1
|
Calderón L, Carbonell-Bejerano P, Muñoz C, Bree L, Sola C, Bergamin D, Tulle W, Gomez-Talquenca S, Lanz C, Royo C, Ibáñez J, Martinez-Zapater JM, Weigel D, Lijavetzky D. Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation. HORTICULTURE RESEARCH 2024; 11:uhae080. [PMID: 38766532 PMCID: PMC11101320 DOI: 10.1093/hr/uhae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/08/2024] [Indexed: 05/22/2024]
Abstract
To preserve their varietal attributes, established grapevine cultivars (Vitis vinifera L. ssp. vinifera) must be clonally propagated, due to their highly heterozygous genomes. Malbec is a France-originated cultivar appreciated for producing high-quality wines and is the offspring of cultivars Prunelard and Magdeleine Noire des Charentes. Here, we have built a diploid genome assembly of Malbec, after trio binning of PacBio long reads into the two haploid complements inherited from either parent. After haplotype-aware deduplication and corrections, complete assemblies for the two haplophases were obtained with a very low haplotype switch-error rate (<0.025). The haplophase alignment identified > 25% of polymorphic regions. Gene annotation including RNA-seq transcriptome assembly and ab initio prediction evidence resulted in similar gene model numbers for both haplophases. The annotated diploid assembly was exploited in the transcriptomic comparison of four clonal accessions of Malbec that exhibited variation in berry composition traits. Analysis of the ripening pericarp transcriptome using either haplophases as a reference yielded similar results, although some differences were observed. Particularly, among the differentially expressed genes identified only with the Magdeleine-inherited haplotype as reference, we observed an over-representation of hypothetically hemizygous genes. The higher berry anthocyanin content of clonal accession 595 was associated with increased abscisic acid responses, possibly leading to the observed overexpression of phenylpropanoid metabolism genes and deregulation of genes associated with abiotic stress response. Overall, the results highlight the importance of producing diploid assemblies to fully represent the genomic diversity of highly heterozygous woody crop cultivars and unveil the molecular bases of clonal phenotypic variation.
Collapse
Affiliation(s)
- Luciano Calderón
- Instituto de Biología Agrícola de Mendoza (CONICET-UNCuyo), Genetica y Genomica de Vid, Chacras de Coria 5505, Mendoza, Argentina
| | - Pablo Carbonell-Bejerano
- Instituto de Ciencias de la Vid y del Vino, ICVV, CSIC - Universidad de La Rioja - Gobierno de La Rioja, Logroño 26007, La Rioja, Spain
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Claudio Muñoz
- Instituto de Biología Agrícola de Mendoza (CONICET-UNCuyo), Genetica y Genomica de Vid, Chacras de Coria 5505, Mendoza, Argentina
- Facultad de Ciencias Agrarias (UNCuyo), Cátedra Fitopatología, Chacras de Coria 5505, Mendoza, Argentina
| | - Laura Bree
- Vivero Mercier Argentina, Perdriel 5500, Mendoza, Argentina
| | - Cristobal Sola
- Vivero Mercier Argentina, Perdriel 5500, Mendoza, Argentina
| | | | - Walter Tulle
- Instituto de Biología Agrícola de Mendoza (CONICET-UNCuyo), Genetica y Genomica de Vid, Chacras de Coria 5505, Mendoza, Argentina
| | - Sebastian Gomez-Talquenca
- Plant Virology Laboratory, Instituto Nacional de Tecnología Agropecuaria, Luján de Cuyo 5534, Mendoza, Argentina
| | - Christa Lanz
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Carolina Royo
- Instituto de Ciencias de la Vid y del Vino, ICVV, CSIC - Universidad de La Rioja - Gobierno de La Rioja, Logroño 26007, La Rioja, Spain
| | - Javier Ibáñez
- Instituto de Ciencias de la Vid y del Vino, ICVV, CSIC - Universidad de La Rioja - Gobierno de La Rioja, Logroño 26007, La Rioja, Spain
| | - José Miguel Martinez-Zapater
- Instituto de Ciencias de la Vid y del Vino, ICVV, CSIC - Universidad de La Rioja - Gobierno de La Rioja, Logroño 26007, La Rioja, Spain
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Diego Lijavetzky
- Instituto de Biología Agrícola de Mendoza (CONICET-UNCuyo), Genetica y Genomica de Vid, Chacras de Coria 5505, Mendoza, Argentina
| |
Collapse
|
2
|
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: 4] [Impact Index Per Article: 4.0] [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.
