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Martina M, Zayas A, Portis E, Di Nardo G, Polli MF, Comino C, Gilardi G, Martin E, Acquadro A. The Dark Side of the pollen: BSA-seq identified genomic regions linked to male sterility in globe artichoke. BMC PLANT BIOLOGY 2024; 24:415. [PMID: 38760683 PMCID: PMC11100218 DOI: 10.1186/s12870-024-05119-z] [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: 12/13/2023] [Accepted: 05/08/2024] [Indexed: 05/19/2024]
Abstract
Globe artichoke (Cynara cardunculus var. scolymus; 2n = 2x = 34) is a food crop consumed for its immature flower heads. Traditionally, globe artichoke varietal types are vegetatively propagated. However, seed propagation makes it possible to treat the crop as annual, increasing field uniformity and reducing farmers costs, as well as pathogens diffusion. Despite globe artichoke's significant agricultural value and the critical role of heterosis in the development of superior varieties, the production of hybrids remains challenging without a reliable system for large-scale industrial seed production. Male sterility (MS) presents a promising avenue for overcoming these challenges by simplifying the hybridization process and enabling cost-effective seed production. However, within the Cynara genus, genic male sterility has been linked to three recessive loci in globe artichoke, with no definitive genetic mechanism elucidated to date. A 250 offsprings F2 population, derived from a cross between a MS globe artichoke and a male fertile (MF) cultivated cardoon (C. cardunculus var. altilis) and fitting a monogenic segregation model (3:1), was analyzed through BSA-seq, aiming at the identification of genomic regions/genes affecting male sterility. Four QTL regions were identified on chromosomes 4, 12, and 14. By analyzing the sequence around the highest pick on chromosome 14, a cytochrome P450 (CYP703A2) was identified, carrying a deleterious substitution (R/Q) fixed in the male sterile parent. A single dCAPS marker was developed around this SNP, allowing the discrimination between MS and MF genotypes within the population, suitable for applications in plant breeding programs. A 3D model of the protein was generated by homology modeling, revealing that the mutated amino acid is part of a highly conserved motif crucial for protein folding.
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Affiliation(s)
- Matteo Martina
- DISAFA, Plant Genetics and Breeding, University of Turin, Turin, Italy
| | - Aldana Zayas
- IICAR (Instituto de Investigaciones en Ciencias Agrarias de Rosario), CONICET, Campo Exp. J.F. Villarino, Zavalla, Santa Fe, Argentina
| | - Ezio Portis
- DISAFA, Plant Genetics and Breeding, University of Turin, Turin, Italy
| | - Giovanna Di Nardo
- DBIOS, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | | | - Cinzia Comino
- DISAFA, Plant Genetics and Breeding, University of Turin, Turin, Italy
| | - Gianfranco Gilardi
- DBIOS, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Eugenia Martin
- IICAR (Instituto de Investigaciones en Ciencias Agrarias de Rosario), CONICET, Campo Exp. J.F. Villarino, Zavalla, Santa Fe, Argentina.
| | - Alberto Acquadro
- DISAFA, Plant Genetics and Breeding, University of Turin, Turin, Italy.
