Genes

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15 pages, 2045 KiB

Open AccessArticle

Genetic Structure and Relationships among Wild and Cultivated Grapevines from Central Europe and Part of the Western Balkan Peninsula

by Goran Zdunić, Katarina Lukšić, Zora Annamaria Nagy, Ana Mucalo, Katarina Hančević, Tomislav Radić, Lukrecija Butorac, Gizella Gyorffyne Jahnke, Erzsebet Kiss, Gloria Ledesma-Krist, Marjana Regvar, Matevž Likar, Andrej Piltaver, Maja Žulj Mihaljević, Edi Maletić, Ivan Pejić, Marion Werling and Erika Maul

Genes 2020, 11(9), 962; https://doi.org/10.3390/genes11090962 - 20 Aug 2020

Cited by 17 | Viewed by 3428

Abstract

The genetic diversity and relationship between wild (Vitis vinifera L. subsp. sylvestris (Gmel.) Hegi and cultivated (V. vinifera L. subsp. vinifera) grapevine in the western Balkan region and Central Europe have not been studied together previously, although this area has [...] Read more.

The genetic diversity and relationship between wild (Vitis vinifera L. subsp. sylvestris (Gmel.) Hegi and cultivated (V. vinifera L. subsp. vinifera) grapevine in the western Balkan region and Central Europe have not been studied together previously, although this area has a rich viticultural past. Here, we studied wild grapevine populations sampled from their natural habitats in several countries of the western Balkan region and Central Europe. Their genetic diversity and structure were compared to cultivars that are traditionally in use in this region. A sample set of 243 accessions was genotyped at 20 nuclear microsatellite loci, including 167 sylvestris and 76 diverse vinifera cultivars. The genetic diversity of the wild grapevines was lower than that of cultivars by all genetic parameters. Both hierarchical and nonhierarchical clustering methods differentiated two main groups, indicating clear separation between wild and cultivated vines but also revealed clear gene flow between the cultivated and wild gene pools through overlaps and admixed ancestry values in the graphs. There was greater affinity to the wild grapes in Central European cultivars than in Balkan cultivars. Fine arrangement of the structure among cultivated grapevines showed differentiation among Central European and Balkan cultivars. These results confirm the divergence of wild grapes from vinifera and highlight the “crossroad” role of the western Balkan peninsula in the broader context of European viticulture. Full article

(This article belongs to the Special Issue Genetics and Diversity of Grapevine)

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18 pages, 2186 KiB

Open AccessArticle

The Potential of HTS Approaches for Accurate Genotyping in Grapevine (Vitis vinifera L.)

by Urban Kunej, Aida Dervishi, Valérie Laucou, Jernej Jakše and Nataša Štajner

Genes 2020, 11(8), 917; https://doi.org/10.3390/genes11080917 - 10 Aug 2020

Cited by 4 | Viewed by 2861

Abstract

The main challenge associated with genotyping based on conventional length polymorphisms is the cross-laboratory standardization of allele sizes. This step requires the inclusion of standards and manual sizing to avoid false results. Capillary electrophoresis (CE) approaches limit the information to the length polymorphism [...] Read more.

The main challenge associated with genotyping based on conventional length polymorphisms is the cross-laboratory standardization of allele sizes. This step requires the inclusion of standards and manual sizing to avoid false results. Capillary electrophoresis (CE) approaches limit the information to the length polymorphism and do not allow the determination of a complete marker sequence. As an alternative, high-throughput sequencing (HTS) offers complete information regarding marker sequences and their flanking regions. In this work, we investigated the suitability of a semi-quantitative sequencing approach for microsatellite genotyping using Illumina paired-end technology. Twelve microsatellite loci that are well established for grapevine CE typing were analysed on 96 grapevine samples from six different countries. We redesigned primers to the length of the amplicon for short sequencing (~100 bp). The primer pair was flanked with a 10 bp overhang for the introduction of barcodes on both sides of the amplicon to enable high multiplexing. The highest data peaks were determined as simple sequence repeat (SSR) alleles and compared with the CE dataset based on 12 reference samples. The comparison showed that HTS SSR genotyping can successfully replace the CE system in further experiments. We believe that, with next-generation sequencing, genotyping can be improved in terms of its speed, accuracy, and price. Full article