Collapse
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
| |
Collapse
|
3
|
Zou C, Sapkota S, Figueroa-Balderas R, Glaubitz J, Cantu D, Kingham BF, Sun Q, Cadle-Davidson L. A multitiered haplotype strategy to enhance phased assembly and fine mapping of a disease resistance locus. PLANT PHYSIOLOGY 2023; 193:2321-2336. [PMID: 37706526 DOI: 10.1093/plphys/kiad494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/10/2023] [Accepted: 08/17/2023] [Indexed: 09/15/2023]
Abstract
Fine mapping of quantitative trait loci (QTL) to dissect the genetic basis of traits of interest is essential to modern breeding practice. Here, we employed a multitiered haplotypic marker system to increase fine mapping accuracy by constructing a chromosome-level, haplotype-resolved parental genome, accurate detection of recombination sites, and allele-specific characterization of the transcriptome. In the first tier of this system, we applied the preexisting panel of 2,000 rhAmpSeq core genome markers that is transferable across the entire Vitis genus and provides a genomic resolution of 200 kb to 1 Mb. The second tier consisted of high-density haplotypic markers generated from Illumina skim sequencing data for samples enriched for relevant recombinations, increasing the potential resolution to hundreds of base pairs. We used this approach to dissect a novel Resistance to Plasmopara viticola-33 (RPV33) locus conferring resistance to grapevine downy mildew, narrowing the candidate region to only 0.46 Mb. In the third tier, we used allele-specific RNA-seq analysis to identify a cluster of 3 putative disease resistance RPP13-like protein 2 genes located tandemly in a nonsyntenic insertion as candidates for the disease resistance trait. In addition, combining the rhAmpSeq core genome haplotype markers and skim sequencing-derived high-density haplotype markers enabled chromosomal-level scaffolding and phasing of the grape Vitis × doaniana 'PI 588149' assembly, initially built solely from Pacific Biosciences (PacBio) high-fidelity (HiFi) reads, leading to the correction of 16 large-scale phasing errors. Our mapping strategy integrates high-density, phased genetic information with individual reference genomes to pinpoint the genetic basis of QTLs and will likely be widely adopted in highly heterozygous species.
Collapse
Affiliation(s)
- Cheng Zou
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Surya Sapkota
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA
- Grape Genetics Research Unit, USDA-ARS, Geneva, NY 14456, USA
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Jeff Glaubitz
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Brewster F Kingham
- DNA Sequencing & Genotyping Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - Qi Sun
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Lance Cadle-Davidson
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA
- Grape Genetics Research Unit, USDA-ARS, Geneva, NY 14456, USA
| |
Collapse
|
4
|
Sichel V, Sarah G, Girollet N, Laucou V, Roux C, Roques M, Mournet P, Cunff LL, Bert P, This P, Lacombe T. Chimeras in Merlot grapevine revealed by phased assembly. BMC Genomics 2023; 24:396. [PMID: 37452318 PMCID: PMC10347889 DOI: 10.1186/s12864-023-09453-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 06/09/2023] [Indexed: 07/18/2023] Open
Abstract
Chimerism is the phenomenon when several genotypes coexist in a single individual. Used to understand plant ontogenesis they also have been valorised through new cultivar breeding. Viticulture has been taking economic advantage out of chimeras when the variant induced an important modification of wine type such as berry skin colour. Crucial agronomic characters may also be impacted by chimeras that aren't identified yet. Periclinal chimera where the variant has entirely colonised a cell layer is the most stable and can be propagated through cuttings. In grapevine, leaves are derived from both meristem layers, L1 and L2. However, lateral roots are formed from the L2 cell layer only. Thus, comparing DNA sequences of roots and leaves allows chimera detection. In this study we used new generation Hifi long reads sequencing, recent bioinformatics tools and trio-binning with parental sequences to detect periclinal chimeras on 'Merlot' grapevine cultivar. Sequencing of cv. 'Magdeleine Noire des Charentes' and 'Cabernet Franc', the parents of cv. 'Merlot', allowed haplotype resolved assembly. Pseudomolecules were built with a total of 33 to 47 contigs and in few occasions a unique contig for one chromosome. This high resolution allowed haplotype comparison. Annotation was transferred from PN40024 VCost.v3 to all pseudomolecules. After strong selection of variants, 51 and 53 'Merlot' specific periclinal chimeras were found on the Merlot-haplotype-CF and Merlot-haplotype-MG respectively, 9 and 7 been located in a coding region. A subset of positions was analysed using Molecular Inversion Probes (MIPseq) and 69% were unambiguously validated, 25% are doubtful because of technological noise or weak depth and 6% invalidated. These results open new perspectives on chimera detection as an important resource to improve cultivars through clonal selection or breeding.
