1
|
Depecker J, Verleysen L, Asimonyio JA, Hatangi Y, Kambale JL, Mwanga Mwanga I, Ebele T, Dhed'a B, Bawin Y, Staelens A, Stoffelen P, Ruttink T, Vandelook F, Honnay O. Genetic diversity and structure in wild Robusta coffee (Coffea canephora A. Froehner) populations in Yangambi (DR Congo) and their relation to forest disturbance. Heredity (Edinb) 2023; 130:145-153. [PMID: 36596880 PMCID: PMC9981769 DOI: 10.1038/s41437-022-00588-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 01/05/2023] Open
Abstract
Degradation and regeneration of tropical forests can strongly affect gene flow in understorey species, resulting in genetic erosion and changes in genetic structure. Yet, these processes remain poorly studied in tropical Africa. Coffea canephora is an economically important species, found in the understorey of tropical rainforests of Central and West Africa, and the genetic diversity harboured in its wild populations is vital for sustainable coffee production worldwide. Here, we aimed to quantify genetic diversity, genetic structure, and pedigree relations in wild C. canephora populations, and we investigated associations between these descriptors and forest disturbance and regeneration. Therefore, we sampled 256 C. canephora individuals within 24 plots across three forest categories in Yangambi (DR Congo), and used genotyping-by-sequencing to identify 18,894 SNPs. Overall, we found high genetic diversity, and no evidence of genetic erosion in C. canephora in disturbed old-growth forest, as compared to undisturbed old-growth forest. In addition, an overall heterozygosity excess was found in all populations, which was expected for a self-incompatible species. Genetic structure was mainly a result of isolation-by-distance, reflecting geographical location, with low to moderate relatedness at finer scales. Populations in regrowth forest had lower allelic richness than populations in old-growth forest and were characterised by a lower inter-individual relatedness and a lack of isolation-by-distance, suggesting that they originated from different neighbouring populations and were subject to founder effects. Wild Robusta coffee populations in the study area still harbour high levels of genetic diversity, yet careful monitoring of their response to ongoing forest degradation remains required.
Collapse
Affiliation(s)
- Jonas Depecker
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium.
- Meise Botanic Garden, Meise, Belgium.
- KU Leuven Plant Institute, Leuven, Belgium.
| | - Lauren Verleysen
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium.
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium.
| | - Justin A Asimonyio
- Centre de Surveillance de la Biodiversité et Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Yves Hatangi
- Meise Botanic Garden, Meise, Belgium
- Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Jean-Léon Kambale
- Centre de Surveillance de la Biodiversité et Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Ithe Mwanga Mwanga
- Centre de Recherche en Science Naturelles, Lwiro, Democratic Republic of the Congo
| | - Tshimi Ebele
- Institut National des Etudes et Recherches, Agronomique, Democratic Republic of the Congo
| | - Benoit Dhed'a
- Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Yves Bawin
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | - Ariane Staelens
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | | | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | - Filip Vandelook
- Meise Botanic Garden, Meise, Belgium
- KU Leuven Plant Institute, Leuven, Belgium
| | - Olivier Honnay
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- KU Leuven Plant Institute, Leuven, Belgium
| |
Collapse
|
2
|
Alkimim ER, Caixeta ET, Sousa TV, Gois IB, Lopes da Silva F, Sakiyama NS, Zambolim L, Alves RS, de Resende MDV. Designing the best breeding strategy for Coffea canephora: Genetic evaluation of pure and hybrid individuals aiming to select for productivity and disease resistance traits. PLoS One 2021; 16:e0260997. [PMID: 34965248 PMCID: PMC8716045 DOI: 10.1371/journal.pone.0260997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/20/2021] [Indexed: 12/03/2022] Open
Abstract
Breeding programs of the species Coffea canephora rely heavily on the significant genetic variability between and within its two varietal groups (conilon and robusta). The use of hybrid families and individuals has been less common. The objectives of this study were to evaluate parents and families from the populations of conilon, robusta, and its hybrids and to define the best breeding and selection strategies for productivity and disease resistance traits. As such, 71 conilon clones, 56 robusta clones, and 20 hybrid families were evaluated over several years for the following traits: vegetative vigor, incidence of rust and cercosporiosis, fruit ripening time, fruit size, plant height, canopy diameter, and yield per plant. Components of variance and genetic parameters were estimated via residual maximum likelihood (REML) and genotypic values were predicted via best linear unbiased prediction (BLUP). Genetic variability among parents (clones) and hybrid families was detected for most of the evaluated traits. The Mulamba-Rank index suggests potential gains up to 17% for the genotypic aggregate of traits in the hybrid population. An intrapopulation recurrent selection within the hybrid population would be the best breeding strategy because the genetic variability, narrow and broad senses heritabilities and selective accuracies for important traits were maximized in the crossed population. Besides, such strategy is simple, low cost and quicker than the concurrent reciprocal recurrent selection in the two parental populations, and this maximizes the genetic gain for unit of time.
