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Zhang W, Zeng Y, Jiao M, Ye C, Li Y, Liu C, Wang J. Integration of high-throughput omics technologies in medicinal plant research: The new era of natural drug discovery. FRONTIERS IN PLANT SCIENCE 2023; 14:1073848. [PMID: 36743502 PMCID: PMC9891177 DOI: 10.3389/fpls.2023.1073848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Medicinal plants are natural sources to unravel novel bioactive compounds to satisfy human pharmacological potentials. The world's demand for herbal medicines is increasing year by year; however, large-scale production of medicinal plants and their derivatives is still limited. The rapid development of modern technology has stimulated multi-omics research in medicinal plants, leading to a series of breakthroughs on key genes, metabolites, enzymes involved in biosynthesis and regulation of active compounds. Here, we summarize the latest research progress on the molecular intricacy of medicinal plants, including the comparison of genomics to demonstrate variation and evolution among species, the application of transcriptomics, proteomics and metabolomics to explore dynamic changes of molecular compounds, and the utilization of potential resources for natural drug discovery. These multi-omics research provide the theoretical basis for environmental adaptation of medicinal plants and allow us to understand the chemical diversity and composition of bioactive compounds. Many medicinal herbs' phytochemical constituents and their potential health benefits are not fully explored. Given their large diversity and global distribution as well as the impacts of growth duration and environmental factors on bioactive phytochemicals in medicinal plants, it is crucial to emphasize the research needs of using multi-omics technologies to address basic and applied problems in medicinal plants to aid in developing new and improved medicinal plant resources and discovering novel medicinal ingredients.
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Affiliation(s)
- Wenting Zhang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Engineering & Technology Research Center for Conservation and Utilization of the Genuine Southern Medicinal Resources, Guangzhou, China
| | - Yuan Zeng
- School of Plant and Environmental Sciences, Virginia Tech, VA, Blacksburg, United States
- Southern Piedmont Agricultural Research and Extension Center, Virginia Tech, VA, Blackstone, United States
| | - Meng Jiao
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Chanjuan Ye
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yanrong Li
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Chuanguang Liu
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jihua Wang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Engineering & Technology Research Center for Conservation and Utilization of the Genuine Southern Medicinal Resources, Guangzhou, China
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Castro MM, Rosa D, Ferro AM, Faustino A, Paulino A, Brás T, Machado E, Cruz CP, Belo ADF, Nozes P, Portugal J, Ramôa S, Mendonça D, Simões F, Duarte MF, Marum L. Genetic diversity and population structure of Cynara cardunculus L. in southern Portugal. PLoS One 2021; 16:e0252792. [PMID: 34106958 PMCID: PMC8189484 DOI: 10.1371/journal.pone.0252792] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 05/21/2021] [Indexed: 11/29/2022] Open
Abstract
Cynara cardunculus L. is a cardoon species native to the Mediterranean region, which is composed of three botanical taxa, each having distinct biological characteristics. The aim of this study was to examine wild populations of C. cardunculus established in Portugal, in order to determine their genetic diversity, geographic distribution, and population structure. Based on SSR markers, 121 individuals of C. cardunculus from 17 wild populations of the Portuguese Alentejo region were identified and analysed. Ten SSRs were found to be efficient markers in the genetic diversity analysis. The total number of alleles ranged from 9 to 17 per locus. The expected and observed means in heterozygosity, by population analysed, were 0.591 and 0.577, respectively. The wild population exhibited a high level of genetic diversity at the species level. The highest proportion of genetic variation was identified within a geographic group, while variation was lower among groups. Geographic areas having highest genetic diversity were identified in Alvito, Herdade da Abóboda, Herdade da Revilheira and Herdade de São Romão populations. Moreover, significant genetic differentiation existed between wild populations from North-Alentejo geographic locations (Arraiolos, Évora, Monte da Chaminé) and Centro Hortofrutícola, compared with other populations. This study reports genetic diversity among a representative number of wild populations and genotypes of C. cardunculus from Portugal. These results will provide valuable information towards future management of C. cardunculus germplasm.