Collapse
Affiliation(s)
- V. Sichel
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398 France
| | - G. Sarah
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398 France
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier, F-34398 France
| | - N. Girollet
- EGFV, Université de Bordeaux, Bordeaux-Sciences Agro, INRAe, ISVV, 210 Chemin de Leysotte, F-33882 Villenave d’Ornon, France
| | - V. Laucou
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398 France
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier, F-34398 France
| | - C. Roux
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398 France
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier, F-34398 France
| | - M. Roques
- Institut Français de la Vigne et du Vin, Montpellier, F-34398 France
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier, F-34398 France
| | - P. Mournet
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398 France
- UMR AGAP Institut, CIRAD, Montpellier, F-34398 France
| | - L. Le Cunff
- Institut Français de la Vigne et du Vin, Montpellier, F-34398 France
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier, F-34398 France
| | - P.F. Bert
- EGFV, Université de Bordeaux, Bordeaux-Sciences Agro, INRAe, ISVV, 210 Chemin de Leysotte, F-33882 Villenave d’Ornon, France
| | - P. 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
| | - T. Lacombe
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398 France
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, Montpellier, F-34398 France
| |
Collapse
|
5
|
Shi X, Cao S, Wang X, Huang S, Wang Y, Liu Z, Liu W, Leng X, Peng Y, Wang N, Wang Y, Ma Z, Xu X, Zhang F, Xue H, Zhong H, Wang Y, Zhang K, Velt A, Avia K, Holtgräwe D, Grimplet J, Matus JT, Ware D, Wu X, Wang H, Liu C, Fang Y, Rustenholz C, Cheng Z, Xiao H, Zhou Y. The complete reference genome for grapevine ( Vitis vinifera L.) genetics and breeding. HORTICULTURE RESEARCH 2023; 10:uhad061. [PMID: 37213686 PMCID: PMC10199708 DOI: 10.1093/hr/uhad061] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/02/2023] [Indexed: 05/23/2023]
Abstract
Grapevine is one of the most economically important crops worldwide. However, the previous versions of the grapevine reference genome tipically consist of thousands of fragments with missing centromeres and telomeres, limiting the accessibility of the repetitive sequences, the centromeric and telomeric regions, and the study of inheritance of important agronomic traits in these regions. Here, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the cultivar PN40024 using PacBio HiFi long reads. The T2T reference genome (PN_T2T) is 69 Mb longer with 9018 more genes identified than the 12X.v0 version. We annotated 67% repetitive sequences, 19 centromeres and 36 telomeres, and incorporated gene annotations of previous versions into the PN_T2T assembly. We detected a total of 377 gene clusters, which showed associations with complex traits, such as aroma and disease resistance. Even though PN40024 derives from nine generations of selfing, we still found nine genomic hotspots of heterozygous sites associated with biological processes, such as the oxidation-reduction process and protein phosphorylation. The fully annotated complete reference genome therefore constitutes an important resource for grapevine genetic studies and breeding programs.
Collapse
Affiliation(s)
| | | | | | - Siyang Huang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Yue Wang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, China
| | - Zhongjie Liu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wenwen Liu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiangpeng Leng
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Yanling Peng
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Nan Wang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yiwen Wang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhiyao Ma
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiaodong Xu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Fan Zhang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hui Xue
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Haixia Zhong
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Yi Wang
- Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing 100093, China
| | - Kekun Zhang
- College of Enology, Northwest A&F University, Yangling 712100, China
| | - Amandine Velt
- SVQV, INRAE - University of Strasbourg, 68000 Colmar, France
| | - Komlan Avia
- SVQV, INRAE - University of Strasbourg, 68000 Colmar, France
| | - Daniela Holtgräwe
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Jérôme Grimplet
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), 50059 Zaragoza, Spain
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Systems Biotech Program, Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- USDA ARS NEA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA
| | - Xinyu Wu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Haibo Wang
- Fruit Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization), Ministry of Agriculture/Key Laboratory of Mineral Nutrition and Fertilizers Efficient Utilization of Deciduous Fruit Tree, Liaoning Province, Xingcheng 125100, China
| | - Chonghuai Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450004, China
| | - Yuling Fang
- College of Enology, Northwest A&F University, Yangling 712100, China
| | | | | | - Hua Xiao
- Corresponding authors: E-mail: ; ; ;
| | | |
Collapse
|
6
|
Tarquini G, Dall'Ara M, Ermacora P, Ratti C. Traditional Approaches and Emerging Biotechnologies in Grapevine Virology. Viruses 2023; 15:v15040826. [PMID: 37112807 PMCID: PMC10142720 DOI: 10.3390/v15040826] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
Environmental changes and global warming may promote the emergence of unknown viruses, whose spread is favored by the trade in plant products. Viruses represent a major threat to viticulture and the wine industry. Their management is challenging and mostly relies on prophylactic measures that are intended to prevent the introduction of viruses into vineyards. Besides the use of virus-free planting material, the employment of agrochemicals is a major strategy to prevent the spread of insect vectors in vineyards. According to the goal of the European Green Deal, a 50% decrease in the use of agrochemicals is expected before 2030. Thus, the development of alternative strategies that allow the sustainable control of viral diseases in vineyards is strongly needed. Here, we present a set of innovative biotechnological tools that have been developed to induce virus resistance in plants. From transgenesis to the still-debated genome editing technologies and RNAi-based strategies, this review discusses numerous illustrative studies that highlight the effectiveness of these promising tools for the management of viral infections in grapevine. Finally, the development of viral vectors from grapevine viruses is described, revealing their positive and unconventional roles, from targets to tools, in emerging biotechnologies.