Collapse
Affiliation(s)
| | - Eveline Teixeira Caixeta
- Brazilian Agricultural Research Corporation—Embrapa Café, Viçosa, MG, Brazil
- * E-mail: (ETC); (MDVR)
| | | | | | | | | | | | - Rodrigo Silva Alves
- National Institute of Coffee Science and Technology—INCT Café, Lavras, MG, Brazil
| | | |
Collapse
|
3
|
From Plantation to Cup: Changes in Bioactive Compounds during Coffee Processing. Foods 2021; 10:foods10112827. [PMID: 34829108 PMCID: PMC8620865 DOI: 10.3390/foods10112827] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 11/17/2022] Open
Abstract
Coffee is consumed not just for its flavor, but also for its health advantages. The quality of coffee beverages is affected by a number of elements and a series of processes, including: the environment, cultivation, post-harvest, fermentation, storage, roasting, and brewing to produce a cup of coffee. The chemical components of coffee beans alter throughout this procedure. The purpose of this article is to present information about changes in chemical components and bioactive compounds in coffee during preharvest and postharvest. The selection of the appropriate cherry maturity level is the first step in the coffee manufacturing process. The coffee cherry has specific flavor-precursor components and other chemical components that become raw materials in the fermentation process. During the fermentation process, there are not many changes in the phenolic or other bioactive components of coffee. Metabolites fermented by microbes diffuse into the seeds, which improves their quality. A germination process occurs during wet processing, which increases the quantity of amino acids, while the dry process induces an increase in non-protein amino acid γ-aminobutyric acid (GABA). In the roasting process, there is a change in the aroma precursors from the phenolic compounds, especially chlorogenic acid, amino acids, and sugars found in coffee beans, to produce a distinctive coffee taste.
Collapse
|
4
|
Homeologous regulation of Frigida-like genes provides insights on reproductive development and somatic embryogenesis in the allotetraploid Coffea arabica. Sci Rep 2019; 9:8446. [PMID: 31186437 PMCID: PMC6560031 DOI: 10.1038/s41598-019-44666-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 05/22/2019] [Indexed: 01/10/2023] Open
Abstract
Coffea arabica is an allotetraploid of high economic importance. C. arabica transcriptome is a combination of the transcripts of two parental genomes (C. eugenioides and C. canephora) that gave rise to the homeologous genes of the species. Previous studies have reported the transcriptional dynamics of C. arabica. In these reports, the ancestry of homeologous genes was identified and the overall regulation of homeologous differential expression (HDE) was explored. One of these genes is part of the FRIGIDA-like family (FRL), which includes the Arabidopsis thaliana flowering-time regulation protein, FRIGIDA (FRI). As nonfunctional FRI proteins give rise to rapid-cycling summer annual ecotypes instead of vernalization-responsive winter-annuals, allelic variation in FRI can modulate flowering time in A. thaliana. Using bioinformatics, genomic analysis, and the evaluation of gene expression of homeologs, we characterized the FRL gene family in C. arabica. Our findings indicate that C. arabica expresses 10 FRL homeologs, and that, throughout flower and fruit development, these genes are differentially transcribed. Strikingly, in addition to confirming the expression of FRL genes during zygotic embryogenesis, we detected FRL expression during direct somatic embryogenesis, a novel finding regarding the FRL gene family. The HDE profile of FRL genes suggests an intertwined homeologous gene regulation. Furthermore, we observed that FLC gene of C. arabica has an expression profile similar to that of CaFRL genes.
