Abstract
Grapevines are challenged by a range of diseases and pests, causing economic losses and requiring often costly approaches to mitigate damage. Public interest in reducing the use of chemicals is a related challenge, along with climate change. Yet, the Vitis gene pool provides vast resources for the development of genetic resistance in rootstock and scion cultivars. Traditional breeding approaches have made great strides in the development of adaptive traits, and recent access to ‘omic technologies has further facilitated the identification of useful loci along with rapid trait introgression from wild species. Moreover, marker technologies are now used to stack multiple genes for the same trait into a single genotype, a heretofore barely accessible technology. Genomic technologies are also impacting germplasm characterization, and thereby facilitating “Breeding by Design” approaches. Genetic transformation and gene-editing technologies are also applicable for both cultivar improvement as well as functional studies of genes. The landscape for acceptance of new resistant cultivars is complex and with wine grapes, subject to high degrees of regulation especially in the European Union. With rootstocks, as well as table/raisin grapes, gaining acceptance in the marketplace for new cultivars developed through either traditional or marker-assisted approaches is routine. Yet even in the highly regulated EU environment, the adoption of new wine cultivars of interspecific origins is beginning to take place in both traditional wine growing regions as well as non-traditional regions nearby.
Reisch and Hausmann: Co-last authors, equally contributed
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Notes
- 1.
COUNCIL REGULATION (EC) No 2100/94 of 27 July 1994 on Community plant variety rights. (OJ L 227, 1.9.1994, p.1).
Abbreviations
- Aaβ-FS:
-
(E)-β-farnesene synthase
- AGO:
-
ARGONAUTE protein
- AM:
-
Association mapping
- AmpSeq:
-
Amplicon sequencing
- ATL:
-
Arabidopsis tóxicos en levadura
- ATP:
-
Adenosine triphosphate
- AUDPC:
-
Area under the disease progress curve
- AWPM:
-
Area wide pest management
- BAC:
-
Bacterial artificial chromosome
- BBR:
-
Botrytis bunch rot
- BCA:
-
Biological control agents
- BES:
-
BAC end sequence
- BLAST:
-
Basic local alignment search tool
- BN:
-
Bois noir
- BR:
-
Black rot
- BSA:
-
Bulked segregant analysis
- BS-seq:
-
Bisulfite sequencing
- bZIP:
-
basic Leucine zipper
- CAP:
-
Common agricultural policy
- CAP:
-
Chimeric antimicrobial protein
- CBF2/DREB1C:
-
C-repeat-binding factor dehydration-responsive element-binding factor 1C
- CBTs:
-
Conventional breeding technologies
- CCD:
-
Carotenoid cleavage dioxygenase
- CDPKs:
-
Calcium-dependent protein kinases
- CGAS:
-
Candidate gene association study
- ChIP-seq:
-
Chromatin immunoprecipitation followed by sequencing
- chr:
-
chromosome
- CIVIT:
-
Consorzio Innovazione Vite
- CMO:
-
Common Market Organization
- CNV:
-
Copy numbers variation
- CPVO:
-
Community Plant Variety Office
- CRISPR/Cas9:
-
Clustered regularly interspaced short palindromic repeats-associated protein 9
- cv.:
-
cultivar
- DAC3:
-
voltage-dependent anion channel 3
- DAMP:
-
Damage-associated molecular pattern
- DCL:
-
DICER-like
- ddRAD-seq:
-
double-digested RAD-seq
- DDS:
-
Decision support system
- DLO :
-
DMR-like oxygenase gene
- DM:
-
Downy mildew
- DMI:
-
Demethylase inhibitor
- DMR :
-
Downy mildew-resistant gene