(This article belongs to the Special Issue Genetics and Diversity of Grapevine)

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20 pages, 2973 KiB

Open AccessArticle

Color Intensity of the Red-Fleshed Berry Phenotype of Vitis vinifera Teinturier Grapes Varies Due to a 408 bp Duplication in the Promoter of VvmybA1

by Franco Röckel, Carina Moock, Ulrike Braun, Florian Schwander, Peter Cousins, Erika Maul, Reinhard Töpfer and Ludger Hausmann

Genes 2020, 11(8), 891; https://doi.org/10.3390/genes11080891 - 05 Aug 2020

Cited by 23 | Viewed by 4364

Abstract

Grapevine (Vitis vinifera) teinturier cultivars are characterized by their typical reddish leaves and red-fleshed berries due to ectopic anthocyanin formation. Wines of these varieties have economic importance as they can be used for blending to enhance the color of red wines. [...] Read more.

Grapevine (Vitis vinifera) teinturier cultivars are characterized by their typical reddish leaves and red-fleshed berries due to ectopic anthocyanin formation. Wines of these varieties have economic importance as they can be used for blending to enhance the color of red wines. The unique and heritable mutation has been known for a long time but the underlying genetic mechanism still is not yet understood. Here we describe the association of the red-fleshed berry phenotype with a 408 bp repetitive DNA element in the promoter of the VvmybA1 gene (grapevine color enhancer, GCE). Three different clones of ‘Teinturier’ were discovered with two, three and five allelic GCE repeats (MybA1t2, MybA1t3 and MybA1t5). All three clones are periclinal chimeras; these clones share the same L1 layer, but have distinct L2 layers with different quantities of GCE repeats. Quantitative real time PCR and HPLC analysis of leaf and berry samples showed that the GCE repeat number strongly correlates with an increase of the expression of VvmybA1 itself and the VvUFGT gene regulated by it and the anthocyanin content. A model is proposed based on autoregulation of VvmybA1t to explain the red phenotype which is similar to that of red-fleshed apples. This study presents results about the generation and modes of action of three MybA1t alleles responsible for the red-fleshed berry phenotype of teinturier grapevines. Full article

(This article belongs to the Special Issue Genetics and Diversity of Grapevine)

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35 pages, 3643 KiB

Open AccessArticle

Genetic Diversity, Population Structure, and Parentage Analysis of Croatian Grapevine Germplasm

by Maja Žulj Mihaljević, Edi Maletić, Darko Preiner, Goran Zdunić, Marijan Bubola, Eva Zyprian and Ivan Pejić

Genes 2020, 11(7), 737; https://doi.org/10.3390/genes11070737 - 02 Jul 2020

Cited by 28 | Viewed by 4968

Abstract

Croatian viticulture was most extensive at the beginning of the 20th century, when about 400 varieties were in use. Autochthonous varieties are the result of spontaneous hybridization from the pre-phylloxera era and are still cultivated today on about 35 % of vineyard area, [...] Read more.

Croatian viticulture was most extensive at the beginning of the 20th century, when about 400 varieties were in use. Autochthonous varieties are the result of spontaneous hybridization from the pre-phylloxera era and are still cultivated today on about 35 % of vineyard area, while some exist only in repositories. We present what is the most comprehensive genetic analysis of all major Croatian national repositories, with a large number of microsatellite, or simple sequence repeat (SSR) markers, and it is also the first study to apply single nucleotide polymorphism (SNP) markers. After 212 accessions were fingerprinted, 95 were classified as unique to Croatian germplasm. Genetic diversity of Croatian germplasm is rather high considering its size. SNP markers proved useful for fingerprinting but less informative and practical than SSRs. Analysis of the genetic structure showed that Croatian germplasm is predominantly part of the Balkan grape gene pool. A high number of admixed varieties and synonyms is a consequence of complex pedigrees and migrations. Parentage analysis confirmed 24 full parentages, as well as 113 half-kinships. Unexpectedly, several key genitors could not be detected within the present Croatian germplasm. The low number of reconstructed parentages (19%) points to severe genetic erosion and stresses the importance of germplasm repositories. Full article