Collapse
|
5
|
Tran HT, Lee LS, Furtado A, Smyth H, Henry RJ. Advances in genomics for the improvement of quality in coffee. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2016; 96:3300-3312. [PMID: 26919810 DOI: 10.1002/jsfa.7692] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 02/08/2016] [Accepted: 02/23/2016] [Indexed: 06/05/2023]
Abstract
Coffee is an important crop that provides a livelihood to millions of people living in developing countries. Production of genotypes with improved coffee quality attributes is a primary target of coffee genetic improvement programmes. Advances in genomics are providing new tools for analysis of coffee quality at the molecular level. The recent report of a genomic sequence for robusta coffee, Coffea canephora, is a major development. However, a reference genome sequence for the genetically more complex arabica coffee (C. arabica) will also be required to fully define the molecular determinants controlling quality in coffee produced from this high quality coffee species. Genes responsible for control of the levels of the major biochemical components in the coffee bean that are known to be important in determining coffee quality can now be identified by association analysis. However, the narrow genetic base of arabica coffee suggests that genomics analysis of the wild relatives of coffee (Coffea spp.) may be required to find the phenotypic diversity required for effective association genetic analysis. The genomic resources available for the study of coffee quality are described and the potential for the application of next generation sequencing and association genetic analysis to advance coffee quality research are explored. © 2016 Society of Chemical Industry.
Collapse
Affiliation(s)
- Hue Tm Tran
- Queensland Alliance for Agri culture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Queensland, Australia
- Western Highlands Agriculture & Forestry Science Institute (WASI), Daklak, Vietnam
| | - L Slade Lee
- Southern Cross University, East Lismore, NSW 2480, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agri culture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Queensland, Australia
| | - Heather Smyth
- Queensland Alliance for Agri culture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Queensland, Australia
| | - Robert J Henry
- Queensland Alliance for Agri culture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Queensland, Australia
| |
Collapse
|
6
|
Abstract
Coffee (Coffea sp.) is a perennial plant widely cultivated in many tropical countries. It is a cash crop for millions of small farmers in these areas. As for other tree species, coffee has long breeding cycles, which makes conventional breeding programs time-consuming. For that matter, genetic transformation can be an effective way to introduce a desired trait in elite varieties or for functional genomics. In this chapter, we describe two highly efficient and reliable Agrobacterium-mediated transformation techniques developed for the C. arabica cultivated species: (1) A. tumefaciens to study and introduce genes conferring resistance/tolerance to biotic (coffee leaf rust, insects) and abiotic stress (drought, heat, seed desiccation) in fully transformed plants and (2) A. rhizogenes to study candidate gene expression for nematode resistance in transformed roots.
Collapse
Affiliation(s)
- Eveline Déchamp
- CIRAD, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR RPB, 911 Avenue Agropolis, BP 64501, 34398, Montpellier, France
| | | | | | | |
Collapse
|
7
|
Leroy T, De Bellis F, Legnate H, Musoli P, Kalonji A, Loor Solórzano RG, Cubry P. Developing core collections to optimize the management and the exploitation of diversity of the coffee Coffea canephora. Genetica 2014; 142:185-99. [PMID: 24792040 DOI: 10.1007/s10709-014-9766-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 04/25/2014] [Indexed: 01/21/2023]
Abstract
The management of diversity for conservation and breeding is of great importance for all plant species and is particularly true in perennial species, such as the coffee Coffea canephora. This species exhibits a large genetic and phenotypic diversity with six different diversity groups. Large field collections are available in the Ivory Coast, Uganda and other Asian, American and African countries but are very expensive and time consuming to establish and maintain in large areas. We propose to improve coffee germplasm management through the construction of genetic core collections derived from a set of 565 accessions that are characterized with 13 microsatellite markers. Core collections of 12, 24 and 48 accessions were defined using two methods aimed to maximize the allelic diversity (Maximization strategy) or genetic distance (Maximum-Length Sub-Tree method). A composite core collection of 77 accessions is proposed for both objectives of an optimal management of diversity and breeding. This core collection presents a gene diversity value of 0.8 and exhibits the totality of the major alleles (i.e., 184) that are present in the initial set. The seven proposed core collections constitute a valuable tool for diversity management and a foundation for breeding programs. The use of these collections for collection management in research centers and breeding perspectives for coffee improvement are discussed.
