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Brault C, Segura V, Roques M, Lamblin P, Bouckenooghe V, Pouzalgues N, Cunty C, Breil M, Frouin M, Garcin L, Camps L, Ducasse MA, Romieu C, Masson G, Julliard S, Flutre T, Le Cunff L. Enhancing grapevine breeding efficiency through genomic prediction and selection index. G3 (BETHESDA, MD.) 2024; 14:jkae038. [PMID: 38401528 PMCID: PMC10989862 DOI: 10.1093/g3journal/jkae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/09/2024] [Accepted: 02/18/2024] [Indexed: 02/26/2024]
Abstract
Grapevine (Vitis vinifera) breeding reaches a critical point. New cultivars are released every year with resistance to powdery and downy mildews. However, the traditional process remains time-consuming, taking 20-25 years, and demands the evaluation of new traits to enhance grapevine adaptation to climate change. Until now, the selection process has relied on phenotypic data and a limited number of molecular markers for simple genetic traits such as resistance to pathogens, without a clearly defined ideotype, and was carried out on a large scale. To accelerate the breeding process and address these challenges, we investigated the use of genomic prediction, a methodology using molecular markers to predict genotypic values. In our study, we focused on 2 existing grapevine breeding programs: Rosé wine and Cognac production. In these programs, several families were created through crosses of emblematic and interspecific resistant varieties to powdery and downy mildews. Thirty traits were evaluated for each program, using 2 genomic prediction methods: Genomic Best Linear Unbiased Predictor and Least Absolute Shrinkage Selection Operator. The results revealed substantial variability in predictive abilities across traits, ranging from 0 to 0.9. These discrepancies could be attributed to factors such as trait heritability and trait characteristics. Moreover, we explored the potential of across-population genomic prediction by leveraging other grapevine populations as training sets. Integrating genomic prediction allowed us to identify superior individuals for each program, using multivariate selection index method. The ideotype for each breeding program was defined collaboratively with representatives from the wine-growing sector.
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Affiliation(s)
- Charlotte Brault
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, Montpellier 34398, France
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
| | - Vincent Segura
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, Montpellier 34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier 34398, France
| | - Maryline Roques
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, Montpellier 34398, France
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
| | - Pauline Lamblin
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
| | - Virginie Bouckenooghe
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, Montpellier 34398, France
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
| | | | - Constance Cunty
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
- Centre du Rosé, Vidauban 83550, France
| | - Matthieu Breil
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, Montpellier 34398, France
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
| | - Marina Frouin
- Conservatoire du Vignoble Charentais, Institut de Formation de Richemont, Cherves-Richemont 16370, France
| | - Léa Garcin
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
- Conservatoire du Vignoble Charentais, Institut de Formation de Richemont, Cherves-Richemont 16370, France
| | - Louise Camps
- Conservatoire du Vignoble Charentais, Institut de Formation de Richemont, Cherves-Richemont 16370, France
| | - Marie-Agnès Ducasse
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
| | - Charles Romieu
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, Montpellier 34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier 34398, France
| | - Gilles Masson
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
- Centre du Rosé, Vidauban 83550, France
| | - Sébastien Julliard
- Conservatoire du Vignoble Charentais, Institut de Formation de Richemont, Cherves-Richemont 16370, France
| | - Timothée Flutre
- INRAE, CNRS, AgroParisTech, Université Paris-Saclay, GQE—Le Moulon, Gif-sur-Yvette 91190, France
| | - Loïc Le Cunff
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, Montpellier 34398, France
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
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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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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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Vargas AM, Fernández-Pastor M, Castro FJ, Martínez MA, Gómez-Cifuentes A, Espinosa-Roldán F, Cabello F, Muñoz-Organero G, de Andrés MT. Strategy to minimize phenotyping in the selection of new table grape varieties. BIO WEB OF CONFERENCES 2023. [DOI: 10.1051/bioconf/20235601030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Morphological evaluation of large progenies is a problem in plant breeding programs, because of the need for skilled labor capable of characterizing various descriptors in a large number of individuals ripening simultaneously. In addition, the maintenance of progenies in the field for evaluation involves an unsustainable consumption of resources that could be reduced. Marker-assisted selection (MAS) offers the possibility of accelerating the process with the consequent saving of resources. The aim of this work is to propose a methodology that minimizes the phenotyping work for thousands of individuals of these breeding programs. The methodology consists of analyzing the complete progeny with a limited number of markers (27 SSR (Simple Sequence Repeat)) and a reduced description of morphological characters on a so-called training collection (27 individuals) obtained with Mstrat software. With this strategy, it was possible to estimate traits such as berry skin color or seedlessness in a progeny of more than 2000 individuals with a probability of 90%, and to discard 50% of individuals without muscat linked alleles.
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Brault C, Lazerges J, Doligez A, Thomas M, Ecarnot M, Roumet P, Bertrand Y, Berger G, Pons T, François P, Le Cunff L, This P, Segura V. Interest of phenomic prediction as an alternative to genomic prediction in grapevine. PLANT METHODS 2022; 18:108. [PMID: 36064570 PMCID: PMC9442960 DOI: 10.1186/s13007-022-00940-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Phenomic prediction has been defined as an alternative to genomic prediction by using spectra instead of molecular markers. A reflectance spectrum provides information on the biochemical composition within a tissue, itself being under genetic determinism. Thus, a relationship matrix built from spectra could potentially capture genetic signal. This new methodology has been mainly applied in several annual crop species but little is known so far about its interest in perennial species. Besides, phenomic prediction has only been tested for a restricted set of traits, mainly related to yield or phenology. This study aims at applying phenomic prediction for the first time in grapevine, using spectra collected on two tissues and over two consecutive years, on two populations and for 15 traits, related to berry composition, phenology, morphological and vigour. A major novelty of this study was to collect spectra and phenotypes several years apart from each other. First, we characterized the genetic signal in spectra and under which condition it could be maximized, then phenomic predictive ability was compared to genomic predictive ability. RESULTS For the first time, we showed that the similarity between spectra and genomic relationship matrices was stable across tissues or years, but variable across populations, with co-inertia around 0.3 and 0.6 for diversity panel and half-diallel populations, respectively. Applying a mixed model on spectra data increased phenomic predictive ability, while using spectra collected on wood or leaves from one year or another had less impact. Differences between populations were also observed for predictive ability of phenomic prediction, with an average of 0.27 for the diversity panel and 0.35 for the half-diallel. For both populations, a significant positive correlation was found across traits between predictive ability of genomic and phenomic predictions. CONCLUSION NIRS is a new low-cost alternative to genotyping for predicting complex traits in perennial species such as grapevine. Having spectra and phenotypes from different years allowed us to exclude genotype-by-environment interactions and confirms that phenomic prediction can rely only on genetics.
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Affiliation(s)
- Charlotte Brault
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
- Institut Français de la vigne et du vin, 34398, Montpellier, France
| | - Juliette Lazerges
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
| | - Agnès Doligez
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
| | - Miguel Thomas
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
| | - Martin Ecarnot
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
| | - Pierre Roumet
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
| | - Yves Bertrand
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
| | - Gilles Berger
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
| | - Thierry Pons
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
| | - Pierre François
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
| | - Loïc Le Cunff
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
- Institut Français de la vigne et du vin, 34398, Montpellier, France
| | - Patrice This
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
| | - Vincent Segura
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France.