- DREBs:
-
Dehydration-responsive element-binding proteins
- DSF:
-
Diffusible signal factor
- DSS:
-
Decision support system
- EcoTILLING:
-
Ecotype-Target induced local lesions in genomes
- ELISA:
-
Enzyme-linked immunosorbent assays
- EPPO:
-
European and Mediterranean Plant Protection Organization
- eQTL:
-
expression QTL
- ERFs:
-
Ethylene-responsive factors
- EST:
-
Expression sequence tag
- ET:
-
Ethylene
- ETGMs:
-
Established techniques of genetic modification
- ETI:
-
Effector-triggered immunity
- EU:
-
European Union
- FAIR:
-
Findability, accessibility, interoperability and reusability
- FAO:
-
Food and Agriculture Organization
- FAOSTAT:
-
Food and Agriculture Organization Corporate Statistical Database
- FD:
-
Flavescence dorée
- FDR:
-
False discovery rate
- FEM:
-
Fondazione Edmund Mach
- Flp:
-
Flippase
- Flp/FRT:
-
Flippase recombinase/Flippase recognition target sites
- GAB:
-
Genomics-assisted breeding
- GBS:
-
Genotyping-by-sequencing
- GC:
-
Guanine-cytosine
- GEM:
-
Grape erineum mite
- GENET:
-
Genetic resources and vine selection
- GFLV:
-
Grapevine Fanleaf Virus
- GINV:
-
Grapevine berry Inner Necrosis Virus
- GLRaV:
-
Grapevine Leafroll associated Virus
- GMO:
-
Genetically modified organisms
- GO:
-
Gene Ontology
- GPGV:
-
Grapevine Pinot gris Virus
- GRBV:
-
Grapevine Red Blotch virus
- GRSPaV:
-
Grapevine Rupestris Stem Pitting associated Virus
- GS:
-
Genomic selection
- GTD:
-
Grapevine trunk diseases
- GVA:
-
Grapevine Virus A
- GVB:
-
Grapevine Virus B
- GWA:
-
Genome wide association
- GWAS:
-
Genome wide association studies
- GxE:
-
Genotype x environment interaction
- GY:
-
Grapevine yellow
- H2O2:
-
Hydrogen peroxide
- H3K27me3:
-
Histone 3 lysine 27 trimethylation
- H3K43me3:
-
Histone 3 lysine 43 trimethylation
- HDR:
-
Homologous direct repair
- HM:
-
Histone modifier
- HR:
-
Hypersensitive response
- IdnDH:
-
L-idonate dehydrogenase enzyme
- IFV:
-
Institut Français de la Vigne et du Vin
- IGGP:
-
International Grapevine Genome Program
- INAO:
-
Institut national de l'origine et de la qualité
- INRA:
-
Institut National de la Recherche Agronomique
- INRAE:
-
France's National Research Institute for Agriculture, Food and Environment
- IPCC:
-
Intergovernmental panel on climate change
- IPM:
-
Integrated pest management
- ITS:
-
Internal transcribed spacer regions
- JA:
-
Jasmonic acid
- JAZ:
-
JASMONATE-ZIM DOMAIN protein
- KASP:
-
Kompetitive allele-specific PCR
- KEGG:
-
Kyoto Encyclopedia of Genes and Genomes
- LAMP:
-
Loop-mediated isothermal amplification
- LD:
-
Linkage disequilibrium
- LRR:
-
Leucine-rich repeat
- MAB:
-
Marker assisted breeding
- MABC:
-
Marker-assisted backcrossing
- MAMP:
-
Microbe-associated molecular pattern
- MAPS:
-
Marker-assisted parent selection
- MAS:
-
Marker-assisted selection
- MASS:
-
Marker-assisted seedling selection
- Mb:
-
Megabases
- MBC:
-
Modified backcross
- MD:
-
Mating disruption
- MIAPPE:
-
Minimum information about a plant phenotyping experiment
- miRNA:
-
microRNA
- MLM:
-
Mixed linear model
- MLMM:
-
Multi-locus mixed model
- MLO :
-
Mildew locus O gene
- mQTL:
-
metabolite QTL
- MSAP:
-
Methylation sensitive amplification polymorphism
- mtmlSEM:
-
multi-trait multi-locus Structural equation modeling
- MTMM:
-
Multi-trait mixed model
- NBS:
-
Nucleotide-binding site
- Nbs:
-
Nanobodies
- NBTs:
-
New breeding techniques
- NCBI:
-
National Center for Biotechnology Information
- ncRNA:
-
non-coding RNA