Collapse
|
8
|
Cação SMB, Silva NV, Domingues DS, Vieira LGE, Diniz LEC, Vinecky F, Alves GSC, Andrade AC, Carpentieri-Pipolo V, Pereira LFP. Construction and characterization of a BAC library from the Coffea arabica genotype Timor Hybrid CIFC 832/2. Genetica 2013; 141:217-26. [PMID: 23677718 DOI: 10.1007/s10709-013-9720-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 05/02/2013] [Indexed: 10/26/2022]
Abstract
Most of the world's coffee production originates from Coffea arabica, an allotetraploid species with low genetic diversity and for which few genomic resources are available. Genomic libraries with large DNA fragment inserts are useful tools for the study of plant genomes, including the production of physical maps, integration studies of physical and genetic maps, genome structure analysis and gene isolation by positional cloning. Here, we report the construction and characterization of a Bacterial Artificial Chromosome (BAC) library from C. arabica Timor Hybrid CIFC 832/2, a parental genotype for several modern coffee cultivars. The BAC library consists of 56,832 clones with an average insert size of 118 kb, which represents a dihaploid genome coverage of five to sixfold. The content of organellar DNA was estimated at 1.04 and 0.5 % for chloroplast and mitochondrial DNA, respectively. The BAC library was screened for the NADPH-dependent mannose-6-phosphate reductase gene (CaM6PR) with markers positioned on four linkage groups of a partial C. arabica genetic map. A mixed approach using PCR and membrane hybridization of BAC pools allowed for the discovery of nine BAC clones with the CaM6PR gene and 53 BAC clones that were anchored to the genetic map with simple sequence repeat markers. This library will be a useful tool for future studies on comparative genomics and the identification of genes and regulatory elements controlling major traits in this economically important crop species.
Collapse
Affiliation(s)
- S M B Cação
- Laboratory of Plant Biotechnology, Instituto Agronomico do Paraná, CP 481 Londrina, Paraná 86001-970, Brazil
| | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Recent advances in the genetic transformation of coffee. BIOTECHNOLOGY RESEARCH INTERNATIONAL 2012; 2012:580857. [PMID: 22970380 PMCID: PMC3437269 DOI: 10.1155/2012/580857] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 06/18/2012] [Accepted: 06/28/2012] [Indexed: 12/29/2022]
Abstract
Coffee is one of the most important plantation crops, grown in about 80 countries across the world. The genus Coffea comprises approximately 100 species of which only two species, that is, Coffea arabica (commonly known as arabica coffee) and Coffea canephora (known as robusta coffee), are commercially cultivated. Genetic improvement of coffee through traditional breeding is slow due to the perennial nature of the plant. Genetic transformation has tremendous potential in developing improved coffee varieties with desired agronomic traits, which are otherwise difficult to achieve through traditional breeding. During the last twenty years, significant progress has been made in coffee biotechnology, particularly in the area of transgenic technology. This paper provides a detailed account of the advances made in the genetic transformation of coffee and their potential applications.
Collapse
|
10
|
Marraccini P, Vinecky F, Alves GS, Ramos HJ, Elbelt S, Vieira NG, Carneiro FA, Sujii PS, Alekcevetch JC, Silva VA, DaMatta FM, Ferrão MA, Leroy T, Pot D, Vieira LG, da Silva FR, Andrade AC. Differentially expressed genes and proteins upon drought acclimation in tolerant and sensitive genotypes of Coffea canephora. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:4191-212. [PMID: 22511801 PMCID: PMC3398449 DOI: 10.1093/jxb/ers103] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The aim of this study was to investigate the molecular mechanisms underlying drought acclimation in coffee plants by the identification of candidate genes (CGs) using different approaches. The first approach used the data generated during the Brazilian Coffee expressed sequence tag (EST) project to select 13 CGs by an in silico analysis (electronic northern). The second approach was based on screening macroarrays spotted with plasmid DNA (coffee ESTs) with separate hybridizations using leaf cDNA probes from drought-tolerant and susceptible clones of Coffea canephora var. Conilon, grown under different water regimes. This allowed the isolation of seven additional CGs. The third approach used two-dimensional gel electrophoresis to identify proteins displaying differential accumulation in leaves of drought-tolerant and susceptible clones of C. canephora. Six of them were characterized by MALDI-TOF-MS/MS (matrix-assisted laser desorption-time of flight-tandem mass spectrometry) and the corresponding proteins were identified. Finally, additional CGs were selected from the literature, and quantitative real-time polymerase chain reaction (qPCR) was performed to analyse the expression of all identified CGs. Altogether, >40 genes presenting differential gene expression during drought acclimation were identified, some of them showing different expression profiles between drought-tolerant and susceptible clones. Based on the obtained results, it can be concluded that factors involved a complex network of responses probably involving the abscisic signalling pathway and nitric oxide are major molecular determinants that might explain the better efficiency in controlling stomata closure and transpiration displayed by drought-tolerant clones of C. canephora.
