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Ricciardi V, Crespan M, Maddalena G, Migliaro D, Brancadoro L, Maghradze D, Failla O, Toffolatti SL, De Lorenzis G. Novel loci associated with resistance to downy and powdery mildew in grapevine. FRONTIERS IN PLANT SCIENCE 2024; 15:1386225. [PMID: 38584944 PMCID: PMC10998452 DOI: 10.3389/fpls.2024.1386225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/06/2024] [Indexed: 04/09/2024]
Abstract
Among the main challenges in current viticulture, there is the increasing demand for sustainability in the protection from fungal diseases, such as downy mildew (DM) and powdery mildew (PM). Breeding disease-resistant grapevine varieties is a key strategy for better managing fungicide inputs. This study explores the diversity of grapevine germplasm (cultivated and wild) from Caucasus and neighboring areas to identify genotypes resistant to DM and PM, based on 13 Simple Sequence Repeat (SSR) loci and phenotypical (artificial pathogen inoculation) analysis, and to identify loci associated with DM and PM resistance, via Genome-Wide Association Analysis (GWAS) on Single Nucleotide Polymorphism (SNP) profiles. SSR analysis revealed resistant alleles for 16 out of 88 genotypes. Phenotypic data identified seven DM and 31 PM resistant genotypes. GWAS identified two new loci associated with DM resistance, located on chromosome 15 and 16 (designated as Rpv36 and Rpv37), and two with PM resistance, located on chromosome 6 and 17 (designated as Ren14 and Ren15). The four novel loci identified genomic regions rich in genes related to biotic stress response, such as genes involved in pathogen recognition, signal transduction and resistance response. This study highlights potential candidate genes associated with resistance to DM and PM, providing valuable insights for breeding programs for resistant varieties. To optimize their utilization, further functional characterization studies are recommended.
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Affiliation(s)
- Valentina Ricciardi
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Manna Crespan
- Centro di Ricerca per la Viticoltura e l'Enologia, Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Conegliano, Italy
| | - Giuliana Maddalena
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Daniele Migliaro
- Centro di Ricerca per la Viticoltura e l'Enologia, Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Conegliano, Italy
| | - Lucio Brancadoro
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milano, Italy
| | - David Maghradze
- Faculty of Viticulture-Winemaking, Caucasus International University, Tbilisi, Georgia
- Faculty of Agricultural Sciences and Biosystems Engineering, Georgian Technical University, Tbilisi, Georgia
| | - Osvaldo Failla
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Silvia Laura Toffolatti
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Gabriella De Lorenzis
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milano, Italy
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Lazaridi E, Kapazoglou A, Gerakari M, Kleftogianni K, Passa K, Sarri E, Papasotiropoulos V, Tani E, Bebeli PJ. Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding. PLANTS (BASEL, SWITZERLAND) 2024; 13:758. [PMID: 38592762 PMCID: PMC10975389 DOI: 10.3390/plants13060758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/23/2024] [Accepted: 03/02/2024] [Indexed: 04/10/2024]
Abstract
Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement of genomic technologies such as deciphering of pangenomes, multi-omics tools, marker-assisted selection (MAS), genome-wide association studies (GWAS), and CRISPR/Cas9 gene editing greatly facilitated the exploitation of landraces in modern plant breeding. In this paper, we present a comprehensive overview of the implementation of new genomic technologies and highlight their importance in pinpointing the genetic basis of desirable traits in landraces and indigenous varieties of annual, perennial herbaceous, and woody crop species cultivated in the Mediterranean region. The need for further employment of advanced -omic technologies to unravel the full potential of landraces and indigenous varieties underutilized genetic diversity is also indicated. Ultimately, the large amount of genomic data emerging from the investigation of landraces and indigenous varieties reveals their potential as a source of valuable genes and traits for breeding. The role of landraces and indigenous varieties in mitigating the ongoing risks posed by climate change in agriculture and food security is also highlighted.
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Affiliation(s)
- Efstathia Lazaridi
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Aliki Kapazoglou
- Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Department of Vitis, Hellenic Agricultural Organization-Dimitra (ELGO-Dimitra), Sofokli Venizelou 1, Lykovrysi, 14123 Athens, Greece;
| | - Maria Gerakari
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Konstantina Kleftogianni
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Kondylia Passa
- Department of Agriculture, University of Patras, Nea Ktiria, 30200 Messolonghi, Greece;
| | - Efi Sarri
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Vasileios Papasotiropoulos
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Penelope J. Bebeli
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
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Magon G, De Rosa V, Martina M, Falchi R, Acquadro A, Barcaccia G, Portis E, Vannozzi A, De Paoli E. Boosting grapevine breeding for climate-smart viticulture: from genetic resources to predictive genomics. FRONTIERS IN PLANT SCIENCE 2023; 14:1293186. [PMID: 38148866 PMCID: PMC10750425 DOI: 10.3389/fpls.2023.1293186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023]
Abstract
The multifaceted nature of climate change is increasing the urgency to select resilient grapevine varieties, or generate new, fitter cultivars, to withstand a multitude of new challenging conditions. The attainment of this goal is hindered by the limiting pace of traditional breeding approaches, which require decades to result in new selections. On the other hand, marker-assisted breeding has proved useful when it comes to traits governed by one or few genes with great effects on the phenotype, but its efficacy is still restricted for complex traits controlled by many loci. On these premises, innovative strategies are emerging which could help guide selection, taking advantage of the genetic diversity within the Vitis genus in its entirety. Multiple germplasm collections are also available as a source of genetic material for the introgression of alleles of interest via adapted and pioneering transformation protocols, which present themselves as promising tools for future applications on a notably recalcitrant species such as grapevine. Genome editing intersects both these strategies, not only by being an alternative to obtain focused changes in a relatively rapid way, but also by supporting a fine-tuning of new genotypes developed with other methods. A review on the state of the art concerning the available genetic resources and the possibilities of use of innovative techniques in aid of selection is presented here to support the production of climate-smart grapevine genotypes.