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France.
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6
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Brault C, Segura V, This P, Le Cunff L, Flutre T, François P, Pons T, Péros JP, Doligez A. Across-population genomic prediction in grapevine opens up promising prospects for breeding. HORTICULTURE RESEARCH 2022; 9:uhac041. [PMID: 35184162 PMCID: PMC9070645 DOI: 10.1093/hr/uhac041] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 02/01/2022] [Indexed: 05/15/2023]
Abstract
Crop breeding involves two selection steps: choosing progenitors and selecting individuals within progenies. Genomic prediction, based on genome-wide marker estimation of genetic values, could facilitate these steps. However, its potential usefulness in grapevine (Vitis vinifera L.) has only been evaluated in non-breeding contexts mainly through cross-validation within a single population. We tested across-population genomic prediction in a more realistic breeding configuration, from a diversity panel to ten bi-parental crosses connected within a half-diallel mating design. Prediction quality was evaluated over 15 traits of interest (related to yield, berry composition, phenology and vigour), for both the average genetic value of each cross (cross mean) and the genetic values of individuals within each cross (individual values). Genomic prediction in these conditions was found useful: for cross mean, average per-trait predictive ability was 0.6, while per-cross predictive ability was halved on average, but reached a maximum of 0.7. Mean predictive ability for individual values within crosses was 0.26, about half the within-half-diallel value taken as a reference. For some traits and/or crosses, these across-population predictive ability values are promising for implementing genomic selection in grapevine breeding. This study also provided key insights on variables affecting predictive ability. Per-cross predictive ability was well predicted by genetic distance between parents and when this predictive ability was below 0.6, it was improved by training set optimization. For individual values, predictive ability mostly depended on trait-related variables (magnitude of the cross effect and heritability). These results will greatly help designing grapevine breeding programs assisted by genomic prediction.
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Affiliation(s)
- Charlotte Brault
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- Institut Français de la Vigne et du Vin, F-34398 Montpellier, France
| | - Vincent Segura
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Patrice This
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Loïc Le Cunff
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- Institut Français de la Vigne et du Vin, F-34398 Montpellier, France
| | - Timothée Flutre
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190, Gif-sur-Yvette, France
| | - Pierre François
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Thierry Pons
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Jean-Pierre Péros
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Agnès Doligez
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
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Brault C, Doligez A, Cunff L, Coupel-Ledru A, Simonneau T, Chiquet J, This P, Flutre T. Harnessing multivariate, penalized regression methods for genomic prediction and QTL detection of drought-related traits in grapevine. G3-GENES GENOMES GENETICS 2021; 11:6325507. [PMID: 34544146 PMCID: PMC8496232 DOI: 10.1093/g3journal/jkab248] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 07/02/2021] [Indexed: 11/13/2022]
Abstract
Viticulture has to cope with climate change and to decrease pesticide inputs, while maintaining yield and wine quality. Breeding is a key lever to meet this challenge, and genomic prediction a promising tool to accelerate breeding programs. Multivariate methods are potentially more accurate than univariate ones. Moreover, some prediction methods also provide marker selection, thus allowing quantitative trait loci (QTLs) detection and the identification of positional candidate genes. To study both genomic prediction and QTL detection for drought-related traits in grapevine, we applied several methods, interval mapping (IM) as well as univariate and multivariate penalized regression, in a bi-parental progeny. With a dense genetic map, we simulated two traits under four QTL configurations. The penalized regression method Elastic Net (EN) for genomic prediction, and controlling the marginal False Discovery Rate on EN selected markers to prioritize the QTLs. Indeed, penalized methods were more powerful than IM for QTL detection across various genetic architectures. Multivariate prediction did not perform better than its univariate counterpart, despite strong genetic correlation between traits. Using 14 traits measured in semi-controlled conditions under different watering conditions, penalized regression methods proved very efficient for intra-population prediction whatever the genetic architecture of the trait, with predictive abilities reaching 0.68. Compared to a previous study on the same traits, these methods applied on a denser map found new QTLs controlling traits linked to drought tolerance and provided relevant candidate genes. Overall, these findings provide a strong evidence base for implementing genomic prediction in grapevine breeding.
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Affiliation(s)
- Charlotte Brault
- Institut Français de la Vigne et du Vin, Montpellier F-34398, France.,UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier F-34398, France.,UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier F-34398, France
| | - Agnès Doligez
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier F-34398, France.,UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier F-34398, France
| | - Le Cunff
- Institut Français de la Vigne et du Vin, Montpellier F-34398, France.,UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier F-34398, France.,UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier F-34398, France
| | - Aude Coupel-Ledru
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier 34000, France
| | - Thierry Simonneau
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier 34000, France
| | | | - Patrice This
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier F-34398, France.,UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier F-34398, France
| | - Timothée Flutre
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
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8
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Gomès É, Maillot P, Duchêne É. Molecular Tools for Adapting Viticulture to Climate Change. FRONTIERS IN PLANT SCIENCE 2021; 12:633846. [PMID: 33643361 PMCID: PMC7902699 DOI: 10.3389/fpls.2021.633846] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/19/2021] [Indexed: 05/04/2023]
Abstract
Adaptation of viticulture to climate change includes exploration of new geographical areas, new training systems, new management practices, or new varieties, both for rootstocks and scions. Molecular tools can be defined as molecular approaches used to study DNAs, RNAs, and proteins in all living organisms. We present here the current knowledge about molecular tools and their potential usefulness in three aspects of grapevine adaptation to the ongoing climate change. (i) Molecular tools for understanding grapevine response to environmental stresses. A fine description of the regulation of gene expression is a powerful tool to understand the physiological mechanisms set up by the grapevine to respond to abiotic stress such as high temperatures or drought. The current knowledge on gene expression is continuously evolving with increasing evidence of the role of alternative splicing, small RNAs, long non-coding RNAs, DNA methylation, or chromatin activity. (ii) Genetics and genomics of grapevine stress tolerance. The description of the grapevine genome is more and more precise. The genetic variations among genotypes are now revealed with new technologies with the sequencing of very long DNA molecules. High throughput technologies for DNA sequencing also allow now the genetic characterization at the same time of hundreds of genotypes for thousands of points in the genome, which provides unprecedented datasets for genotype-phenotype associations studies. We review the current knowledge on the genetic determinism of traits for the adaptation to climate change. We focus on quantitative trait loci and molecular markers available for developmental stages, tolerance to water stress/water use efficiency, sugar content, acidity, and secondary metabolism of the berries. (iii) Controlling the genome and its expression to allow breeding of better-adapted genotypes. High-density DNA genotyping can be used to select genotypes with specific interesting alleles but genomic selection is also a powerful method able to take into account the genetic information along the whole genome to predict a phenotype. Modern technologies are also able to generate mutations that are possibly interesting for generating new phenotypes but the most promising one is the direct editing of the genome at a precise location.