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Affiliation(s)
- Maria Miguel Castro
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL)/Instituto Politécnico de Beja (IPBeja), Beja, Portugal
| | - Daniela Rosa
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL)/Instituto Politécnico de Beja (IPBeja), Beja, Portugal
- MED – Mediterranean Institute for Agriculture, Environment and Development – CEBAL, Beja, Portugal
| | - Ana M. Ferro
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL)/Instituto Politécnico de Beja (IPBeja), Beja, Portugal
- MED – Mediterranean Institute for Agriculture, Environment and Development – CEBAL, Beja, Portugal
| | - Ana Faustino
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL)/Instituto Politécnico de Beja (IPBeja), Beja, Portugal
- MED – Mediterranean Institute for Agriculture, Environment and Development – CEBAL, Beja, Portugal
| | - Ana Paulino
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL)/Instituto Politécnico de Beja (IPBeja), Beja, Portugal
- Centre for Ecology, Faculdade de Ciência, Evolution and Environmental Changes (cE3c), Universidade de Lisboa, Lisboa, Portugal
| | - Teresa Brás
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL)/Instituto Politécnico de Beja (IPBeja), Beja, Portugal
- LAQV/ REQUIMTE, FCT, Universidade Nova de Lisboa, Caparica, Portugal
| | - Eliana Machado
- MED-Instituto Mediterrâneo para a Agricultura, Ambiente e Desenvolvimento, Universidade de Évora, Ap 94, Évora, Portugal
| | - Carla Pinto Cruz
- Ambiente e Desenvolvimento & Departamento de Biologia, MED - Instituto Mediterrâneo para a Agricultura, Escola de Ciências e Tecnologia, Universidade de Évora, Ap 94, Évora, Portugal
| | - Anabela D. F. Belo
- Ambiente e Desenvolvimento & Departamento de Biologia, MED - Instituto Mediterrâneo para a Agricultura, Escola de Ciências e Tecnologia, Universidade de Évora, Ap 94, Évora, Portugal
| | - Paula Nozes
- Departamento de Biociências/Instituto Politécnico de Beja (IPBeja), Beja, Portugal
| | - João Portugal
- Departamento de Biociências/Instituto Politécnico de Beja (IPBeja), Beja, Portugal
- VALORIZA – Centro de Investigação para a Valorização dos Recursos Endógenos, Instituto Politécnico de Portalegre, Portalegre, Portugal
| | - Sofia Ramôa
- Departamento de Biociências/Instituto Politécnico de Beja (IPBeja), Beja, Portugal
| | - Diogo Mendonça
- Instituto Nacional de Investigação Agrária e Veterinária I.P. (INIAV IP), Unidade Estratégica de Biotecnologia e Recursos Genéticos, I.P., Oeiras, Portugal
| | - Fernanda Simões
- Instituto Nacional de Investigação Agrária e Veterinária I.P. (INIAV IP), Unidade Estratégica de Biotecnologia e Recursos Genéticos, I.P., Oeiras, Portugal
| | - Maria F. Duarte
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL)/Instituto Politécnico de Beja (IPBeja), Beja, Portugal
- MED – Mediterranean Institute for Agriculture, Environment and Development – CEBAL, Beja, Portugal
| | - Liliana Marum
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL)/Instituto Politécnico de Beja (IPBeja), Beja, Portugal
- MED – Mediterranean Institute for Agriculture, Environment and Development – CEBAL, Beja, Portugal
- * E-mail:
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Fate of Nitrogen from Artichoke (Cynara cardunculus L. var. scolymus (L.)) Crop Residues: A Review and Lysimeter Study. NITROGEN 2021. [DOI: 10.3390/nitrogen2010004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The goal of the European Nitrate Directive 91/676/CEE is to mitigate or prevent water pollution associated with the nitrogen (N) cascade. Vegetable crops have a high risk of nitrate leaching during autumn and winter. Information about the fate of N from artichoke (Cynara cardunculus L. var. scolymus (L.)) residues is reviewed and then supplemented with a three-year study with 15N-labelled residues in an artichoke-cauliflower (Brassica oleracea L. cv. botrytis) rotation in six lysimeters. After three years, 6% of N in artichoke residues was leached, 8% was exported by crops, while 86% remained in the lysimeter. Summed over the rotation, 16% of artichoke-residue N was absorbed by artichoke and 14% by cauliflower. Total aboveground N uptake by all crops during the entire rotation ranged from 370 to 534 kg N ha−1, of which 207–311 kg N ha−1 returned to the soil as residues. Increasing N-recycling efficiency and reducing the risk of N leaching while conserving crop productivity requires capturing N mineralized from soil organic N. Cauliflower performs this capture effectively during the drainage period. A break crop should be introduced after the first and second harvests of artichoke to further synchronize N mineralization and uptake and reduce leaching risk during the rotation.
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Sheeja TE, Kumar IPV, Giridhari A, Minoo D, Rajesh MK, Babu KN. Amplified Fragment Length Polymorphism: Applications and Recent Developments. Methods Mol Biol 2021; 2222:187-218. [PMID: 33301096 DOI: 10.1007/978-1-0716-0997-2_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
AFLP or amplified fragment length polymorphism is a PCR-based molecular technique that uses selective amplification of a subset of digested DNA fragments from any source to generate and compare unique fingerprints of genomes. It is more efficient in terms of time, economy, reproducibility, informativeness, resolution, and sensitivity, compared to other popular DNA markers. Besides, it requires very small quantities of DNA and no prior genome information. This technique is widely used in plants for taxonomy, genetic diversity, phylogenetic analysis, construction of high-resolution genetic maps, and positional cloning of genes, to determine relatedness among cultivars and varietal identity, etc. The review encompasses in detail the various applications of AFLP in plants and the major advantages and disadvantages. The review also considers various modifications of this technique and novel developments in detection of polymorphism. A wet-lab protocol is also provided.
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Affiliation(s)
- Thotten Elampilay Sheeja
- Indian Institute of Spices Research, Kozhikode, Kerala, India.