(This article belongs to the Special Issue Genetics and Diversity of Grapevine)

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19 pages, 1092 KiB

Open AccessArticle

VviUCC1 Nucleotide Diversity, Linkage Disequilibrium and Association with Rachis Architecture Traits in Grapevine

by Javier Tello, Rafael Torres-Pérez, Timothée Flutre, Jérôme Grimplet and Javier Ibáñez

Genes 2020, 11(6), 598; https://doi.org/10.3390/genes11060598 - 29 May 2020

Cited by 8 | Viewed by 2923

Abstract

Cluster compactness is a trait with high agronomic relevance, affecting crop yield and grape composition. Rachis architecture is a major component of cluster compactness determinism, and is a target trait toward the breeding of grapevine varieties less susceptible to pests and diseases. Although [...] Read more.

Cluster compactness is a trait with high agronomic relevance, affecting crop yield and grape composition. Rachis architecture is a major component of cluster compactness determinism, and is a target trait toward the breeding of grapevine varieties less susceptible to pests and diseases. Although its genetic basis is scarcely understood, a preliminary result indicated a possible involvement of the VviUCC1 gene. The aim of this study was to characterize the VviUCC1 gene in grapevine and to test the association between the natural variation observed for a series of rachis architecture traits and the polymorphisms detected in the VviUCC1 sequence. This gene encodes an uclacyanin plant-specific cell-wall protein involved in fiber formation and/or lignification processes. A high nucleotide diversity in the VviUCC1 gene promoter and coding regions was observed, but no critical effects were predicted in the protein domains, indicating a high level of conservation of its function in the cultivated grapevine. After correcting statistical models for genetic stratification and linkage disequilibrium effects, marker-trait association results revealed a series of single nucleotide polymorphisms (SNPs) significantly associated with cluster compactness and rachis traits variation. Two of them (Y-984 and K-88) affected two common cis-transcriptional regulatory elements, suggesting an effect on phenotype via gene expression regulation. This work reinforces the interest of further studies aiming to reveal the functional effect of the detected VviUCC1 variants on grapevine rachis architecture. Full article

(This article belongs to the Special Issue Genetics and Diversity of Grapevine)

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23 pages, 3100 KiB

Open AccessArticle

VviWRKY40, a WRKY Transcription Factor, Regulates Glycosylated Monoterpenoid Production by VviGT14 in Grape Berry

by Xiangyi Li, Lei He, Xiaohui An, Keji Yu, Nan Meng, Changqing Duan and Qiu-Hong Pan

Genes 2020, 11(5), 485; https://doi.org/10.3390/genes11050485 - 29 Apr 2020

Cited by 16 | Viewed by 3632

Abstract

Glycosylated volatile precursors are important, particularly in wine grape berries, as they contribute to the final aroma in wines by releasing volatile aglycones during yeast fermentation and wine storage. Previous study demonstrated that VviGT14 was functioned as a critical monoterpene glucosyltransferase in grape [...] Read more.

Glycosylated volatile precursors are important, particularly in wine grape berries, as they contribute to the final aroma in wines by releasing volatile aglycones during yeast fermentation and wine storage. Previous study demonstrated that VviGT14 was functioned as a critical monoterpene glucosyltransferase in grape berry, while the transcriptional regulation mechanism of VviGT14 was still unknown. Here we identified VviWRKY40 as a binding factor of VviGT14 promoter by both DNA pull-down and yeast one-hybrid screening, followed by a series of in vitro verification. VviWRKY40 expression pattern negatively correlated with that of VviGT14 in grape berries. And the suppressor role of VviWRKY40 was further confirmed by using the dual luciferase assay with Arabidopsis protoplast and grape cell suspension system. Furthermore, the grape suspension cell ABA treatment study showed that ABA downregulated VviWRKY40 transcript level but promoted that of VviGT14, indicating that VviWRKY40 was at the downstream of ABA signal transduction network to regulate monoterpenoid glycosylation. These data extend our knowledge of transcriptional regulation of VviGT14, and provide new targets for grape breeding to alter monoterpenoid composition. Full article