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Affiliation(s)
- Éric Gomès
- EGFV, University of Bordeaux – Bordeaux Sciences-Agro – INRAE, Villenave d’Ornon, France
| | - Pascale Maillot
- SVQV, INRAE – University of Strasbourg, Colmar, France
- University of Haute Alsace, Mulhouse, France
| | - Éric Duchêne
- SVQV, INRAE – University of Strasbourg, Colmar, France
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9
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Trenti M, Lorenzi S, Bianchedi PL, Grossi D, Failla O, Grando MS, Emanuelli F. Candidate genes and SNPs associated with stomatal conductance under drought stress in Vitis. BMC PLANT BIOLOGY 2021; 21:7. [PMID: 33407127 PMCID: PMC7789618 DOI: 10.1186/s12870-020-02739-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 11/16/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Understanding the complexity of the vine plant's response to water deficit represents a major challenge for sustainable winegrowing. Regulation of water use requires a coordinated action between scions and rootstocks on which cultivars are generally grafted to cope with phylloxera infestations. In this regard, a genome-wide association study (GWAS) approach was applied on an 'ad hoc' association mapping panel including different Vitis species, in order to dissect the genetic basis of transpiration-related traits and to identify genomic regions of grape rootstocks associated with drought tolerance mechanisms. The panel was genotyped with the GrapeReSeq Illumina 20 K SNP array and SSR markers, and infrared thermography was applied to estimate stomatal conductance values during progressive water deficit. RESULTS In the association panel the level of genetic diversity was substantially lower for SNPs loci (0.32) than for SSR (0.87). GWAS detected 24 significant marker-trait associations along the various stages of drought-stress experiment and 13 candidate genes with a feasible role in drought response were identified. Gene expression analysis proved that three of these genes (VIT_13s0019g03040, VIT_17s0000g08960, VIT_18s0001g15390) were actually induced by drought stress. Genetic variation of VIT_17s0000g08960 coding for a raffinose synthase was further investigated by resequencing the gene of 85 individuals since a SNP located in the region (chr17_10,497,222_C_T) was significantly associated with stomatal conductance. CONCLUSIONS Our results represent a step forward towards the dissection of genetic basis that modulate the response to water deprivation in grape rootstocks. The knowledge derived from this study may be useful to exploit genotypic and phenotypic diversity in practical applications and to assist further investigations.
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Affiliation(s)
- Massimiliano Trenti
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all’Adige, Italy
| | - Silvia Lorenzi
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all’Adige, Italy
| | - Pier Luigi Bianchedi
- Technology Transfer Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all’Adige, Italy
| | - Daniele Grossi
- Department of Agricultural and Environmental Sciences, University of Milano, via Celoria 2, 20133 Milan, Italy
| | - Osvaldo Failla
- Department of Agricultural and Environmental Sciences, University of Milano, via Celoria 2, 20133 Milan, Italy
| | - Maria Stella Grando
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all’Adige, Italy
- Center Agriculture Food Environment (C3A), University of Trento, via E. Mach 1, 38010 San Michele all’Adige, Italy
| | - Francesco Emanuelli
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all’Adige, Italy
- Department of Agricultural and Environmental Sciences, University of Milano, via Celoria 2, 20133 Milan, Italy
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Adoption and Optimization of Genomic Selection To Sustain Breeding for Apricot Fruit Quality. G3-GENES GENOMES GENETICS 2020; 10:4513-4529. [PMID: 33067307 PMCID: PMC7718743 DOI: 10.1534/g3.120.401452] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Genomic selection (GS) is a breeding approach which exploits genome-wide information and whose unprecedented success has shaped several animal and plant breeding schemes through delivering their genetic progress. This is the first study assessing the potential of GS in apricot (Prunus armeniaca) to enhance postharvest fruit quality attributes. Genomic predictions were based on a F1 pseudo-testcross population, comprising 153 individuals with contrasting fruit quality traits. They were phenotyped for physical and biochemical fruit metrics in contrasting climatic conditions over two years. Prediction accuracy (PA) varied from 0.31 for glucose content with the Bayesian LASSO (BL) to 0.78 for ethylene production with RR-BLUP, which yielded the most accurate predictions in comparison to Bayesian models and only 10% out of 61,030 SNPs were sufficient to reach accurate predictions. Useful insights were provided on the genetic architecture of apricot fruit quality whose integration in prediction models improved their performance, notably for traits governed by major QTL. Furthermore, multivariate modeling yielded promising outcomes in terms of PA within training partitions partially phenotyped for target traits. This provides a useful framework for the implementation of indirect selection based on easy-to-measure traits. Thus, we highlighted the main levers to take into account for the implementation of GS for fruit quality in apricot, but also to improve the genetic gain in perennial species.
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11
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Janni M, Gullì M, Maestri E, Marmiroli M, Valliyodan B, Nguyen HT, Marmiroli N. Molecular and genetic bases of heat stress responses in crop plants and breeding for increased resilience and productivity. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3780-3802. [PMID: 31970395 PMCID: PMC7316970 DOI: 10.1093/jxb/eraa034] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 01/20/2020] [Indexed: 05/21/2023]
Abstract
To ensure the food security of future generations and to address the challenge of the 'no hunger zone' proposed by the FAO (Food and Agriculture Organization), crop production must be doubled by 2050, but environmental stresses are counteracting this goal. Heat stress in particular is affecting agricultural crops more frequently and more severely. Since the discovery of the physiological, molecular, and genetic bases of heat stress responses, cultivated plants have become the subject of intense research on how they may avoid or tolerate heat stress by either using natural genetic variation or creating new variation with DNA technologies, mutational breeding, or genome editing. This review reports current understanding of the genetic and molecular bases of heat stress in crops together with recent approaches to creating heat-tolerant varieties. Research is close to a breakthrough of global relevance, breeding plants fitter to face the biggest challenge of our time.
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Affiliation(s)
- Michela Janni
- Institute of Bioscience and Bioresources (IBBR), National Research Council (CNR), Via Amendola, Bari, Italy
- Institute of Materials for Electronics and Magnetism (IMEM), National Research Council (CNR), Parco Area delle Scienze, Parma, Italy
| | - Mariolina Gullì
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Elena Maestri
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Marta Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Babu Valliyodan
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
- Lincoln University, Jefferson City, MO, USA
| | - Henry T Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
- CINSA Interuniversity Consortium for Environmental Sciences, Parma/Venice, Italy
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12
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Tello J, Roux C, Chouiki H, Laucou V, Sarah G, Weber A, Santoni S, Flutre T, Pons T, This P, Péros JP, Doligez A. A novel high-density grapevine (Vitis vinifera L.) integrated linkage map using GBS in a half-diallel population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2237-2252. [PMID: 31049634 DOI: 10.1007/s00122-019-03351-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/20/2019] [Indexed: 05/21/2023]
Abstract
A half-diallel population involving five elite grapevine cultivars was generated and genotyped by GBS, and highly-informative segregation data was used to construct a high-density genetic map for Vitis vinifera L. Grapevine is one of the most relevant fruit crops in the world. Deeper genetic knowledge could assist modern grapevine breeding programs to develop new wine grape varieties able to face climate change effects. To assist in the rapid identification of markers for crop yield components, grape quality traits and adaptation potential, we generated a large Vitis vinifera L. population (N = 624) by crossing five red wine cultivars in a half-diallel scheme, which was subsequently sequenced by an efficient GBS procedure. A high number of fully informative genetic variants was detected using a novel mapping approach capable of reconstructing local haplotypes from adjacent biallelic SNPs, which were subsequently used to construct the densest consensus genetic map available for the cultivated grapevine to date. This 1378.3-cM map integrates 10 bi-parental consensus maps and orders 4437 markers in 3353 unique positions on 19 chromosomes. Markers are well distributed all along the grapevine reference genome, covering up to 98.8% of its genomic sequence. Additionally, a good agreement was observed between genetic and physical orders, adding confidence in the quality of this map. Collectively, our results pave the way for future genetic studies (such as fine QTL mapping) aimed to understand the complex relationship between genotypic and phenotypic variation in the cultivated grapevine. In addition, the method used (which efficiently delivers a high number of fully informative markers) could be of interest to other outbred organisms, notably perennial fruit crops.