- Division of Crop Improvement and Biotechnology, ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, India.
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Pancaldi F, Trindade LM. Marginal Lands to Grow Novel Bio-Based Crops: A Plant Breeding Perspective. FRONTIERS IN PLANT SCIENCE 2020; 11:227. [PMID: 32194604 PMCID: PMC7062921 DOI: 10.3389/fpls.2020.00227] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/13/2020] [Indexed: 05/09/2023]
Abstract
The biomass demand to fuel a growing global bio-based economy is expected to tremendously increase over the next decades, and projections indicate that dedicated biomass crops will satisfy a large portion of it. The establishment of dedicated biomass crops raises huge concerns, as they can subtract land that is required for food production, undermining food security. In this context, perennial biomass crops suitable for cultivation on marginal lands (MALs) raise attraction, as they could supply biomass without competing for land with food supply. While these crops withstand marginal conditions well, their biomass yield and quality do not ensure acceptable economic returns to farmers and cost-effective biomass conversion into bio-based products, claiming genetic improvement. However, this is constrained by the lack of genetic resources for most of these crops. Here we first review the advantages of cultivating novel perennial biomass crops on MALs, highlighting management practices to enhance the environmental and economic sustainability of these agro-systems. Subsequently, we discuss the preeminent breeding targets to improve the yield and quality of the biomass obtainable from these crops, as well as the stability of biomass production under MALs conditions. These targets include crop architecture and phenology, efficiency in the use of resources, lignocellulose composition in relation to bio-based applications, and tolerance to abiotic stresses. For each target trait, we outline optimal ideotypes, discuss the available breeding resources in the context of (orphan) biomass crops, and provide meaningful examples of genetic improvement. Finally, we discuss the available tools to breed novel perennial biomass crops. These comprise conventional breeding methods (recurrent selection and hybridization), molecular techniques to dissect the genetics of complex traits, speed up selection, and perform transgenic modification (genetic mapping, QTL and GWAS analysis, marker-assisted selection, genomic selection, transformation protocols), and novel high-throughput phenotyping platforms. Furthermore, novel tools to transfer genetic knowledge from model to orphan crops (i.e., universal markers) are also conceptualized, with the belief that their development will enhance the efficiency of plant breeding in orphan biomass crops, enabling a sustainable use of MALs for biomass provision.
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Affiliation(s)
| | - Luisa M. Trindade
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
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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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7
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Wang L, Bao Y, Wang H, He C, Wang P, Sheng L, Tang Z. Slow stamen movement in a perennial herb decreases male-male and male-female interference. AOB PLANTS 2017; 9:plx018. [PMID: 28702163 PMCID: PMC5501957 DOI: 10.1093/aobpla/plx018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 05/30/2017] [Indexed: 06/07/2023]
Abstract
Approximately 80 % of angiosperm species produce hermaphroditic flowers, which face the problem of male-male sexual interference (one or more anthers gets in the way of disseminating pollen from other anthers) or male-female sexual interference (the pistil interferes with disseminating pollen from the anthers by preventing the anther from touching a pollinator, or the anther prevents pollinator from depositing outcross pollen on the stigma). Slow stamen movement in hermaphrodite flowers has been interpreted as an adaptation for reducing male-male sexual interference. Using slow stamen movement in Lychnis cognata (Caryophyllaceae), this study presents new evidence that this phenomenon can reduce both male-male and male-female sexual interference. Ten stamens in L. cognata flowers vertically elongated their filaments in two batches and displayed similar patterns in pollen dispensing. More importantly, 10 stamens bend out of the floral centre by curving the filament also in 2 batches and pollen grains located at the flower centre displayed the highest viability. Thus, three stages of stamen movement can be identified, comprising two male stages (M1 and M2) and one female stage (F). We found that the main pollinator for L. cognata, Bhutanitis yulongensis (Papilionodae) generally preferred M1 flowers. Manipulation experiments show that vertical stamen movement enabled the anthers to dehisce at different times to prolong the presentation of pollen grains. Horizontal movement of the stamen decreased both male-male and male-female interference. However, vertical stamen movement had a minor role in increasing amount of pollen received by the stigma. This study provides the first direct experimental evidence of concurrent male-male and male-female interference in a flower. We suggest that the selection pressure to reduce such interference might be a strong force in floral evolution. We also propose that other selective pressure, including pollen dispensing mechanisms, pollen longevity, pollinator behaviour and weather, might contribute to floral evolution.