(This article belongs to the Special Issue Genetics and Diversity of Grapevine)

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9 pages, 998 KiB

Open AccessArticle

Grape-RNA: A Database for the Collection, Evaluation, Treatment, and Data Sharing of Grape RNA-Seq Datasets

by Yi Wang, Rui Zhang, Zhenchang Liang and Shaohua Li

Genes 2020, 11(3), 315; https://doi.org/10.3390/genes11030315 - 16 Mar 2020

Cited by 11 | Viewed by 3167

Abstract

Since its inception, RNA sequencing (RNA-seq) has become the most effective way to study gene expression. After more than a decade of development, numerous RNA-seq datasets have been created, and the full utilization of these datasets has emerged as a major issue. In [...] Read more.

Since its inception, RNA sequencing (RNA-seq) has become the most effective way to study gene expression. After more than a decade of development, numerous RNA-seq datasets have been created, and the full utilization of these datasets has emerged as a major issue. In this study, we built a comprehensive database named Grape-RNA, which is focused on the collection, evaluation, treatment, and data sharing of grape RNA-seq datasets. This database contains 1529 RNA-seq samples, 112 microRNA samples from the public platform, and 485 RNA-seq in-house datasets sequenced by our lab. We classified these data into 25 conditions and provide the sample information, cleaned raw data, expression level, assembled unigenes, useful tools, and other relevant information to the users. Thus, this study provides data and tools that should be beneficial for researchers by allowing them to easily use the RNA-seq. The provided information can greatly contribute to grape breeding and genomic and biological research. This study may improve the usage of RNA-seq. Full article

(This article belongs to the Special Issue Genetics and Diversity of Grapevine)

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23 pages, 1465 KiB

Open AccessArticle

Novel Aspects on The Interaction Between Grapevine and Plasmopara viticola: Dual-RNA-Seq Analysis Highlights Gene Expression Dynamics in The Pathogen and The Plant During The Battle For Infection

by Silvia Laura Toffolatti, Gabriella De Lorenzis, Matteo Brilli, Mirko Moser, Vahid Shariati, Elahe Tavakol, Giuliana Maddalena, Alessandro Passera, Paola Casati, Massimo Pindo, Alessandro Cestaro, David Maghradze, Osvaldo Failla, Piero Attilio Bianco and Fabio Quaglino

Genes 2020, 11(3), 261; https://doi.org/10.3390/genes11030261 - 28 Feb 2020

Cited by 28 | Viewed by 5551

Abstract

Mgaloblishvili, a Vitis vinifera cultivar, exhibits unique resistance traits against Plasmopara viticola, the downy mildew agent. This offers the unique opportunity of exploring the molecular responses in compatible and incompatible plant-pathogen interaction. In this study, whole transcriptomes of Mgaloblishvili, Pinot noir (a [...] Read more.

Mgaloblishvili, a Vitis vinifera cultivar, exhibits unique resistance traits against Plasmopara viticola, the downy mildew agent. This offers the unique opportunity of exploring the molecular responses in compatible and incompatible plant-pathogen interaction. In this study, whole transcriptomes of Mgaloblishvili, Pinot noir (a V. vinifera susceptible cultivar), and Bianca (a resistant hybrid) leaves, inoculated and non-inoculated with the pathogen, were used to identify P. viticola effector-encoding genes and plant susceptibility/resistance genes. Multiple effector-encoding genes were identified in P. viticola transcriptome, with remarkable expression differences in relation to the inoculated grapevine cultivar. Intriguingly, five apoplastic effectors specifically associated with resistance in V. vinifera. Gene coexpression network analysis identified specific modules and metabolic changes occurring during infection in the three grapevine cultivars. Analysis of these data allowed, for the first time, the detection in V. vinifera of a putative P. viticola susceptibility gene, encoding a LOB domain-containing protein. Finally, the de novo assembly of Mgaloblishvili, Pinot noir, and Bianca transcriptomes and their comparison highlighted novel candidate genes that might be at the basis of the resistant phenotype. These results open the way to functional analysis studies and to new perspectives in molecular breeding of grapevine for resistance to P. viticola. Full article

(This article belongs to the Special Issue Genetics and Diversity of Grapevine)

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