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Affiliation(s)
- Javier Tello
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Catherine Roux
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Hajar Chouiki
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
| | - Valérie Laucou
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Gautier Sarah
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Audrey Weber
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
| | - Sylvain Santoni
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
| | - Timothée Flutre
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Thierry Pons
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Patrice This
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Jean-Pierre Péros
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Agnès Doligez
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France.
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France.
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13
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Zini E, Dolzani C, Stefanini M, Gratl V, Bettinelli P, Nicolini D, Betta G, Dorigatti C, Velasco R, Letschka T, Vezzulli S. R-Loci Arrangement Versus Downy and Powdery Mildew Resistance Level: A Vitis Hybrid Survey. Int J Mol Sci 2019; 20:ijms20143526. [PMID: 31323823 PMCID: PMC6679420 DOI: 10.3390/ijms20143526] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/01/2019] [Accepted: 07/16/2019] [Indexed: 12/14/2022] Open
Abstract
For the viticulture of the future, it will be an essential prerequisite to manage grapevine diseases with fewer chemical inputs. The development and the deployment of novel mildew resistant varieties are considered one of the most promising strategies towards a sustainable viticulture. In this regard, a collection of 102 accessions derived from crossing Vitis hybrids with V. vinifera varieties was studied. In addition to the true-to-type analysis, an exhaustive genetic characterization was carried out at the 11 reliable mildew resistance (R) loci available in the literature to date. Our findings highlight the pyramiding of R-loci against downy mildew in 15.7% and against powdery mildew in 39.2% of the total accessions. The genetic analysis was coupled with a three-year evaluation of disease symptoms in an untreated field in order to assess the impact of the R-loci arrangement on the disease resistance degree at leaf and bunch level. Overall, our results strongly suggest that R-loci pyramiding does not necessarily mean to increase the overall disease resistance, but it guarantees the presence of further barriers in case of pathogens overcoming the first. Moreover, our survey allows the discovery of new mildew resistance sources useful for novel QTL identifications towards marker-assisted breeding.
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Affiliation(s)
- Elena Zini
- Laimburg Research Centre, Laimburg 6, 39052 Vadena (BZ), Italy
| | - Chiara Dolzani
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Marco Stefanini
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Verena Gratl
- Institute of Pharmacy/Pharmacognosy, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | | | - Daniela Nicolini
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Giulia Betta
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Cinzia Dorigatti
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Riccardo Velasco
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
- CREA Research Centre for Viticulture and Enology, Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
| | - Thomas Letschka
- Laimburg Research Centre, Laimburg 6, 39052 Vadena (BZ), Italy.
| | - Silvia Vezzulli
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige (TN), Italy.
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14
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Patel S, Lu Z, Jin X, Swaminathan P, Zeng E, Fennell AY. Comparison of three assembly strategies for a heterozygous seedless grapevine genome assembly. BMC Genomics 2018; 19:57. [PMID: 29343235 PMCID: PMC5773036 DOI: 10.1186/s12864-018-4434-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/04/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND De novo heterozygous assembly is an ongoing challenge requiring improved assembly approaches. In this study, three strategies were used to develop de novo Vitis vinifera 'Sultanina' genome assemblies for comparison with the inbred V. vinifera (PN40024 12X.v2) reference genome and a published Sultanina ALLPATHS-LG assembly (AP). The strategies were: 1) a default PLATANUS assembly (PLAT_d) for direct comparison with AP assembly, 2) an iterative merging strategy using METASSEMBLER to combine PLAT_d and AP assemblies (MERGE) and 3) PLATANUS parameter modifications plus GapCloser (PLAT*_GC). RESULTS The three new assemblies were greater in size than the AP assembly. PLAT*_GC had the greatest number of scaffolds aligning with a minimum of 95% identity and ≥1000 bp alignment length to V. vinifera (PN40024 12X.v2) reference genome. SNP analysis also identified additional high quality SNPs. A greater number of sequence reads mapped back with zero-mismatch to the PLAT_d, MERGE, and PLAT*_GC (>94%) than was found in the AP assembly (87%) indicating a greater fidelity to the original sequence data in the new assemblies than in AP assembly. A de novo gene prediction conducted using seedless RNA-seq data predicted > 30,000 coding sequences for the three new de novo assemblies, with the greatest number (30,544) in PLAT*_GC and only 26,515 for the AP assembly. Transcription factor analysis indicated good family coverage, but some genes found in the VCOST.v3 annotation were not identified in any of the de novo assemblies, particularly some from the MYB and ERF families. CONCLUSIONS The PLAT_d and PLAT*_GC had a greater number of synteny blocks with the V. vinifera (PN40024 12X.v2) reference genome than AP or MERGE. PLAT*_GC provided the most contiguous assembly with only 1.2% scaffold N, in contrast to AP (10.7% N), PLAT_d (6.6% N) and Merge (6.4% N). A PLAT*_GC pseudo-chromosome assembly with chromosome alignment to the reference genome V. vinifera, (PN40024 12X.v2) provides new information for use in seedless grape genetic mapping studies. An annotated de novo gene prediction for the PLAT*_GC assembly, aligned with VitisNet pathways provides new seedless grapevine specific transcriptomic resource that has excellent fidelity with the seedless short read sequence data.
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Affiliation(s)
- Sagar Patel
- Agronomy, Horticulture and Plant Science Department and BioSNTR, 247 McFadden BioStress Laboratory, South Dakota State University, Brookings, SD, 57006, USA
| | - Zhixiu Lu
- Department of Computer Science, University of South Dakota, Vermillion, SD, USA
| | - Xiaozhu Jin
- Agronomy, Horticulture and Plant Science Department and BioSNTR, 247 McFadden BioStress Laboratory, South Dakota State University, Brookings, SD, 57006, USA
| | - Padmapriya Swaminathan
- Agronomy, Horticulture and Plant Science Department and BioSNTR, 247 McFadden BioStress Laboratory, South Dakota State University, Brookings, SD, 57006, USA
| | - Erliang Zeng
- Department of Computer Science, University of South Dakota, Vermillion, SD, USA.,Department of Biology, University of South Dakota, Vermillion, SD, USA
| | - Anne Y Fennell
- Agronomy, Horticulture and Plant Science Department and BioSNTR, 247 McFadden BioStress Laboratory, South Dakota State University, Brookings, SD, 57006, USA.