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Affiliation(s)
- Lingyan Wang
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Jingyue Street 2555, Changchun 130024, China
| | - Yu Bao
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Jingyue Street 2555, Changchun 130024, China
| | - Hanxi Wang
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Jingyue Street 2555, Changchun 130024, China
| | - Chunguang He
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Jingyue Street 2555, Changchun 130024, China
| | - Ping Wang
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Jingyue Street 2555, Changchun 130024, China
| | - Lianxi Sheng
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Jingyue Street 2555, Changchun 130024, China
| | - Zhanhui Tang
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Jingyue Street 2555, Changchun 130024, China
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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 first genetic linkage map of Primulina eburnea (Gesneriaceae) based on EST-derived SNP markers. J Genet 2016; 95:377-82. [PMID: 27350682 DOI: 10.1007/s12041-016-0650-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Primulina eburnea is a promising candidate for domestication and floriculture, since it is easy to culture and has beautiful flowers. An F₂ population of 189 individuals was established for the construction of first-generation linkage maps based on expressed sequence tags-derived single-nucleotide polymorphism markers using the massARRAY genotyping platform. Of the 232 screened markers, 215 were assigned to 18 LG according to the haploid number of chromosomes in the species. The linkage map spanned a total of 3774.7 cM with an average distance of 17.6 cM between adjacent markers. This linkage map provides a framework for identification of important genes in breeding programmes.
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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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Huang HP, Li JC, Huang LQ, Wang DL, Huang P, Nie JS. The application of biotechnology in medicinal plants breeding research in China. Chin J Integr Med 2015; 21:551-60. [PMID: 25804198 DOI: 10.1007/s11655-015-2072-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Indexed: 11/29/2022]
Abstract
Breeding is not only an important area of medicinal plants research but also the foundation for the superior varieties acquirement of medicinal plants. The rise of modern biotechnology provides good opportunities and new means for medicinal plants breeding research in China. Biotechnology shows its technical advantages and new development prospects in breeding of new medicinal plants varieties with high and stable yield, good quality, as well as stress-resistance. In this paper, we describe recent advances, problems, and development prospects about the application of modern biotechnology in medicinal plants breeding research in China.
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Affiliation(s)
- He-Ping Huang
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230031, China
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12
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Development of Ty1-copia retrotransposon-based SSAP molecular markers for the study of genetic diversity in peach. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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13
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Alzohairy AM, Gyulai GB, Ramadan MF, Edris S, Sabir JSM, Jansen RK, Eissa HF, Bahieldin A. Retrotransposon-based molecular markers for assessment of genomic diversity. FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:781-789. [PMID: 32481032 DOI: 10.1071/fp13351] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 02/19/2014] [Indexed: 06/11/2023]
Abstract
Retrotransposons (RTs) are major components of most eukaryotic genomes. They are ubiquitous, dispersed throughout the genome, and their abundance correlates with genome size. Their copy-and-paste lifestyle in the genome consists of three molecular steps involving transcription of an RNA copy from the genomic RT, followed by reverse transcription to generate cDNA, and finally, reintegration into a new location in the genome. This process leads to new genomic insertions without excision of the original element. The target sites of insertions are relatively random and independent for different taxa; however, some elements cluster together in 'repeat seas' or have a tendency to cluster around the centromeres and telomeres. The structure and copy number of retrotransposon families are strongly influenced by the evolutionary history of the host genome. Molecular markers play an essential role in all aspects of genetics and genomics, and RTs represent a powerful tool compared with other molecular and morphological markers. All features of integration activity, persistence, dispersion, conserved structure and sequence motifs, and high copy number suggest that RTs are appropriate genomic features for building molecular marker systems. To detect polymorphisms for RTs, marker systems generally rely on the amplification of sequences between the ends of the RT, such as (long-terminal repeat)-retrotransposons and the flanking genomic DNA. Here, we review the utility of some commonly used PCR retrotransposon-based molecular markers, including inter-primer binding sequence (IPBS), sequence-specific amplified polymorphism (SSAP), retrotransposon-based insertion polymorphism (RBIP), inter retrotransposon amplified polymorphism (IRAP), and retrotransposon-microsatellite amplified polymorphism (REMAP).
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Affiliation(s)
- Ahmed M Alzohairy
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - G Bor Gyulai
- Institute of Genetics and Biotechnology, St. István University, Gödöll?, H-2103, Hungary
| | - Mohamed F Ramadan
- Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Sherif Edris
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Genomics and Biotechnology Section, Jeddah 21589, Saudi Arabia
| | - Jamal S M Sabir
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Genomics and Biotechnology Section, Jeddah 21589, Saudi Arabia
| | - Robert K Jansen
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Genomics and Biotechnology Section, Jeddah 21589, Saudi Arabia
| | - Hala F Eissa
- Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt
| | - Ahmed Bahieldin
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Genomics and Biotechnology Section, Jeddah 21589, Saudi Arabia
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Pandino G, Lombardo S, Moglia A, Portis E, Lanteri S, Mauromicale G. Leaf polyphenol profile and SSR-based fingerprinting of new segregant Cynara cardunculus genotypes. FRONTIERS IN PLANT SCIENCE 2014; 5:800. [PMID: 25653660 PMCID: PMC4300902 DOI: 10.3389/fpls.2014.00800] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 12/22/2014] [Indexed: 05/03/2023]
Abstract
The dietary value of many plant polyphenols lies in the protection given against degenerative pathologies. Their in planta role is associated with the host's defense response against biotic and abiotic stress. The polyphenol content of a given plant tissue is strongly influenced by the growing environment, but is also genetically determined. Plants belonging to the Cynara cardunculus species (globe artichoke and the cultivated and wild cardoon) accumulate substantial quantities of polyphenols mainly mono and di-caffeoylquinic acid (CQA) in their foliage. Transgressive segregation for CQA content in an F1 population bred from a cross between a globe artichoke and a cultivated cardoon led to the selection of eight segregants which accumulated more CQA in their leaves than did those of either of their parental genotypes. The selections were grown over two seasons to assess their polyphenol profile (CQAs, apigenin and luteolin derivatives and narirutin), and were also fingerprinted using a set of 217 microsatellite markers. The growing environment exerted a strong effect on polyphenol content, but two of the selections were able to accumulate up to an order of magnitude more CQA than either parent in both growing seasons. Since the species is readily vegetatively propagable, such genotypes can be straightforwardly exploited as a source of pharmaceutically valuable compounds, while their SSR-based fingerprinting will allow the genetic identity of clonally propagated material to be easily verified.