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Alicandri E, Paolacci AR, Catarcione G, Del Lungo A, Iacoponi V, Pati F, Scarascia Mugnozza G, Ciaffi M. Morphological, Molecular, and Nutritional Characterisation of the Globe Artichoke Landrace "Carciofo Ortano". PLANTS (BASEL, SWITZERLAND) 2023; 12:1844. [PMID: 37176903 PMCID: PMC10180589 DOI: 10.3390/plants12091844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
The present study focused on the molecular, morphological, and nutritional characterisation of a globe artichoke landrace at risk of genetic erosion still cultivated in the municipality of Orte (Lazio Region, Central Italy) and therefore named "Carciofo Ortano". Molecular analysis based on SSR and ISSR markers was carried out on 73 genotypes selected at random from 20 smallholdings located in the Orte countryside and 17 accessions of landraces/clones belonging to the main varietal types cultivated in Italy. The results confirmed that "Carciofo Ortano" belongs to the "Romanesco" varietal typology and revealed the presence within the landrace of two distinct genetic populations named Orte 1 and Orte 2. Despite the high level of within-population genetic variation detected, the two populations were genetically differentiated from each other and from the landraces/clones of the main varietal types cultivated in Italy. Morphological and nutritional characterisation was performed on representative genotypes for each of the two populations of the "Carciofo Ortano" and the four landraces/clones included in the varietal platform of the PGI "CARCIOFO ROMANESCO DEL LAZIO" used as reference genotypes ("Campagnano", "Castellammare", "C3", and "Grato 1"). Principal component analysis showed that, of the 43 morphological descriptors considered, 12, including plant height, head shape index, head yield, and earliness, allowed a clear grouping of genotypes, distinguishing Orte 1 and Orte 2 populations from the reference genotypes. Regarding the nutritional composition of heads, particular attention should be devoted to the Orte 2 genotypes for their high dietary fibre, inulin, flavonoid, and phenol content, a feature that could be highly appreciated by the market.
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Affiliation(s)
- Enrica Alicandri
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100 Viterbo, Italy
| | - Anna Rita Paolacci
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100 Viterbo, Italy
| | - Giulio Catarcione
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100 Viterbo, Italy
| | - Alberto Del Lungo
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100 Viterbo, Italy
| | - Valentina Iacoponi
- Agenzia Regionale per lo Sviluppo e l’Innovazione dell’Agricoltura del Lazio (ARSIAL), Via Rodolfo Lanciani, 38, 00162 Rome, Italy
| | - Francesco Pati
- Agenzia Regionale per lo Sviluppo e l’Innovazione dell’Agricoltura del Lazio (ARSIAL), Via Rodolfo Lanciani, 38, 00162 Rome, Italy
| | - Giuseppe Scarascia Mugnozza
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100 Viterbo, Italy
| | - Mario Ciaffi
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100 Viterbo, Italy
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Spanò R, Fortunato S, Linsalata V, D’Antuono I, Cardinali A, de Pinto MC, Mascia T. Comparative Analysis of Bioactive Compounds in Two Globe Artichoke Ecotypes Sanitized and Non-Sanitized from Viral Infections. PLANTS (BASEL, SWITZERLAND) 2023; 12:1600. [PMID: 37111825 PMCID: PMC10145195 DOI: 10.3390/plants12081600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 06/19/2023]
Abstract
Globe artichoke ecotypes sanitized from plant pathogen infections are characterized by high vegetative vigor, productivity, and quality of capitula. The recent availability on the market of these plants has renewed the interest of farmers and pharmaceutical industries in the crop. Globe artichoke exhibits interesting nutraceutical properties due to the high content of health-promoting bioactive compounds (BACs), such as polyphenols, that could be extracted from waste biomass. The production of BACs depends on several factors including the plant portion considered, the globe artichoke variety/ecotype, and the physiological status of the plants, linked to biotic and abiotic stresses. We investigated the influence of viral infections on polyphenol accumulation in two Apulian late-flowering ecotypes "Locale di Mola tardivo" and "Troianella", comparing sanitized virus-free material (S) vs. naturally virus-infected (non-sanitized, NS) plants. Transcriptome analysis of the two ecotypes highlighted that differentially expressed genes (DEGs), in the two tested conditions, were mainly involved in primary metabolism and processing of genetic/environmental information. The up-regulation of the genes related to the biosynthesis of secondary metabolites and the analysis of peroxidase activity suggested that their modulation is influenced by the phytosanitary status of the plant and is ecotype-dependent. Conversely, the phytochemical analysis showed a remarkable decrease in polyphenols and lignin accumulation in S artichokes compared to NS plants. This unique study analyzes the potential of growing vigorous, sanitized plants, in order to have high amounts of 'soft and clean' biomass, finalized for BAC extraction for nutraceutical purposes. This, in turn, opens new perspectives for a circular economy of sanitized artichokes, in line with the current phytosanitary standards and sustainable development goals.