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Minamikawa MF, Nonaka K, Kaminuma E, Kajiya-Kanegae H, Onogi A, Goto S, Yoshioka T, Imai A, Hamada H, Hayashi T, Matsumoto S, Katayose Y, Toyoda A, Fujiyama A, Nakamura Y, Shimizu T, Iwata H. Genome-wide association study and genomic prediction in citrus: Potential of genomics-assisted breeding for fruit quality traits. Sci Rep 2017; 7:4721. [PMID: 28680114 PMCID: PMC5498537 DOI: 10.1038/s41598-017-05100-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/24/2017] [Indexed: 01/08/2023] Open
Abstract
Novel genomics-based approaches such as genome-wide association studies (GWAS) and genomic selection (GS) are expected to be useful in fruit tree breeding, which requires much time from the cross to the release of a cultivar because of the long generation time. In this study, a citrus parental population (111 varieties) and a breeding population (676 individuals from 35 full-sib families) were genotyped for 1,841 single nucleotide polymorphisms (SNPs) and phenotyped for 17 fruit quality traits. GWAS power and prediction accuracy were increased by combining the parental and breeding populations. A multi-kernel model considering both additive and dominance effects improved prediction accuracy for acidity and juiciness, implying that the effects of both types are important for these traits. Genomic best linear unbiased prediction (GBLUP) with linear ridge kernel regression (RR) was more robust and accurate than GBLUP with non-linear Gaussian kernel regression (GAUSS) in the tails of the phenotypic distribution. The results of this study suggest that both GWAS and GS are effective for genetic improvement of citrus fruit traits. Furthermore, the data collected from breeding populations are beneficial for increasing the detection power of GWAS and the prediction accuracy of GS.
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Affiliation(s)
- Mai F Minamikawa
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Keisuke Nonaka
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 485-6 Okitsu Nakacho, Shimizu, Shizuoka, 424-0292, Japan
| | - Eli Kaminuma
- Genome Informatics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Hiromi Kajiya-Kanegae
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Akio Onogi
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Shingo Goto
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 485-6 Okitsu Nakacho, Shimizu, Shizuoka, 424-0292, Japan
| | - Terutaka Yoshioka
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 485-6 Okitsu Nakacho, Shimizu, Shizuoka, 424-0292, Japan
| | - Atsushi Imai
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| | - Hiroko Hamada
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 485-6 Okitsu Nakacho, Shimizu, Shizuoka, 424-0292, Japan
| | - Takeshi Hayashi
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Satomi Matsumoto
- Institute of Crop Science, NARO, 1-2 Ohwashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Yuichi Katayose
- Institute of Crop Science, NARO, 1-2 Ohwashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
- Advanced Genomics Center, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Asao Fujiyama
- Advanced Genomics Center, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Yasukazu Nakamura
- Genome Informatics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Tokurou Shimizu
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 485-6 Okitsu Nakacho, Shimizu, Shizuoka, 424-0292, Japan
| | - Hiroyoshi Iwata
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan.
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16
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Biscarini F, Nazzicari N, Bink M, Arús P, Aranzana MJ, Verde I, Micali S, Pascal T, Quilot-Turion B, Lambert P, da Silva Linge C, Pacheco I, Bassi D, Stella A, Rossini L. Genome-enabled predictions for fruit weight and quality from repeated records in European peach progenies. BMC Genomics 2017; 18:432. [PMID: 28583089 PMCID: PMC5460546 DOI: 10.1186/s12864-017-3781-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 05/10/2017] [Indexed: 11/16/2022] Open
Abstract
Background Highly polygenic traits such as fruit weight, sugar content and acidity strongly influence the agroeconomic value of peach varieties. Genomic Selection (GS) can accelerate peach yield and quality gain if predictions show higher levels of accuracy compared to phenotypic selection. The available IPSC 9K SNP array V1 allows standardized and highly reliable genotyping, preparing the ground for GS in peach. Results A repeatability model (multiple records per individual plant) for genome-enabled predictions in eleven European peach populations is presented. The analysis included 1147 individuals derived from both commercial and non-commercial peach or peach-related accessions. Considered traits were average fruit weight (FW), sugar content (SC) and titratable acidity (TA). Plants were genotyped with the 9K IPSC array, grown in three countries (France, Italy, Spain) and phenotyped for 3–5 years. An analysis of imputation accuracy of missing genotypic data was conducted using the software Beagle, showing that two of the eleven populations were highly sensitive to increasing levels of missing data. The regression model produced, for each trait and each population, estimates of heritability (FW:0.35, SC:0.48, TA:0.53, on average) and repeatability (FW:0.56, SC:0.63, TA:0.62, on average). Predictive ability was estimated in a five-fold cross validation scheme within population as the correlation of true and predicted phenotypes. Results differed by populations and traits, but predictive abilities were in general high (FW:0.60, SC:0.72, TA:0.65, on average). Conclusions This study assessed the feasibility of Genomic Selection in peach for highly polygenic traits linked to yield and fruit quality. The accuracy of imputing missing genotypes was as high as 96%, and the genomic predictive ability was on average 0.65, but could be as high as 0.84 for fruit weight or 0.83 for titratable acidity. The estimated repeatability may prove very useful in the management of the typical long cycles involved in peach productions. All together, these results are very promising for the application of genomic selection to peach breeding programmes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3781-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Filippo Biscarini
- PTP Science Park, Via Einstein - Loc. Cascina Codazza, Lodi, Italy.,IBBA-CNR, Via Edoardo Bassini, 15, Milan, 20133, Italy
| | - Nelson Nazzicari
- PTP Science Park, Via Einstein - Loc. Cascina Codazza, Lodi, Italy.,Council for Agricultural Research and Economics (CREA) Research Centre for Fodder Crops and Dairy Productions, Lodi, Italy
| | - Marco Bink
- Wageningen UR Biometris, Wageningen, The Netherlands.,Present Address: Hendrix Genetics Research, Technology & Services B.V., P.O. Box 114, Boxmeer NL, 5830AC, The Netherlands
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| | - Maria José Aranzana
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| | - Ignazio Verde
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA) - Centro di Ricerca per la Frutticoltura (CREA-FRU), Via di Fioranello 52, Roma, Italy
| | - Sabrina Micali
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA) - Centro di Ricerca per la Frutticoltura (CREA-FRU), Via di Fioranello 52, Roma, Italy
| | | | | | - Patrick Lambert
- Università degli Studi di Milano - DiSAA, Via Celoria 2, Milano, Italy
| | | | - Igor Pacheco
- Università degli Studi di Milano - DiSAA, Via Celoria 2, Milano, Italy.,Institute of Nutrition and Food Technology - INTA, Universidad de Chile, Av El Líbano 5524, Santiago, Chile
| | - Daniele Bassi
- Università degli Studi di Milano - DiSAA, Via Celoria 2, Milano, Italy
| | - Alessandra Stella
- PTP Science Park, Via Einstein - Loc. Cascina Codazza, Lodi, Italy.,IBBA-CNR, Via Edoardo Bassini, 15, Milan, 20133, Italy
| | - Laura Rossini
- PTP Science Park, Via Einstein - Loc. Cascina Codazza, Lodi, Italy. .,Università degli Studi di Milano - DiSAA, Via Celoria 2, Milano, Italy.