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Affiliation(s)
- Gaetano Pandino
- Dipartimento di Agricoltura, Alimentazione e Ambiente Università degli Studi di CataniaCatania, Italy
| | - Sara Lombardo
- Dipartimento di Agricoltura, Alimentazione e Ambiente Università degli Studi di CataniaCatania, Italy
| | - Andrea Moglia
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di TorinoGrugliasco, Italy
- *Correspondence: Andrea Moglia, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Italy e-mail:
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di TorinoGrugliasco, Italy
| | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di TorinoGrugliasco, Italy
| | - Giovanni Mauromicale
- Dipartimento di Agricoltura, Alimentazione e Ambiente Università degli Studi di CataniaCatania, Italy
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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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Genetic mapping and identification of QTL for earliness in the globe artichoke/cultivated cardoon complex. BMC Res Notes 2012; 5:252. [PMID: 22621324 PMCID: PMC3434057 DOI: 10.1186/1756-0500-5-252] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 05/10/2012] [Indexed: 11/18/2022] Open
Abstract
Background The Asteraceae species Cynara cardunculus (2n = 2x = 34) includes the two fully cross-compatible domesticated taxa globe artichoke (var. scolymus L.) and cultivated cardoon (var. altilis DC). As both are out-pollinators and suffer from marked inbreeding depression, linkage analysis has focussed on the use of a two way pseudo-test cross approach. Results A set of 172 microsatellite (SSR) loci derived from expressed sequence tag DNA sequence were integrated into the reference C. cardunculus genetic maps, based on segregation among the F1 progeny of a cross between a globe artichoke and a cultivated cardoon. The resulting maps each detected 17 major linkage groups, corresponding to the species’ haploid chromosome number. A consensus map based on 66 co-dominant shared loci (64 SSRs and two SNPs) assembled 694 loci, with a mean inter-marker spacing of 2.5 cM. When the maps were used to elucidate the pattern of inheritance of head production earliness, a key commercial trait, seven regions were shown to harbour relevant quantitative trait loci (QTL). Together, these QTL accounted for up to 74% of the overall phenotypic variance. Conclusion The newly developed consensus as well as the parental genetic maps can accelerate the process of tagging and eventually isolating the genes underlying earliness in both the domesticated C. cardunculus forms. The largest single effect mapped to the same linkage group in each parental maps, and explained about one half of the phenotypic variance, thus representing a good candidate for marker assisted selection.
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Scaglione D, Acquadro A, Portis E, Tirone M, Knapp SJ, Lanteri S. RAD tag sequencing as a source of SNP markers in Cynara cardunculus L. BMC Genomics 2012; 13:3. [PMID: 22214349 PMCID: PMC3269995 DOI: 10.1186/1471-2164-13-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2011] [Accepted: 01/03/2012] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The globe artichoke (Cynara cardunculus L. var. scolymus) genome is relatively poorly explored, especially compared to those of the other major Asteraceae crops sunflower and lettuce. No SNP markers are in the public domain. We have combined the recently developed restriction-site associated DNA (RAD) approach with the Illumina DNA sequencing platform to effect the rapid and mass discovery of SNP markers for C. cardunculus. RESULTS RAD tags were sequenced from the genomic DNA of three C. cardunculus mapping population parents, generating 9.7 million reads, corresponding to ~1 Gbp of sequence. An assembly based on paired ends produced ~6.0 Mbp of genomic sequence, separated into ~19,000 contigs (mean length 312 bp), of which ~21% were fragments of putative coding sequence. The shared sequences allowed for the discovery of ~34,000 SNPs and nearly 800 indels, equivalent to a SNP frequency of 5.6 per 1,000 nt, and an indel frequency of 0.2 per 1,000 nt. A sample of heterozygous SNP loci was mapped by CAPS assays and this exercise provided validation of our mining criteria. The repetitive fraction of the genome had a high representation of retrotransposon sequence, followed by simple repeats, AT-low complexity regions and mobile DNA elements. The genomic k-mers distribution and CpG rate of C. cardunculus, compared with data derived from three whole genome-sequenced dicots species, provided a further evidence of the random representation of the C. cardunculus genome generated by RAD sampling. CONCLUSION The RAD tag sequencing approach is a cost-effective and rapid method to develop SNP markers in a highly heterozygous species. Our approach permitted to generate a large and robust SNP datasets by the adoption of optimized filtering criteria.