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Affiliation(s)
- Roberta Spanò
- Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy
| | - Stefania Fortunato
- Department of Bioscience, Biotechnology and Environment, University of Bari “Aldo Moro”, Via E. Orabona 4, 70124 Bari, Italy
| | - Vito Linsalata
- Institute of Science of Foods Production (ISPA), CNR Via Amendola 122/O, 70126 Bari, Italy
| | - Isabella D’Antuono
- Institute of Science of Foods Production (ISPA), CNR Via Amendola 122/O, 70126 Bari, Italy
| | - Angela Cardinali
- Institute of Science of Foods Production (ISPA), CNR Via Amendola 122/O, 70126 Bari, Italy
| | - Maria Concetta de Pinto
- Department of Bioscience, Biotechnology and Environment, University of Bari “Aldo Moro”, Via E. Orabona 4, 70124 Bari, Italy
| | - Tiziana Mascia
- Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy
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Pagliari S, Cannavacciuolo C, Celano R, Carabetta S, Russo M, Labra M, Campone L. Valorisation, Green Extraction Development, and Metabolomic Analysis of Wild Artichoke By-Product Using Pressurised Liquid Extraction UPLC-HRMS and Multivariate Data Analysis. Molecules 2022; 27:7157. [PMID: 36363983 PMCID: PMC9656714 DOI: 10.3390/molecules27217157] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 08/13/2023] Open
Abstract
Valorisation of food by-products has recently attracted considerable attention due to the opportunities to improve the economic and environmental sustainability of the food production chain. Large quantities of non-edible parts of the artichoke plant (Cynara cardunculus L.) comprising leaves, stems, roots, bracts, and seeds are discarded annually during industrial processing. These by-products contain many phytochemicals such as dietary fibres, phenolic acids, and flavonoids, whereby the most challenging issue concerns about the recovery of high-added value components from these by-products. The aim of this work is to develop a novel valorisation strategy for the sustainable utilisation of artichoke leaves' waste, combining green pressurised-liquid extraction (PLE), spectrophotometric assays and UPLC-HRMS phytochemical characterization, to obtain bioactive-rich extract with high antioxidant capacity. Multivariate analysis of the major selected metabolites was used to compare different solvent extraction used in PLE.
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Affiliation(s)
- Stefania Pagliari
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126 Milano, Italy
| | - Ciro Cannavacciuolo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126 Milano, Italy
| | - Rita Celano
- Department of Pharmacy, University of Salerno, Via Giovanni Paola II 132, Fisciano, 84084 Salerno, Italy
| | - Sonia Carabetta
- Safety and Sensoromic Laboratory (FoCuSS Lab), Department of Agriculture Science, Food Chemistry, University of Reggio Calabria, Via dell’Università 25, 89124 Reggio Calabria, Italy
| | - Mariateresa Russo
- Safety and Sensoromic Laboratory (FoCuSS Lab), Department of Agriculture Science, Food Chemistry, University of Reggio Calabria, Via dell’Università 25, 89124 Reggio Calabria, Italy
| | - Massimo Labra
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126 Milano, Italy
| | - Luca Campone
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126 Milano, Italy
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Seaweed Extract Improves Lagenaria siceraria Young Shoot Production, Mineral Profile and Functional Quality. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7120549] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Vegetable landraces represent the main source of biodiversity in Sicily. Lagenaria siceraria is appreciated by Southern Mediterranean consumers for its immature fruits and young shoots. Plant-based biostimulants supply, such as seaweed extract (SwE), is a contemporary and green agricultural practice applied to ameliorate the yield and quality of vegetables. However, there are no studies concerning the effects of SwE on L. siceraria. The current study evaluated the effects of SwE foliar application (0 or 3 mL L−1) on five L. siceraria landraces (G1, G2, G3, G4 and G5) grown in greenhouses. Growth traits, first female flower emission, fruit yield, young shoot yield, fruit firmness, young shoot