYTOL GENET+ 2009. [DOI: 10.3103/s0095452709060024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Molecular and cellular mechanisms of diversity within grapevine varieties. Heredity (Edinb) 2009; 104:331-40. [PMID: 19935824 DOI: 10.1038/hdy.2009.161] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
A grapevine variety consists of an array of clones descended by vegetative propagation from a single selected vine grown from a single seedling. A majority of the clones within a variety are identical, but some can show divergent genotypes and, to some extent, divergent phenotypes. Polymorphism results mainly from somatic mutations that occur naturally during plant growth. Various types of mutations were shown to be responsible for genetic diversity among clones: point mutations, large deletions, illegitimate recombination or variable number of repeats in microsatellite sequences. In most cases, somatic mutations do not affect the whole plant; rather, they affect only one cell layer, leading to periclinal chimeras. Such structures do not threaten the plant's fitness and are stable through vegetative propagation. Occasionally, cellular rearrangements in the chimera lead to homogenization of the genotype of the whole plant. Through these molecular and cellular mechanisms, the genotypes of clones drift over time and grapevine varieties evolve.
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27
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Fournier-Level A, Lacombe T, Le Cunff L, Boursiquot JM, This P. Evolution of the VvMybA gene family, the major determinant of berry colour in cultivated grapevine (Vitis vinifera L.). Heredity (Edinb) 2009; 104:351-62. [PMID: 19920856 DOI: 10.1038/hdy.2009.148] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Polymorphisms in the grape transcription factor family VvMybA are responsible for variation in anthocyanin content in the berries of cultivated grapevine (Vitis vinifera L. subsp. sativa). Previous study has shown that white grapes arose through the mutation of two adjacent genes: a retroelement insertion in VvMybA1 and a single-nucleotide polymorphism mutation in VvMybA2. The purpose of this study was to understand how these mutations emerged and affected genetic diversity at neighbouring sites and how they structured the genetic diversity of cultivated grapevines. We sequenced a total of 3225 bp of these genes in a core collection of genetic resources, and carried out empirical selection tests, phylogenetic- and coalescence-based demographic analyses. The insertion in the VvMybA1 promoter was shown to have occurred recently, after the mutation of VvMybA2, both mutations followed by a selective sweep. The mutational pattern for these colour genes is consistent with progressively relaxed selection from constrained ancestral coloured haplotypes to light coloured and finally white haplotypes. Dynamics of population size in the VvMybA genes showed an initial exponential growth, followed by population size stabilization. Most ancestral haplotypes are found in cultivars from western region, whereas recent haplotypes are essentially present in table cultivars from eastern regions where intense breeding practices may have replaced the original diversity. Finally, the emergence of the white allele was followed by a recent strong exponential growth, showing a very fast diffusion of the initial white allele.
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Affiliation(s)
- A Fournier-Level
- INRA UMR 1097 Diversité et Adaptation des Plantes Cultivées, Montpellier, France
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Salmaso M, Valle RD, Lucchin M. Gene pool variation and phylogenetic relationships of an indigenous northeast Italian grapevine collection revealed by nuclear and chloroplast SSRs. Genome 2009; 51:838-55. [PMID: 18923535 DOI: 10.1139/g08-064] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A germplasm safeguard programme was set up with 19 grapevine varieties considered as indigenous to northeastern Italy. To better estimate how genetic structure can be used to obtain a conservation perspective of local varieties, genetic variability was examined at 30 nuclear and 3 chloroplast polymorphic microsatellite loci in the native varieties plus 7 European cultivars taken as reference. The genetic profiles of all the cultivars were searched for possible parentage relationships and several suspected cases of the same variety having different names were investigated. The alleles shared at the loci suggest a parent-offspring relationship between Merlot and Cabernet Franc, 'Gruaja' and 'Negrara Veronese', and Marzemina Nera and Marzemina Bianca. Alleles at the 30 nuclear loci are consistent with Raboso Veronese being the progeny of Marzemina Bianca and Raboso Piave. Chloroplast-specific haplotypes were singled out for the first time in this indigenous germplasm and should be considered typical of the region. It is hypothesized that there are many specific haplotypes for the local varieties due to a past contribution of wild grapevine to the cultivated gene pool. The majority of investigated cultivars were demonstrated to constitute an independent source of genetic variation, and therefore a possible valuable resource of genetic traits for breeders.
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Affiliation(s)
- Marzia Salmaso
- Department of Environmental Agronomy and Crop Production, Agripolis, University of Padova, Viale Universita 16, 35020 Legnaro, Padova, Italy.
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Carmona MJ, Chaïb J, Martínez-Zapater JM, Thomas MR. A molecular genetic perspective of reproductive development in grapevine. JOURNAL OF EXPERIMENTAL BOTANY 2008; 59:2579-96. [PMID: 18596111 DOI: 10.1093/jxb/ern160] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The grapevine reproductive cycle has a number of unique features. Inflorescences develop from lateral meristems (anlagen) in latent buds during spring and summer and enter a dormant state at a very immature stage before completing development and producing flowers and berries the following spring. Lateral meristems are unique structures derived from the shoot apical meristem and can either develop into an inflorescence or a tendril. How the grapevine plant controls these processes at the molecular level is not understood, but some progress has been made by isolating and studying the expression of flowering genes in wild-type and mutant grapevine plants. Interestingly, a number of flowering genes are also expressed during berry development. This paper reviews the current understanding of the genetic control of grapevine flowering and the impact of viticulture management treatments and environmental variables on yield. While the availability of the draft genome sequence of grapevine will greatly assist future molecular genetic studies, a number of issues are identified that need to be addressed--particularly rapid methods for confirming gene function and linking genes to biological processes and traits. Understanding the key interactions between environmental factors and genetic mechanisms controlling the induction and development of inflorescences, flowers, and berries is also an important area that requires increased emphasis, especially given the large seasonal fluctuations in yield experienced by the crop and the increasing concern about the effect of climate change on existing wine-producing regions.
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Affiliation(s)
- María José Carmona
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria, 28003 Madrid, Spain
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