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Affiliation(s)
- Gabriele Magon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padova, Agripolis, Viale dell’Università 16, Legnaro, Italy
| | - Valeria De Rosa
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Via delle Scienze, 206, Udine, Italy
| | - Matteo Martina
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - Rachele Falchi
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Via delle Scienze, 206, Udine, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padova, Agripolis, Viale dell’Università 16, Legnaro, Italy
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padova, Agripolis, Viale dell’Università 16, Legnaro, Italy
| | - Emanuele De Paoli
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Via delle Scienze, 206, Udine, Italy
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Blois L, de Miguel M, Bert PF, Ollat N, Rubio B, Voss-Fels KP, Schmid J, Marguerit E. Dissecting the genetic architecture of root-related traits in a grafted wild Vitis berlandieri population for grapevine rootstock breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:223. [PMID: 37838631 PMCID: PMC10576685 DOI: 10.1007/s00122-023-04472-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/25/2023] [Indexed: 10/16/2023]
Abstract
In woody perennial plants, quantitative genetics and association studies remain scarce for root-related traits, due to the time required to obtain mature plants and the complexity of phenotyping. In grapevine, a grafted cultivated plant, most of the rootstocks used are hybrids between American Vitis species (V. rupestris, V. riparia, and V. berlandieri). In this study, we used a wild population of an American Vitis species (V. berlandieri) to analyze the genetic architecture of the root-related traits of rootstocks in a grafted context. We studied a population consisting of 211 genotypes, with one to five replicates each (n = 846 individuals), plus four commercial rootstocks as control genotypes (110R, 5BB, Börner, and SO4). After two independent years of experimentation, the best linear unbiased estimates method revealed root-related traits with a moderate-to-high heritability (0.36-0.82) and coefficient of genetic variation (0.15-0.45). A genome-wide association study was performed with the BLINK model, leading to the detection of 11 QTL associated with four root-related traits (one QTL was associated with the total number of roots, four were associated with the number of small roots (< 1 mm in diameter), two were associated with the number of medium-sized roots (1 mm < diameter < 2 mm), and four were associated with mean diameter) accounting for up to 25.1% of the variance. Three genotypes were found to have better root-related trait performances than the commercial rootstocks and therefore constitute possible new candidates for use in grapevine rootstock breeding programs.
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Affiliation(s)
- Louis Blois
- EGFV, Bordeaux Sciences Agro, INRAE, ISVV, Univ. Bordeaux, 33882, Villenave d'Ornon, France.
- Department of Grapevine Breeding, Geisenheim University, Von Lade Str. 1, 65366, Geisenheim, Germany.
| | - Marina de Miguel
- EGFV, Bordeaux Sciences Agro, INRAE, ISVV, Univ. Bordeaux, 33882, Villenave d'Ornon, France
| | - Pierre-François Bert
- EGFV, Bordeaux Sciences Agro, INRAE, ISVV, Univ. Bordeaux, 33882, Villenave d'Ornon, France
| | - Nathalie Ollat
- EGFV, Bordeaux Sciences Agro, INRAE, ISVV, Univ. Bordeaux, 33882, Villenave d'Ornon, France
| | - Bernadette Rubio
- EGFV, Bordeaux Sciences Agro, INRAE, ISVV, Univ. Bordeaux, 33882, Villenave d'Ornon, France
| | - Kai P Voss-Fels
- Department of Grapevine Breeding, Geisenheim University, Von Lade Str. 1, 65366, Geisenheim, Germany
| | - Joachim Schmid
- Department of Grapevine Breeding, Geisenheim University, Von Lade Str. 1, 65366, Geisenheim, Germany
| | - Elisa Marguerit
- EGFV, Bordeaux Sciences Agro, INRAE, ISVV, Univ. Bordeaux, 33882, Villenave d'Ornon, France
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Tello J, Ibáñez J. Review: Status and prospects of association mapping in grapevine. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 327:111539. [PMID: 36410567 DOI: 10.1016/j.plantsci.2022.111539] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
Thanks to current advances in sequencing technologies, novel bioinformatics tools, and efficient modeling solutions, association mapping has become a widely accepted approach to unravel the link between genotype and phenotype diversity in numerous crops. In grapevine, this strategy has been used in the last decades to understand the genetic basis of traits of agronomic interest (fruit quality, crop yield, biotic and abiotic resistance), of special relevance nowadays to improve crop resilience to cope with future climate scenarios. Genome-wide association studies have identified many putative causative loci for different traits, some of them overlapping well-known causal genes identified by conventional quantitative trait loci studies in biparental progenies, and/or validated by functional approaches. In addition, candidate-gene association studies have been useful to pinpoint the causal mutation underlying phenotypic variation for several traits of high interest in breeding programs (like berry color, seedlessness, and muscat flavor), information that has been used to develop highly informative and useful markers already in use in marker-assisted selection processes. Thus, association mapping has proved to represent a valuable step towards high quality and sustainable grape production. This review summarizes current applications of association mapping in grapevine research and discusses future prospects in view of current viticulture challenges.
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Affiliation(s)
- Javier Tello
- Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), Logroño 26007, Spain.
| | - Javier Ibáñez
- Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), Logroño 26007, Spain
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