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Affiliation(s)
- Davide Scaglione
- Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy
| | - Alberto Acquadro
- Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy
| | - Ezio Portis
- Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy
| | - Matteo Tirone
- Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy
| | - Steven J Knapp
- Institute for Plant Breeding, Genetics, and Genomics, University of Georgia, 111 Riverbend Rd., 30602 Athens, Georgia USA
| | - Sergio Lanteri
- Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy
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Sonnante G, Gatto A, Morgese A, Montemurro F, Sarli G, Blanco E, Pignone D. Genetic map of artichoke × wild cardoon: toward a consensus map for Cynara cardunculus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:1215-29. [PMID: 21800142 DOI: 10.1007/s00122-011-1661-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 07/09/2011] [Indexed: 05/07/2023]
Abstract
An integrated consensus linkage map is proposed for globe artichoke. Maternal and paternal genetic maps were constructed on the basis of an F(1) progeny derived from crossing an artichoke genotype (Mola) with its progenitor, the wild cardoon (Tolfa), using EST-derived SSRs, genomic SSRs, AFLPs, ten genes, and two morphological traits. For most genes, mainly belonging to the chlorogenic acid pathway, new markers were developed. Five of these were SNP markers analyzed through high-resolution melt technology. From the maternal (Mola) and paternal (Tolfa) maps, an integrated map was obtained, containing 337 molecular and one morphological markers ordered in 17 linkage groups (LGs), linked between Mola and Tolfa. The integrated map covers 1,488.8 cM, with an average distance of 4.4 cM between markers. The map was aligned with already existing maps for artichoke, and 12 LGs were linked via 31 bridge markers. LG numbering has been proposed. A total of 124 EST-SSRs and two genes were mapped here for the first time, providing a framework for the construction of a functional map in artichoke. The establishment of a consensus map represents a necessary condition to plan a complete sequencing of the globe artichoke genome.
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Affiliation(s)
- Gabriella Sonnante
- Institute of Plant Genetics, National Research Council, Via Amendola, 165/A, 70126, Bari, Italy.
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Kalendar R, Flavell AJ, Ellis THN, Sjakste T, Moisy C, Schulman AH. Analysis of plant diversity with retrotransposon-based molecular markers. Heredity (Edinb) 2010; 106:520-30. [PMID: 20683483 DOI: 10.1038/hdy.2010.93] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Retrotransposons are both major generators of genetic diversity and tools for detecting the genomic changes associated with their activity because they create large and stable insertions in the genome. After the demonstration that retrotransposons are ubiquitous, active and abundant in plant genomes, various marker systems were developed to exploit polymorphisms in retrotransposon insertion patterns. These have found applications ranging from the mapping of genes responsible for particular traits and the management of backcrossing programs to analysis of population structure and diversity of wild species. This review provides an insight into the spectrum of retrotransposon-based marker systems developed for plant species and evaluates the contributions of retrotransposon markers to the analysis of population diversity in plants.
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Affiliation(s)
- R Kalendar
- MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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GAO LX, LIU N, HUANG BH. Linkage Maps of the Genus Hedychium (Zingiberaceae) Based on SRAP. ACTA ACUST UNITED AC 2010. [DOI: 10.3724/sp.j.1143.2009.09036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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The linkage maps of Dendrobium species based on RAPD and SRAP markers. J Genet Genomics 2010; 37:197-204. [DOI: 10.1016/s1673-8527(09)60038-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Revised: 12/21/2009] [Accepted: 12/30/2009] [Indexed: 11/17/2022]
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Portis E, Mauromicale G, Mauro R, Acquadro A, Scaglione D, Lanteri S. Construction of a reference molecular linkage map of globe artichoke (Cynara cardunculus var. scolymus). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 120:59-70. [PMID: 19787331 DOI: 10.1007/s00122-009-1159-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Accepted: 09/11/2009] [Indexed: 05/07/2023]
Abstract
The genome organization of globe artichoke (Cynara cardunculus var. scolymus), unlike other species belonging to Asteraceae (=Compositae) family (i.e. sunflower, lettuce and chicory), remains largely unexplored. The species is highly heterozygous and suffers marked inbreeding depression when forced to self-fertilize. Thus a two-way pseudo-testcross represents the optimal strategy for linkage analysis. Here, we report linkage maps based on the progeny of a cross between globe artichoke (C. cardunculus var. scolymus) and cultivated cardoon (C. cardunculus var. altilis). The population was genotyped using a variety of PCR-based marker platforms, resulting in the identification of 708 testcross markers suitable for map construction. The male map consisted of 177 loci arranged in 17 major linkage groups, spanning 1,015.5 cM, while female map was built with 326 loci arranged into 20 major linkage groups, spanning 1,486.8 cM. The presence of 84 loci shared between these maps and those previously developed from a cross within globe artichoke allowed for map alignment and the definition of 17 homologous linkage groups, corresponding to the haploid number of the species. This will provide a favourable property for QTL scanning; furthermore, as 25 mapped markers (8%) correspond to coding regions, it has an additional value as functional map and might represent an important genetic tool for candidate gene studies in globe artichoke.