nitrogen use efficiency (NUEys) and specific young shoot quality parameters, such as soluble solids content (SSC), mineral profile, ascorbic acid, and polyphenols, were appraised. Plant height and number of leaves at 10, 20 and 30 days after transplant (DAT) were significantly higher in plants treated with SwE as compared with untreated plants. Treating plants with SwE increased marketable fruit yield, fruit mean mass, young shoot yield and number of young shoots by 14.4%, 15.0%, 22.2%, 32.4%, and 32.0%, respectively as compared with untreated plants. Relevant increments were also recorded for NUEys, P, K, Ca, Mg, ascorbic acid and polyphenols concentration. SwE application did not significantly affect total yield and SSC. Furthermore, SwE treated plants produced a lower number of marketable fruits than non-treated plants. The present study showed that SwE at 3 mL L−1 can fruitfully enhance crop performance, young shoot yield and quality of L. siceraria.
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The Beneficial Health Effects of Vegetables and Wild Edible Greens: The Case of the Mediterranean Diet and Its Sustainability. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10249144] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The Mediterranean diet (MD) concept as currently known describes the dietary patterns that were followed in specific regions of the area in the 1950s and 1960s. The broad recognition of its positive effects on the longevity of Mediterranean populations also led to the adoption of this diet in other regions of the world, and scientific interest focused on revealing its health effects. MD is not only linked with eating specific nutritional food products but also with social, religious, environmental, and cultural aspects, thus representing a healthy lifestyle in general. However, modern lifestyles adhere to less healthy diets, alienating people from their heritage. Therefore, considering the increasing evidence of the beneficial health effects of adherence to the MD and the ongoing transitions in consumers’ behavior, the present review focuses on updating the scientific knowledge regarding this diet and its relevance to agrobiodiversity. In addition, it also considers a sustainable approach for new marketing opportunities and consumer trends of the MD.
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"Mind the Gap": Hi-C Technology Boosts Contiguity of the Globe Artichoke Genome in Low-Recombination Regions. G3-GENES GENOMES GENETICS 2020; 10:3557-3564. [PMID: 32817122 PMCID: PMC7534446 DOI: 10.1534/g3.120.401446] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Globe artichoke (Cynara cardunculus var. scolymus; 2n2x=34) is cropped largely in the Mediterranean region, being Italy the leading world producer; however, over time, its cultivation has spread to the Americas and China. In 2016, we released the first (v1.0) globe artichoke genome sequence (http://www.artichokegenome.unito.it/). Its assembly was generated using ∼133-fold Illumina sequencing data, covering 725 of the 1,084 Mb genome, of which 526 Mb (73%) were anchored to 17 chromosomal pseudomolecules. Based on v1.0 sequencing data, we generated a new genome assembly (v2.0), obtained from a Hi-C (Dovetail) genomic library, and which improves the scaffold N50 from 126 kb to 44.8 Mb (∼356-fold increase) and N90 from 29 kb to 17.8 Mb (∼685-fold increase). While the L90 of the v1.0 sequence included 6,123 scaffolds, the new v2.0 just 15 super-scaffolds, a number close to the haploid chromosome number of the species. The newly generated super-scaffolds were assigned to pseudomolecules using reciprocal blast procedures. The cumulative size of unplaced scaffolds in v2.0 was reduced of 165 Mb, increasing to 94% the anchored genome sequence. The marked improvement is mainly attributable to the ability of the proximity ligation-based approach to deal with both heterochromatic (e.g.: peri-centromeric) and euchromatic regions during the assembly procedure, which allowed to physically locate low recombination regions. The new high-quality reference genome enhances the taxonomic breadth of the data available for comparative plant genomics and led to a new accurate gene prediction (28,632 genes), thus promoting the map-based cloning of economically important genes.