- NGR:
-
National Grapevine Register
- NGS:
-
Next-generation sequencing
- NHEJ:
-
Non-homologous end joining
- NO:
-
Nitric oxide
- NPTII:
-
Neomycin phosphotransferase
- nSSR:
-
nuclear SSR
- OIV:
-
Organisation Internationale de la Vigne et du Vin
- ORF:
-
Open reading frame
- PAM:
-
Protospacer-adjacent motif
- PAMP:
-
Pathogen-associated molecular pattern
- PCLS:
-
Phomopsis cane and leaf spot
- PCR:
-
Polymerase chain reaction
- PD:
-
Pierce's disease
- PDO:
-
Protected designation of origin
- pegRNA:
-
Prime editing guide RNA
- PGI:
-
Protected geographical indication
- PGIP:
-
Polygalacturonase inhibitory protein
- PIWI:
-
pilzwiderstandsfähig
- PM:
-
Powdery mildew
- PNN:
-
Plant-parasitic nematode
- PR4b:
-
Pathogenesis Related 4b protein
- PR:
-
Pathogenesis-related protein
- PRR:
-
Pattern recognition receptor
- PTI:
-
PAMP-triggered immunity
- pv.:
-
pathovar
- QoI:
-
Quinone outside inhibitor
- qPCR:
-
quantitative PCR
- QTL:
-
Quantitative trait locus
- QTLs:
-
Quantitative trait loci
- QTN:
-
Quantitative trait nucleotide
- RAD-seq:
-
Restriction site-associated DNA sequencing
- RAPD:
-
Random amplified polymorphic DNA
- RDR:
-
RNA-dependent RNA polymerase
- RGA:
-
Resistance gene analog
- R-gene :
-
Resistance gene
- rhAmpSeq:
-
RNase H2 enzyme-dependent amplicon sequencing
- RISC:
-
RNA-induced silencing complex
- RLK:
-
Receptor-like protein kinase
- RNA-seq:
-
RNA sequencing
- RNP:
-
Ribonucleoprotein
- rpfF:
-
regulation of pathogenicity factor F
- RPW8 :
-
Resistance to powdery mildew 8 gene
- RRBS:
-
Reduced representation bisulfite sequencing
- RT:
-
Reverse transcriptase enzyme
- SA:
-
Salicylic acid
- SEM:
-
Structural equation modeling
- sgRNA:
-
single guide RNA
- siRNA:
-
small interfering RNA
- SLAF:
-
Specific length amplified fragment
- SNAT:
-
Serotonin N-acetyltransferase
- SNP:
-
Single nucleotide polymorphism
- SNV:
-
Single nucleotide variant
- SSR:
-
Simple sequence repeat
- STS:
-
Stilbene synthase
- syn.:
-
synonymous
- TALEN:
-
Transcription activator like effector nuclease
- TAS4b :
-
Trans-acting small interfering RNA gene 4
- T-DNA:
-
Transfer DNA
- TIR:
-
Toll/interleukin-1 receptor
- TIR-NB-ARC-LRR:
-
Toll-interleukin-1-receptor - nucleotide-binding - adaptor shared by APAF-1 (apoptotic protease-activating factor-1), R proteins, and CED-4 (Caenorhabditis elegans death-4 protein) - leucine-rich repeat
- TLP:
-
Thaumatin-like protein
- TMT:
-
Tonoplastic monosaccharide transporter
- UBQ:
-
Ubiquitin
- UPOV:
-
International Union for the Protection of New Varieties of Plants
- USDA:
-
United States Department of Agriculture
- VCR:
-
Vivai Cooperativi Rauscedo
- VESPUCCI:
-
Vitis Expression Studies Platform Using COLOMBOS Compendia Instances
- VIVC:
-
Vitis International Variety Catalog
- VpGRP2A :
-
Vitis pseudoreticulata glycine-rich protein 2A gene
- VpRH2 :
-
Vitis pseudoreticulata RING-H2-type ubiquitin ligase gene
- VpTNL1 :
-
Vitis pseudoreticulata TIR-NB-LRR gene 1
- VOC:
-
Volatile organic compound
- WGS:
-
Whole genome shotgun
- WRKY:
-
WRKY family protein
- XVE:
-
LexA-VP16-ER
- ZFN:
-
Zinc finger nuclease
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Vezzulli, S. et al. (2022). Genomic Designing for Biotic Stress Resistant Grapevine. In: Kole, C. (eds) Genomic Designing for Biotic Stress Resistant Fruit Crops. Springer, Cham. https://doi.org/10.1007/978-3-030-91802-6_4
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