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Affiliation(s)
- E Portis
- DIVAPRA Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095, Grugliasco (Turin), Italy
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Scaglione D, Acquadro A, Portis E, Taylor CA, Lanteri S, Knapp SJ. Ontology and diversity of transcript-associated microsatellites mined from a globe artichoke EST database. BMC Genomics 2009; 10:454. [PMID: 19785740 PMCID: PMC2760586 DOI: 10.1186/1471-2164-10-454] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Accepted: 09/28/2009] [Indexed: 12/02/2022] Open
Abstract
Background The globe artichoke (Cynara cardunculus var. scolymus L.) is a significant crop in the Mediterranean basin. Despite its commercial importance and its both dietary and pharmaceutical value, knowledge of its genetics and genomics remains scant. Microsatellite markers have become a key tool in genetic and genomic analysis, and we have exploited recently acquired EST (expressed sequence tag) sequence data (Composite Genome Project - CGP) to develop an extensive set of microsatellite markers. Results A unigene assembly was created from over 36,000 globe artichoke EST sequences, containing 6,621 contigs and 12,434 singletons. Over 12,000 of these unigenes were functionally assigned on the basis of homology with Arabidopsis thaliana reference proteins. A total of 4,219 perfect repeats, located within 3,308 unigenes was identified and the gene ontology (GO) analysis highlighted some GO term's enrichments among different classes of microsatellites with respect to their position. Sufficient flanking sequence was available to enable the design of primers to amplify 2,311 of these microsatellites, and a set of 300 was tested against a DNA panel derived from 28 C. cardunculus genotypes. Consistent amplification and polymorphism was obtained from 236 of these assays. Their polymorphic information content (PIC) ranged from 0.04 to 0.90 (mean 0.66). Between 176 and 198 of the assays were informative in at least one of the three available mapping populations. Conclusion EST-based microsatellites have provided a large set of de novo genetic markers, which show significant amounts of polymorphism both between and within the three taxa of C. cardunculus. They are thus well suited as assays for phylogenetic analysis, the construction of genetic maps, marker-assisted breeding, transcript mapping and other genomic applications in the species.
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Affiliation(s)
- Davide Scaglione
- DiVaPRA Plant Genetics and Breeding, University of Torino, via L, da Vinci 44, 10095 Grugliasco, Torino, Italy.
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Moglia A, Comino C, Portis E, Acquadro A, De Vos RCH, Beekwilder J, Lanteri S. Isolation and mapping of a C3'H gene (CYP98A49) from globe artichoke, and its expression upon UV-C stress. PLANT CELL REPORTS 2009; 28:963-74. [PMID: 19301010 DOI: 10.1007/s00299-009-0695-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 02/10/2009] [Accepted: 03/01/2009] [Indexed: 05/04/2023]
Abstract
Globe artichoke represents a natural source of phenolic compounds with dicaffeoylquinic acids along with their biosynthetic precursor chlorogenic acid (5-caffeoylquinic acid) as the predominant molecules. We report the isolation and characterization of a full-length cDNA and promoter of a globe artichoke p-coumaroyl ester 3'-hydroxylase (CYP98A49), which is involved in both chlorogenic acid and lignin biosynthesis. Phylogenetic analyses demonstrated that this gene belongs to the CYP98 family. CYP98A49 was also heterologously expressed in yeast, in order to perform an enzymatic assay with p-coumaroylshikimate and p-coumaroylquinate as substrates. Real Time quantitative PCR analysis revealed that CYP98A49 expression is induced upon exposure to UV-C radiation. A single nucleotide polymorphism in the CYP98A49 gene sequence of two globe artichoke varieties used for genetic mapping allowed the localization of this gene to linkage group 10 within the previously developed maps.