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Pesce GR, Mauromicale G. Cynara cardunculus L.: Historical and Economic Importance, Botanical Descriptions, Genetic Resources and Traditional Uses. COMPENDIUM OF PLANT GENOMES 2019. [DOI: 10.1007/978-3-030-20012-1_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation. Sci Rep 2017; 7:5617. [PMID: 28717205 PMCID: PMC5514137 DOI: 10.1038/s41598-017-05085-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 05/24/2017] [Indexed: 11/12/2022] Open
Abstract
The genome sequence of globe artichoke (Cynara cardunculus L. var. scolymus, 2n = 2x = 34) is now available for use. A survey of C. cardunculus genetic resources is essential for understanding the evolution of the species, carrying out genetic studies and for application of breeding strategies. We report on the resequencing analyses (~35×) of four globe artichoke genotypes, representative of the core varietal types, as well as a genotype of the related taxa cultivated cardoon. The genomes were reconstructed at a chromosomal scale and structurally/functionally annotated. Gene prediction indicated a similar number of genes, while distinctive variations in miRNAs and resistance gene analogues (RGAs) were detected. Overall, 23,5 M SNP/indel were discovered (range 6,34 M –14,50 M). The impact of some missense SNPs on the biological functions of genes involved in the biosynthesis of phenylpropanoid and sesquiterpene lactone secondary metabolites was predicted. The identified variants contribute to infer on globe artichoke domestication of the different varietal types, and represent key tools for dissecting the path from sequence variation to phenotype. The new genomic sequences are fully searchable through independent Jbrowse interfaces (www.artichokegenome.unito.it), which allow the analysis of collinearity and the discovery of genomic variants, thus representing a one-stop resource for C. cardunculus genomics.
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Genetic diversity and accession structure in European Cynara cardunculus collections. PLoS One 2017; 12:e0178770. [PMID: 28570688 PMCID: PMC5453587 DOI: 10.1371/journal.pone.0178770] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/18/2017] [Indexed: 11/19/2022] Open
Abstract
Understanding the distribution of genetic variations and accession structures is an important factor for managing genetic resources, but also for using proper germplasm in association map analyses and breeding programs. The globe artichoke is the fourth most important horticultural crop in Europe. Here, we report the results of a molecular analysis of a collection including globe artichoke and leafy cardoon germplasm present in the Italian, French and Spanish gene banks. The aims of this study were to: (i) assess the diversity present in European collections, (ii) determine the population structure, (iii) measure the genetic distance between accessions; (iv) cluster the accessions; (v) properly distinguish accessions present in the different national collections carrying the same name; and (vi) understand the diversity distribution in relation to the gene bank and the geographic origin of the germplasm. A total of 556 individuals grouped into 174 accessions of distinct typologies were analyzed by different types of molecular markers, i.e. dominant (ISSR and AFLP) and co-dominant (SSR). The data of the two crops (globe artichoke and leafy cardoon) were analyzed jointly and separately to compute, among other aims, the gene diversity, heterozygosity (He, Ho), fixation indexes, AMOVA, genetic distance and structure. The findings underline the huge diversity present in the analyzed material, and the existence of alleles that are able to discriminate among accessions. The accessions were clustered not only on the basis of their typology, but also on the basis of the gene bank they come from. Probably, the environmental conditions of the different field gene banks affected germplasm conservation. These outcomes will be useful in plant breeding to select accessions and to fingerprint varieties. Moreover, the results highlight the particular attention that should be paid to the method used to conserve the Cynara cardunculus germplasm and suggest to the preference of using accessions from different gene banks to run an association map.