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17
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Gascuel Q, Diretto G, Monforte AJ, Fortes AM, Granell A. Use of Natural Diversity and Biotechnology to Increase the Quality and Nutritional Content of Tomato and Grape. FRONTIERS IN PLANT SCIENCE 2017; 8:652. [PMID: 28553296 PMCID: PMC5427129 DOI: 10.3389/fpls.2017.00652] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/10/2017] [Indexed: 05/18/2023]
Abstract
Improving fruit quality has become a major goal in plant breeding. Direct approaches to tackling fruit quality traits specifically linked to consumer preferences and environmental friendliness, such as improved flavor, nutraceutical compounds, and sustainability, have slowly been added to a breeder priority list that already includes traits like productivity, efficiency, and, especially, pest and disease control. Breeders already use molecular genetic tools to improve fruit quality although most advances have been made in producer and industrial quality standards. Furthermore, progress has largely been limited to simple agronomic traits easy-to-observe, whereas the vast majority of quality attributes, specifically those relating to flavor and nutrition, are complex and have mostly been neglected. Fortunately, wild germplasm, which is used for resistance against/tolerance of environmental stresses (including pathogens), is still available and harbors significant genetic variation for taste and health-promoting traits. Similarly, heirloom/traditional varieties could be used to identify which genes contribute to flavor and health quality and, at the same time, serve as a good source of the best alleles for organoleptic quality improvement. Grape (Vitis vinifera L.) and tomato (Solanum lycopersicum L.) produce fleshy, berry-type fruits, among the most consumed in the world. Both have undergone important domestication and selection processes, that have dramatically reduced their genetic variability, and strongly standardized fruit traits. Moreover, more and more consumers are asking for sustainable production, incompatible with the wide range of chemical inputs. In the present paper, we review the genetic resources available to tomato/grape breeders, and the recent technological progresses that facilitate the identification of genes/alleles of interest within the natural or generated variability gene pool. These technologies include omics, high-throughput phenotyping/phenomics, and biotech approaches. Our review also covers a range of technologies used to transfer to tomato and grape those alleles considered of interest for fruit quality. These include traditional breeding, TILLING (Targeting Induced Local Lesions in Genomes), genetic engineering, or NPBT (New Plant Breeding Technologies). Altogether, the combined exploitation of genetic variability and innovative biotechnological tools may facilitate breeders to improve fruit quality tacking more into account the consumer standards and the needs to move forward into more sustainable farming practices.
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Affiliation(s)
- Quentin Gascuel
- Laboratory of Plant-Microbe Interactions, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Toulouse UniversityCastanet Tolosan, France
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy, and Sustainable Development, Casaccia Research CentreRome, Italy
| | - Antonio J. Monforte
- Instituto de Biología Molecular y Celular de Plantas, Agencia Estatal Consejo Superior de Investigaciones Científicas, Universidad Politécnica de ValenciaValencia, Spain
| | - Ana M. Fortes
- Faculdade de Ciências de Lisboa, Instituto de Biossistemas e Ciências Integrativas (BioISI), Universidade de LisboaLisboa, Portugal
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas, Agencia Estatal Consejo Superior de Investigaciones Científicas, Universidad Politécnica de ValenciaValencia, Spain
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18
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Migault V, Pallas B, Costes E. Combining Genome-Wide Information with a Functional Structural Plant Model to Simulate 1-Year-Old Apple Tree Architecture. FRONTIERS IN PLANT SCIENCE 2017; 7:2065. [PMID: 28127302 PMCID: PMC5226960 DOI: 10.3389/fpls.2016.02065] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 12/26/2016] [Indexed: 05/26/2023]
Abstract
In crops, optimizing target traits in breeding programs can be fostered by selecting appropriate combinations of architectural traits which determine light interception and carbon acquisition. In apple tree, architectural traits were observed to be under genetic control. However, architectural traits also result from many organogenetic and morphological processes interacting with the environment. The present study aimed at combining a FSPM built for apple tree, MAppleT, with genetic determinisms of architectural traits, previously described in a bi-parental population. We focused on parameters related to organogenesis (phyllochron and immediate branching) and morphogenesis processes (internode length and leaf area) during the first year of tree growth. Two independent datasets collected in 2004 and 2007 on 116 genotypes, issued from a 'Starkrimson' × 'Granny Smith' cross, were used. The phyllochron was estimated as a function of thermal time and sylleptic branching was modeled subsequently depending on phyllochron. From a genetic map built with SNPs, marker effects were estimated on four MAppleT parameters with rrBLUP, using 2007 data. These effects were then considered in MAppleT to simulate tree development in the two climatic conditions. The genome wide prediction model gave consistent estimations of parameter values with correlation coefficients between observed values and estimated values from SNP markers ranging from 0.79 to 0.96. However, the accuracy of the prediction model following cross validation schemas was lower. Three integrative traits (the number of leaves, trunk length, and number of sylleptic laterals) were considered for validating MAppleT simulations. In 2007 climatic conditions, simulated values were close to observations, highlighting the correct simulation of genetic variability. However, in 2004 conditions which were not used for model calibration, the simulations differed from observations. This study demonstrates the possibility of integrating genome-based information in a FSPM for a perennial fruit tree. It also showed that further improvements are required for improving the prediction ability. Especially temperature effect should be extended and other factors taken into account for modeling GxE interactions. Improvements could also be expected by considering larger populations and by testing other genome wide prediction models. Despite these limitations, this study opens new possibilities for supporting plant breeding by in silico evaluations of the impact of genotypic polymorphisms on plant integrative phenotypes.
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Affiliation(s)
| | | | - Evelyne Costes
- INRA, UMR 1334 AGAP, Equipe Architecture et Fonctionnement des Espèces FruitièresMontpellier, France
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19
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Gezan SA, Osorio LF, Verma S, Whitaker VM. An experimental validation of genomic selection in octoploid strawberry. HORTICULTURE RESEARCH 2017; 4:16070. [PMID: 28090334 PMCID: PMC5225750 DOI: 10.1038/hortres.2016.70] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 12/06/2016] [Accepted: 12/08/2016] [Indexed: 05/03/2023]
Abstract
The primary goal of genomic selection is to increase genetic gains for complex traits by predicting performance of individuals for which phenotypic data are not available. The objective of this study was to experimentally evaluate the potential of genomic selection in strawberry breeding and to define a strategy for its implementation. Four clonally replicated field trials, two in each of 2 years comprised of a total of 1628 individuals, were established in 2013-2014 and 2014-2015. Five complex yield and fruit quality traits with moderate to low heritability were assessed in each trial. High-density genotyping was performed with the Affymetrix Axiom IStraw90 single-nucleotide polymorphism array, and 17 479 polymorphic markers were chosen for analysis. Several methods were compared, including Genomic BLUP, Bayes B, Bayes C, Bayesian LASSO Regression, Bayesian Ridge Regression and Reproducing Kernel Hilbert Spaces. Cross-validation within training populations resulted in higher values than for true validations across trials. For true validations, Bayes B gave the highest predictive abilities on average and also the highest selection efficiencies, particularly for yield traits that were the lowest heritability traits. Selection efficiencies using Bayes B for parent selection ranged from 74% for average fruit weight to 34% for early marketable yield. A breeding strategy is proposed in which advanced selection trials are utilized as training populations and in which genomic selection can reduce the breeding cycle from 3 to 2 years for a subset of untested parents based on their predicted genomic breeding values.