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Affiliation(s)
- Andrea Moglia
- DiVaPRA, Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095, Grugliasco (TO), Italy
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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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Acquadro A, Falvo S, Mila S, Giuliano Albo A, Comino C, Moglia A, Lanteri S. Proteomics in globe artichoke: Protein extraction and sample complexity reduction by PEG fractionation. Electrophoresis 2009; 30:1594-602. [DOI: 10.1002/elps.200800549] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Comino C, Hehn A, Moglia A, Menin B, Bourgaud F, Lanteri S, Portis E. The isolation and mapping of a novel hydroxycinnamoyltransferase in the globe artichoke chlorogenic acid pathway. BMC PLANT BIOLOGY 2009; 9:30. [PMID: 19292932 PMCID: PMC2664813 DOI: 10.1186/1471-2229-9-30] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Accepted: 03/18/2009] [Indexed: 05/19/2023]
Abstract
BACKGROUND The leaves of globe artichoke and cultivated cardoon (Cynara cardunculus L.) have significant pharmaceutical properties, which mainly result from their high content of polyphenolic compounds such as monocaffeoylquinic and dicaffeoylquinic acid (DCQ), and a range of flavonoid compounds. RESULTS Hydroxycinnamoyl-CoA:quinate hydroxycinnamoyltransferase (HQT) encoding genes have been isolated from both globe artichoke and cultivated cardoon (GenBank accessions DQ915589 and DQ915590, respectively) using CODEHOP and PCR-RACE. A phylogenetic analysis revealed that their sequences belong to one of the major acyltransferase groups (anthranilate N-hydroxycinnamoyl/benzoyltransferase). The heterologous expression of globe artichoke HQT in E. coli showed that this enzyme can catalyze the esterification of quinic acid with caffeoyl-CoA or p-coumaroyl-CoA to generate, respectively, chlorogenic acid (CGA) and p-coumaroyl quinate. Real time PCR experiments demonstrated an increase in the expression level of HQT in UV-C treated leaves, and established a correlation between the synthesis of phenolic acids and protection against damage due to abiotic stress. The HQT gene, together with a gene encoding hydroxycinnamoyl-CoA:shikimate/quinate hydroxycinnamoyltransferase (HCT) previously isolated from globe artichoke, have been incorporated within the developing globe artichoke linkage maps. CONCLUSION A novel acyltransferase involved in the biosynthesis of CGA in globe artichoke has been isolated, characterized and mapped. This is a good basis for our effort to understand the genetic basis of phenylpropanoid (PP) biosynthesis in C. cardunculus.
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Affiliation(s)
- Cinzia Comino
- DiVaPRA Plant Genetics and Breeding, University of Torino 10095, Grugliasco (Torino), Italy
| | - Alain Hehn
- UMR 1121 Nancy Université (INPL)-INRA, Agronomie Environnement Nancy-Colmar 2 avenue de la Forêt de Haye 54505 Vandoeuvre-lès-Nancy, France
| | - Andrea Moglia
- DiVaPRA Plant Genetics and Breeding, University of Torino 10095, Grugliasco (Torino), Italy
| | - Barbara Menin
- DiVaPRA Plant Genetics and Breeding, University of Torino 10095, Grugliasco (Torino), Italy
| | - Frédéric Bourgaud
- UMR 1121 Nancy Université (INPL)-INRA, Agronomie Environnement Nancy-Colmar 2 avenue de la Forêt de Haye 54505 Vandoeuvre-lès-Nancy, France
| | - Sergio Lanteri
- DiVaPRA Plant Genetics and Breeding, University of Torino 10095, Grugliasco (Torino), Italy
| | - Ezio Portis
- DiVaPRA Plant Genetics and Breeding, University of Torino 10095, Grugliasco (Torino), Italy
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Abstract
Retrotransposons can be used as markers because their integration creates new joints between genomic DNA and their conserved ends. To detect polymorphisms for retrotransposon insertion, marker systems generally rely on PCR amplification between these ends and some component of flanking genomic DNA. We have developed two methods, retrotransposon-microsatellite amplified polymorphism (REMAP) analysis and inter-retrotransposon amplified polymorphism (IRAP) analysis, that require neither restriction enzyme digestion nor ligation to generate the marker bands. The IRAP products are generated from two nearby retrotransposons using outward-facing primers. In REMAP, amplification between retrotransposons proximal to simple sequence repeats (microsatellites) produces the marker bands. Here, we describe protocols for the IRAP and REMAP techniques, including methods for PCR amplification with a single primer or with two primers and for agarose gel electrophoresis of the product using optimal electrophoresis buffers and conditions. This protocol can be completed in 1-2 d.
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Affiliation(s)
- Ruslan Kalendar
- MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, P.O. Box 56, Viikinkaari 4, FIN-00014 Helsinki, Finland
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Acquadro A, Portis E, Moglia A, Magurno F, Lanteri S. Retrotransposon-based S-SAP as a platform for the analysis of genetic variation and linkage in globe artichoke. Genome 2006; 49:1149-59. [PMID: 17110995 DOI: 10.1139/g06-074] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A high copy number of retrotransposon sequences are present and widely dispersed in plant genomes. Their activity generates a considerable degree of sequence polymorphism. Here, we report the cloning of CYRE-5, a long-terminal repeat carrying retrotransposon-like sequence in Cynara cardunculus L., and its exploitation to develop a DNA fingerprinting assay across 22 accessions, including both cultivated (globe artichoke and cultivated cardoon) and wild (wild cardoon) types. The effectiveness of the sequence-specific amplified polymorphism (S-SAP) platform is compared with that of amplified fragment length polymorphism (AFLP). A genetic linkage analysis, based on a hybrid population between 2 globe artichoke varietal types, resulted in the inclusion of 29 S-SAP loci in the core genetic map, confirming their dispersed distribution across the globe artichoke genome.
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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, I-10095 Grugliasco (Turin), Italy
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