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A Genome-Wide Survey of the Microsatellite Content of the Globe Artichoke Genome and the Development of a Web-Based Database. PLoS One 2016; 11:e0162841. [PMID: 27648830 PMCID: PMC5029897 DOI: 10.1371/journal.pone.0162841] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 08/29/2016] [Indexed: 11/19/2022] Open
Abstract
The recently acquired genome sequence of globe artichoke (Cynara cardunculus var. scolymus) has been used to catalog the genome’s content of simple sequence repeat (SSR) markers. More than 177,000 perfect SSRs were revealed, equivalent to an overall density across the genome of 244.5 SSRs/Mbp, but some 224,000 imperfect SSRs were also identified. About 21% of these SSRs were complex (two stretches of repeats separated by <100 nt). Some 73% of the SSRs were composed of dinucleotide motifs. The SSRs were categorized for the numbers of repeats present, their overall length and were allocated to their linkage group. A total of 4,761 perfect and 6,583 imperfect SSRs were present in 3,781 genes (14.11% of the total), corresponding to an overall density across the gene space of 32,5 and 44,9 SSRs/Mbp for perfect and imperfect motifs, respectively. A putative function has been assigned, using the gene ontology approach, to the set of genes harboring at least one SSR. The same search parameters were applied to reveal the SSR content of 14 other plant species for which genome sequence is available. Certain species-specific SSR motifs were identified, along with a hexa-nucleotide motif shared only with the other two Compositae species (sunflower (Helianthus annuus) and horseweed (Conyza canadensis)) included in the study. Finally, a database, called “Cynara cardunculus MicroSatellite DataBase” (CyMSatDB) was developed to provide a searchable interface to the SSR data. CyMSatDB facilitates the retrieval of SSR markers, as well as suggested forward and reverse primers, on the basis of genomic location, genomic vs genic context, perfect vs imperfect repeat, motif type, motif sequence and repeat number. The SSR markers were validated via an in silico based PCR analysis adopting two available assembled transcriptomes, derived from contrasting globe artichoke accessions, as templates.
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The genome sequence of the outbreeding globe artichoke constructed de novo incorporating a phase-aware low-pass sequencing strategy of F1 progeny. Sci Rep 2016; 6:19427. [PMID: 26786968 PMCID: PMC4726258 DOI: 10.1038/srep19427] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 12/11/2015] [Indexed: 12/13/2022] Open
Abstract
Globe artichoke (Cynara cardunculus var. scolymus) is an out-crossing, perennial, multi-use crop species that is grown worldwide and belongs to the Compositae, one of the most successful Angiosperm families. We describe the first genome sequence of globe artichoke. The assembly, comprising of 13,588 scaffolds covering 725 of the 1,084 Mb genome, was generated using ~133-fold Illumina sequencing data and encodes 26,889 predicted genes. Re-sequencing (30×) of globe artichoke and cultivated cardoon (C. cardunculus var. altilis) parental genotypes and low-coverage (0.5 to 1×) genotyping-by-sequencing of 163 F1 individuals resulted in 73% of the assembled genome being anchored in 2,178 genetic bins ordered along 17 chromosomal pseudomolecules. This was achieved using a novel pipeline, SOILoCo (Scaffold Ordering by Imputation with Low Coverage), to detect heterozygous regions and assign parental haplotypes with low sequencing read depth and of unknown phase. SOILoCo provides a powerful tool for de novo genome analysis of outcrossing species. Our data will enable genome-scale analyses of evolutionary processes among crops, weeds, and wild species within and beyond the Compositae, and will facilitate the identification of economically important genes from related species.