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Affiliation(s)
- Salvador A Gezan
- School of Forest Resources and Conservation, University of Florida, 363 Newins-Ziegler Hall, PO Box 110410, Gainesville, FL 32611-0410, USA
| | - Luis F Osorio
- Gulf Coast Research and Education Center, University of Florida, 14625 CR 672, Wimauma, FL 33598, USA
| | - Sujeet Verma
- Gulf Coast Research and Education Center, University of Florida, 14625 CR 672, Wimauma, FL 33598, USA
| | - Vance M Whitaker
- Gulf Coast Research and Education Center, University of Florida, 14625 CR 672, Wimauma, FL 33598, USA
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20
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Bhat JA, Ali S, Salgotra RK, Mir ZA, Dutta S, Jadon V, Tyagi A, Mushtaq M, Jain N, Singh PK, Singh GP, Prabhu KV. Genomic Selection in the Era of Next Generation Sequencing for Complex Traits in Plant Breeding. Front Genet 2016; 7:221. [PMID: 28083016 PMCID: PMC5186759 DOI: 10.3389/fgene.2016.00221] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 12/12/2016] [Indexed: 12/31/2022] Open
Abstract
Genomic selection (GS) is a promising approach exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. In plant breeding, it provides opportunities to increase genetic gain of complex traits per unit time and cost. The cost-benefit balance was an important consideration for GS to work in crop plants. Availability of genome-wide high-throughput, cost-effective and flexible markers, having low ascertainment bias, suitable for large population size as well for both model and non-model crop species with or without the reference genome sequence was the most important factor for its successful and effective implementation in crop species. These factors were the major limitations to earlier marker systems viz., SSR and array-based, and was unimaginable before the availability of next-generation sequencing (NGS) technologies which have provided novel SNP genotyping platforms especially the genotyping by sequencing. These marker technologies have changed the entire scenario of marker applications and made the use of GS a routine work for crop improvement in both model and non-model crop species. The NGS-based genotyping have increased genomic-estimated breeding value prediction accuracies over other established marker platform in cereals and other crop species, and made the dream of GS true in crop breeding. But to harness the true benefits from GS, these marker technologies will be combined with high-throughput phenotyping for achieving the valuable genetic gain from complex traits. Moreover, the continuous decline in sequencing cost will make the WGS feasible and cost effective for GS in near future. Till that time matures the targeted sequencing seems to be more cost-effective option for large scale marker discovery and GS, particularly in case of large and un-decoded genomes.
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Affiliation(s)
- Javaid A Bhat
- Division of Genetics, Indian Agricultural Research Institute New Delhi, India
| | - Sajad Ali
- National Research Centre for Plant Biotechnology New Delhi, India
| | - Romesh K Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu Chatha, India
| | - Zahoor A Mir
- National Research Centre for Plant Biotechnology New Delhi, India
| | - Sutapa Dutta
- Division of Genetics, Indian Agricultural Research Institute New Delhi, India
| | - Vasudha Jadon
- Division of Genetics, Indian Agricultural Research Institute New Delhi, India
| | - Anshika Tyagi
- National Research Centre for Plant Biotechnology New Delhi, India
| | - Muntazir Mushtaq
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu Chatha, India
| | - Neelu Jain
- Division of Genetics, Indian Agricultural Research Institute New Delhi, India
| | - Pradeep K Singh
- Division of Genetics, Indian Agricultural Research Institute New Delhi, India
| | - Gyanendra P Singh
- Division of Genetics, Indian Agricultural Research Institute New Delhi, India
| | - K V Prabhu
- Division of Genetics, Indian Agricultural Research Institute New Delhi, India
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21
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Nicolas SD, Péros JP, Lacombe T, Launay A, Le Paslier MC, Bérard A, Mangin B, Valière S, Martins F, Le Cunff L, Laucou V, Bacilieri R, Dereeper A, Chatelet P, This P, Doligez A. Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies. BMC PLANT BIOLOGY 2016; 16:74. [PMID: 27005772 PMCID: PMC4802926 DOI: 10.1186/s12870-016-0754-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/14/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND As for many crops, new high-quality grapevine varieties requiring less pesticide and adapted to climate change are needed. In perennial species, breeding is a long process which can be speeded up by gaining knowledge about quantitative trait loci linked to agronomic traits variation. However, due to the long juvenile period of these species, establishing numerous highly recombinant populations for high resolution mapping is both costly and time-consuming. Genome wide association studies in germplasm panels is an alternative method of choice, since it allows identifying the main quantitative trait loci with high resolution by exploiting past recombination events between cultivars. Such studies require adequate panel design to represent most of the available genetic and phenotypic diversity. Assessing linkage disequilibrium extent and panel power is also needed to determine the marker density required for association studies. RESULTS Starting from the largest grapevine collection worldwide maintained in Vassal (France), we designed a diversity panel of 279 cultivars with limited relatedness, reflecting the low structuration in three genetic pools resulting from different uses (table vs wine) and geographical origin (East vs West), and including the major founders of modern cultivars. With 20 simple sequence repeat markers and five quantitative traits, we showed that our panel adequately captured most of the genetic and phenotypic diversity existing within the entire Vassal collection. To assess linkage disequilibrium extent and panel power, we genotyped single nucleotide polymorphisms: 372 over four genomic regions and 129 distributed over the whole genome. Linkage disequilibrium, measured by correlation corrected for kinship, reached 0.2 for a physical distance between 9 and 458 Kb depending on genetic pool and genomic region, with varying size of linkage disequilibrium blocks. This panel achieved reasonable power to detect associations between traits with high broad-sense heritability (> 0.7) and causal loci with intermediate allelic frequency and strong effect (explaining > 10 % of total variance). CONCLUSIONS Our association panel constitutes a new, highly valuable resource for genetic association studies in grapevine, and deserves dissemination to diverse field and greenhouse trials to gain more insight into the genetic control of many agronomic traits and their interaction with the environment.