Collapse
Affiliation(s)
- Giulia Tarquini
- Department of Agricultural, Environmental, Food and Animal Sciences (Di4A), University of Udine, 33100 Udine, Italy
| | - Mattia Dall'Ara
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, 40127 Bologna, Italy
| | - Paolo Ermacora
- Department of Agricultural, Environmental, Food and Animal Sciences (Di4A), University of Udine, 33100 Udine, Italy
| | - Claudio Ratti
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, 40127 Bologna, Italy
| |
Collapse
|
7
|
CRISPR/Cas9-Mediated Enrichment Coupled to Nanopore Sequencing Provides a Valuable Tool for the Precise Reconstruction of Large Genomic Target Regions. Int J Mol Sci 2023; 24:ijms24021076. [PMID: 36674592 PMCID: PMC9863143 DOI: 10.3390/ijms24021076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 01/09/2023] Open
Abstract
Complete and accurate identification of genetic variants associated with specific phenotypes can be challenging when there is a high level of genomic divergence between individuals in a study and the corresponding reference genome. We have applied the Cas9-mediated enrichment coupled to nanopore sequencing to perform a targeted de novo assembly and accurately reconstruct a genomic region of interest. This approach was used to reconstruct a 250-kbp target region on chromosome 5 of the common bean genome (Phaseolus vulgaris) associated with the shattering phenotype. Comparing a non-shattering cultivar (Midas) with the reference genome revealed many single-nucleotide variants and structural variants in this region. We cut five 50-kbp tiled sub-regions of Midas genomic DNA using Cas9, followed by sequencing on a MinION device and de novo assembly, generating a single contig spanning the whole 250-kbp region. This assembly increased the number of Illumina reads mapping to genes in the region, improving their genotypability for downstream analysis. The Cas9 tiling approach for target enrichment and sequencing is a valuable alternative to whole-genome sequencing for the assembly of ultra-long regions of interest, improving the accuracy of downstream genotype-phenotype association analysis.
Collapse
|
8
|
Nuzzo F, Gambino G, Perrone I. Unlocking grapevine in vitro regeneration: Issues and perspectives for genetic improvement and functional genomic studies. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 193:99-109. [PMID: 36343465 DOI: 10.1016/j.plaphy.2022.10.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
In vitro plant regeneration is a pivotal process in genetic engineering to obtain large numbers of transgenic, cisgenic and gene edited plants in the frame of functional gene or genetic improvement studies. However, several issues emerge as regeneration is not universally possible across the plant kingdom and many variables must be considered. In grapevine (Vitis spp.), as in other woody and fruit tree species, the regeneration process is impaired by a recalcitrance that depends on numerous factors such as genotype and explant-dependent responses. This is one of the major obstacles in developing gene editing approaches and functional genome studies in grapevine and it is therefore crucial to understand how to achieve efficient regeneration across different genotypes. Further issues that emerge in regeneration need to be addressed, such as somaclonal mutations which do not allow the regeneration of individuals identical to the original mother plant, an essential factor for commercial use of the improved grapevines obtained through the New Breeding Techniques. Over the years, the evolution of protocols to achieve plant regeneration has relied mainly on optimizing protocols for genotypes of interest whilst nowadays with new genomic data available there is an emerging opportunity to have a clearer picture of its molecular regulation. The goal of this review is to discuss the latest information available about different aspects of grapevine in vitro regeneration, to address the main factors that can impair the efficiency of the plant regeneration process and cause post-regeneration problems and to propose strategies for investigating and solving them.
Collapse
Affiliation(s)
- Floriana Nuzzo
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Strada Delle Cacce 73, 10135, Torino, Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Strada Delle Cacce 73, 10135, Torino, Italy.
| | - Irene Perrone
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Strada Delle Cacce 73, 10135, Torino, Italy
| |
Collapse
|