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Scaglione D, Lanteri S, Acquadro A, Lai Z, Knapp SJ, Rieseberg L, Portis E. Large-scale transcriptome characterization and mass discovery of SNPs in globe artichoke and its related taxa. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:956-69. [PMID: 22849342 DOI: 10.1111/j.1467-7652.2012.00725.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Cynara cardunculus (2n = 2× = 34) is a member of the Asteraceae family that contributes significantly to the agricultural economy of the Mediterranean basin. The species includes two cultivated varieties, globe artichoke and cardoon, which are grown mainly for food. Cynara cardunculus is an orphan crop species whose genome/transcriptome has been relatively unexplored, especially in comparison to other Asteraceae crops. Hence, there is a significant need to improve its genomic resources through the identification of novel genes and sequence-based markers, to design new breeding schemes aimed at increasing quality and crop productivity. We report the outcome of cDNA sequencing and assembly for eleven accessions of C. cardunculus. Sequencing of three mapping parental genotypes using Roche 454-Titanium technology generated 1.7 × 10⁶ reads, which were assembled into 38,726 reference transcripts covering 32 Mbp. Putative enzyme-encoding genes were annotated using the KEGG-database. Transcription factors and candidate resistance genes were surveyed as well. Paired-end sequencing was done for cDNA libraries of eight other representative C. cardunculus accessions on an Illumina Genome Analyzer IIx, generating 46 × 10⁶ reads. Alignment of the IGA and 454 reads to reference transcripts led to the identification of 195,400 SNPs with a Bayesian probability exceeding 95%; a validation rate of 90% was obtained by Sanger-sequencing of a subset of contigs. These results demonstrate that the integration of data from different NGS platforms enables large-scale transcriptome characterization, along with massive SNP discovery. This information will contribute to the dissection of key agricultural traits in C. cardunculus and facilitate the implementation of marker-assisted selection programs.
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Aguirre-Dugua X, Eguiarte LE, González-Rodríguez A, Casas A. Round and large: morphological and genetic consequences of artificial selection on the gourd tree Crescentia cujete by the Maya of the Yucatan Peninsula, Mexico. ANNALS OF BOTANY 2012; 109:1297-306. [PMID: 22499854 PMCID: PMC3359923 DOI: 10.1093/aob/mcs068] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
BACKGROUND AND AIMS Artificial selection, the main driving force of domestication, depends on human perception of intraspecific variation and operates through management practices that drive morphological and genetic divergences with respect to wild populations. This study analysed the recognition of varieties of Crescentia cujete by Maya people in relation to preferred plant characters and documents ongoing processes of artificial selection influencing differential chloroplast DNA haplotype distribution in sympatric wild and home-garden populations. METHODS Fifty-three home gardens in seven villages (93 trees) and two putative wild populations (43 trees) were sampled. Through semi-structured interviews we documented the nomenclature of varieties, their distinctive characters, provenance, frequency and management. Phenotypic divergence of fruits was assessed with morphometric analyses. Genetic analyses were performed through five cpDNA microsatellites. KEY RESULTS The Maya recognize two generic (wild/domesticated) and two specific domesticated (white/green) varieties of Crescentia cujete. In home gardens, most trees (68 %) were from domesticated varieties while some wild individuals (32 %) were tolerated. Cultivation involves mainly vegetative propagation (76 %). Domesticated fruits were significantly rounder, larger and with thicker pericarp than wild fruits. Haplotype A was dominant in home gardens (76 %) but absent in wild populations. Haplotypes B-F were found common in the wild but at low frequency (24 %) in home gardens. CONCLUSIONS The gourd tree is managed through clonal and sexual propagules, fruit form and size being the main targets of artificial selection. Domesticated varieties belong to a lineage preserved by vegetative propagation but propagation by seeds and tolerance of spontaneous trees favour gene flow from wild populations. Five mutational steps between haplotypes A and D suggest that domesticated germplasm has been introduced to the region. The close relationship between Maya nomenclature and artificial selection has maintained the morphological and haplotypic identity (probably for centuries) of domesticated Crescentia despite gene flow from wild populations.