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Affiliation(s)
- Stéphane D. Nicolas
- />INRA, UMR AGAP, F-34060 Montpellier, France
- />GQE-Le Moulon, INRA - Univ. Paris-Sud - CNRS - AgroParisTech - Université Paris-Saclay, Ferme du Moulon, F-91190 Gif-sur-Yvette, France
| | | | | | | | | | | | | | - Sophie Valière
- />INRA, Plateforme Génomique, F-31326 Castanet-Tolosan, France
| | - Frédéric Martins
- />INRA, Plateforme Génomique, F-31326 Castanet-Tolosan, France
- />INSERM, UMR1048, F-31432 Toulouse, France
| | | | | | | | - Alexis Dereeper
- />INRA, UMR AGAP, F-34060 Montpellier, France
- />IRD, UMR IPME, F-34394 Montpellier 5, France
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22
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Yang S, Fresnedo-Ramírez J, Wang M, Cote L, Schweitzer P, Barba P, Takacs EM, Clark M, Luby J, Manns DC, Sacks G, Mansfield AK, Londo J, Fennell A, Gadoury D, Reisch B, Cadle-Davidson L, Sun Q. A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker-assisted selection in grapevine. HORTICULTURE RESEARCH 2016; 3:16002. [PMID: 27257505 PMCID: PMC4879517 DOI: 10.1038/hortres.2016.2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/06/2016] [Accepted: 01/08/2016] [Indexed: 05/07/2023]
Abstract
Marker-assisted selection (MAS) is often employed in crop breeding programs to accelerate and enhance cultivar development, via selection during the juvenile phase and parental selection prior to crossing. Next-generation sequencing and its derivative technologies have been used for genome-wide molecular marker discovery. To bridge the gap between marker development and MAS implementation, this study developed a novel practical strategy with a semi-automated pipeline that incorporates trait-associated single nucleotide polymorphism marker discovery, low-cost genotyping through amplicon sequencing (AmpSeq) and decision making. The results document the development of a MAS package derived from genotyping-by-sequencing using three traits (flower sex, disease resistance and acylated anthocyanins) in grapevine breeding. The vast majority of sequence reads (⩾99%) were from the targeted regions. Across 380 individuals and up to 31 amplicons sequenced in each lane of MiSeq data, most amplicons (83 to 87%) had <10% missing data, and read depth had a median of 220-244×. Several strengths of the AmpSeq platform that make this approach of broad interest in diverse crop species include accuracy, flexibility, speed, high-throughput, low-cost and easily automated analysis.
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Affiliation(s)
- Shanshan Yang
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | | | - Minghui Wang
- Bioinformatics Facility, Cornell University, Ithaca, NY 14853, USA
| | - Linda Cote
- Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Peter Schweitzer
- Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Paola Barba
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Elizabeth M Takacs
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - Matthew Clark
- Department of Horticultural Science, University of Minnesota, St Paul, MN 55108, USA
| | - James Luby
- Department of Horticultural Science, University of Minnesota, St Paul, MN 55108, USA
| | - David C Manns
- Department of Food Science, Cornell University, Geneva, NY 14456, USA
| | - Gavin Sacks
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | | | - Jason Londo
- USDA-ARS Grape Genetics Research Unit, Geneva, NY 14456, USA
| | - Anne Fennell
- Plant Science Department, South Dakota State University, Brookings, SD 57007, USA
| | - David Gadoury
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - Bruce Reisch
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | | | - Qi Sun
- Bioinformatics Facility, Cornell University, Ithaca, NY 14853, USA
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23
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Gorjanc G, Jenko J, Hearne SJ, Hickey JM. Initiating maize pre-breeding programs using genomic selection to harness polygenic variation from landrace populations. BMC Genomics 2016; 17:30. [PMID: 26732811 PMCID: PMC4702314 DOI: 10.1186/s12864-015-2345-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/21/2015] [Indexed: 11/23/2022] Open
Abstract
Background The limited genetic diversity of elite maize germplasms raises concerns about the potential to breed for new challenges. Initiatives have been formed over the years to identify and utilize useful diversity from landraces to overcome this issue. The aim of this study was to evaluate the proposed designs to initiate a pre-breeding program within the Seeds of Discovery (SeeD) initiative with emphasis on harnessing polygenic variation from landraces using genomic selection. We evaluated these designs with stochastic simulation to provide decision support about the effect of several design factors on the quality of resulting (pre-bridging) germplasm. The evaluated design factors were: i) the approach to initiate a pre-breeding program from the selected landraces, doubled haploids of the selected landraces, or testcrosses of the elite hybrid and selected landraces, ii) the genetic parameters of landraces and phenotypes, and iii) logistical factors related to the size and management of a pre-breeding program. Results The results suggest a pre-breeding program should be initiated directly from landraces. Initiating from testcrosses leads to a rapid reconstruction of the elite donor genome during further improvement of the pre-bridging germplasm. The analysis of accuracy of genomic predictions across the various design factors indicate the power of genomic selection for pre-breeding programs with large genetic diversity and constrained resources for data recording. The joint effect of design factors was summarized with decision trees with easy to follow guidelines to optimize pre-breeding efforts of SeeD and similar initiatives. Conclusions Results of this study provide guidelines for SeeD and similar initiatives on how to initiate pre-breeding programs that aim to harness polygenic variation from landraces. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2345-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gregor Gorjanc
- Biotechnical Faculty, University of Ljubljana, 1000, Ljubljana, Slovenia. .,The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK.
| | - Janez Jenko
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK. .,Agricultural Institute of Slovenia, 1000, Ljubljana, Slovenia.
| | - Sarah J Hearne
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo, 06600, México, D.F., México.
| | - John M Hickey
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK.
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24
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Iwata H, Minamikawa MF, Kajiya-Kanegae H, Ishimori M, Hayashi T. Genomics-assisted breeding in fruit trees. BREEDING SCIENCE 2016; 66:100-15. [PMID: 27069395 PMCID: PMC4780794 DOI: 10.1270/jsbbs.66.100] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/12/2016] [Indexed: 05/03/2023]
Abstract
Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the plant to assess the marketable product (fruit). In this article, we describe the potential of genomics-assisted breeding, which uses these novel genomics-based approaches, to break through these barriers in conventional fruit tree breeding. We first introduce the molecular marker systems and whole-genome sequence data that are available for fruit tree breeding. Next we introduce the statistical methods for biparental linkage and quantitative trait locus (QTL) mapping as well as GWAS and GS. We then review QTL mapping, GWAS, and GS studies conducted on fruit trees. We also review novel technologies for rapid generation advancement. Finally, we note the future prospects of genomics-assisted fruit tree breeding and problems that need to be overcome in the breeding.
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Affiliation(s)
- Hiroyoshi Iwata
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo,
1-1-1 Yayoi, Bunkyo, Tokyo 113-8657,
Japan
- Corresponding author (e-mail: )
| | - Mai F. Minamikawa
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo,
1-1-1 Yayoi, Bunkyo, Tokyo 113-8657,
Japan
| | - Hiromi Kajiya-Kanegae
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo,
1-1-1 Yayoi, Bunkyo, Tokyo 113-8657,
Japan
| | - Motoyuki Ishimori
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo,
1-1-1 Yayoi, Bunkyo, Tokyo 113-8657,
Japan
| | - Takeshi Hayashi
- Agroinfomatics Division, NARO Agricultural Research Center (NARC),
3-1-1 Kannondai, Tsukuba, Ibaraki 305-8666,
Japan
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