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Affiliation(s)
- Xitlali Aguirre-Dugua
- Centro de Investigaciones en Ecosistemas, Universidad Nacional Autónoma de México, campus Morelia, Apartado Postal 27-3 (Santa María de Guido), Morelia, Michoacán, 58190, México
| | - Luis E. Eguiarte
- Departamento de Biología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán, México, D. F. 04510, México
| | - Antonio González-Rodríguez
- Centro de Investigaciones en Ecosistemas, Universidad Nacional Autónoma de México, campus Morelia, Apartado Postal 27-3 (Santa María de Guido), Morelia, Michoacán, 58190, México
| | - Alejandro Casas
- Centro de Investigaciones en Ecosistemas, Universidad Nacional Autónoma de México, campus Morelia, Apartado Postal 27-3 (Santa María de Guido), Morelia, Michoacán, 58190, México
- For correspondence. E-mail
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Pandino G, Lombardo S, Mauromicale G. Chemical and morphological characteristics of new clones and commercial varieties of globe artichoke (Cynara cardunculus var. scolymus). PLANT FOODS FOR HUMAN NUTRITION (DORDRECHT, NETHERLANDS) 2011; 66:291-7. [PMID: 21792680 DOI: 10.1007/s11130-011-0247-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The globe artichoke is a widely consumed vegetable in the Mediterranean Basin, with Italy being the leading producer. In southern Italy, its cultivation contributes to local economic stability and social development. The producers are increasingly choosing to replace autochthonous varieties, such as 'Violetto di Sicilia', with cultivars bred or selected outside of the region, putting pressure on the maintenance of traditional varieties. Here, we have undertaken a detailed morphological and chemical analysis of a group of clones selected from a population of 'Violetto di Sicilia'. All the traits measured displayed genetic variation, particularly the total content of phenolics and minerals. The capitula of the 'Violetto di Sicilia' clones contained, on average, 6.3 g kg(-1) of fresh weight total phenolics, compared with 4.5 g kg(-1) in the two commercial varieties. The clones also had more inulin than commercial varieties (254 vs. 225 g kg(-1) of dry matter), as well as a good mineral content. The set of clones is of interest in the context of the proposed improvement of the crop through breeding and selection of genotypes with high nutritional quality and a specific end-use (industrial processing or fresh consumption).
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Affiliation(s)
- Gaetano Pandino
- Dipartimento di Scienze delle Produzioni Agrarie e Alimentari, Università degli Studi di Catania, Catania, Italy
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Sarwat M, Nabi G, Das S, Srivastava PS. Molecular markers in medicinal plant biotechnology: past and present. Crit Rev Biotechnol 2011; 32:74-92. [DOI: 10.3109/07388551.2011.551872] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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17
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Acquadro A, Lanteri S, Scaglione D, Arens P, Vosman B, Portis E. Genetic mapping and annotation of genomic microsatellites isolated from globe artichoke. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 118:1573-87. [PMID: 19326092 DOI: 10.1007/s00122-009-1005-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2008] [Accepted: 03/08/2009] [Indexed: 05/14/2023]
Abstract
Cynara cardunculus includes three taxa, the globe artichoke (subsp. scolymus L. Hegi), the cultivated cardoon (var. altilis) and their progenitor, the wild cardoon (var. sylvestris). Globe artichoke is an important component of the Mediterranean rural economy, but its improvement through breeding has been rather limited and its genome organization remains largely unexplored. Here, we report the isolation of 61 new microsatellite loci which amplified a total of 208 alleles in a panel of 22 C. cardunculus genotypes. Of these, 51 were informative for linkage analysis and 39 were used to increase marker density in the available globe artichoke genetic maps. Sequence analysis of the 22 loci associated with genes showed that 9 are located within coding sequence, with the repetitive domain probably being involved in DNA binding or in protein-protein interactions. The expression of the genes associated with 9 of the 22 microsatellite loci was demonstrated by RT-PCR.
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Affiliation(s)
- Alberto Acquadro
- Di.Va.P.R.A. Plant Genetics and Breeding, University of Turin, via L. da Vinci 44, 10095, Grugliasco, Turin, Italy
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