Collapse
Affiliation(s)
- Pierre Marraccini
- EMBRAPA Recursos Genéticos e Biotecnologia (LGM), Parque EB, CP 02372, 70770-917 Brasilia, DF, Brazil
- CIRAD, UMR AGAP, Avenue d’Agropolis, F 34398 Montpellier, France
| | - Felipe Vinecky
- EMBRAPA Recursos Genéticos e Biotecnologia (LGM), Parque EB, CP 02372, 70770-917 Brasilia, DF, Brazil
| | - Gabriel S.C. Alves
- EMBRAPA Recursos Genéticos e Biotecnologia (LGM), Parque EB, CP 02372, 70770-917 Brasilia, DF, Brazil
| | | | - Sonia Elbelt
- EMBRAPA Recursos Genéticos e Biotecnologia (LGM), Parque EB, CP 02372, 70770-917 Brasilia, DF, Brazil
- CIRAD, UMR AGAP, Avenue d’Agropolis, F 34398 Montpellier, France
| | - Natalia G. Vieira
- EMBRAPA Recursos Genéticos e Biotecnologia (LGM), Parque EB, CP 02372, 70770-917 Brasilia, DF, Brazil
| | - Fernanda A. Carneiro
- EMBRAPA Recursos Genéticos e Biotecnologia (LGM), Parque EB, CP 02372, 70770-917 Brasilia, DF, Brazil
| | - Patricia S. Sujii
- EMBRAPA Recursos Genéticos e Biotecnologia (LGM), Parque EB, CP 02372, 70770-917 Brasilia, DF, Brazil
| | - Jean C. Alekcevetch
- EMBRAPA Recursos Genéticos e Biotecnologia (LGM), Parque EB, CP 02372, 70770-917 Brasilia, DF, Brazil
| | - Vânia A. Silva
- UFV, Departamento de Biologia Vegetal, 36570-000 Viçosa, MG, Brazil
| | - Fábio M. DaMatta
- UFV, Departamento de Biologia Vegetal, 36570-000 Viçosa, MG, Brazil
| | - Maria A.G. Ferrão
- INCAPER/EMBRAPA CAFÉ, Rod. BR 363, km 94, 29375-000 Domingos Martins, ES, Brazil
| | - Thierry Leroy
- CIRAD, UMR AGAP, Avenue d’Agropolis, F 34398 Montpellier, France
| | - David Pot
- CIRAD, UMR AGAP, Avenue d’Agropolis, F 34398 Montpellier, France
| | - Luiz G.E. Vieira
- INCAPER/EMBRAPA CAFÉ, Rod. BR 363, km 94, 29375-000 Domingos Martins, ES, Brazil
| | - Felipe R. da Silva
- EMBRAPA Recursos Genéticos e Biotecnologia (LGM), Parque EB, CP 02372, 70770-917 Brasilia, DF, Brazil
| | - Alan C. Andrade
- EMBRAPA Recursos Genéticos e Biotecnologia (LGM), Parque EB, CP 02372, 70770-917 Brasilia, DF, Brazil
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|
11
|
Guyot R, Lefebvre-Pautigny F, Tranchant-Dubreuil C, Rigoreau M, Hamon P, Leroy T, Hamon S, Poncet V, Crouzillat D, de Kochko A. Ancestral synteny shared between distantly-related plant species from the asterid (Coffea canephora and Solanum Sp.) and rosid (Vitis vinifera) clades. BMC Genomics 2012; 13:103. [PMID: 22433423 PMCID: PMC3372433 DOI: 10.1186/1471-2164-13-103] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 03/20/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Coffee trees (Rubiaceae) and tomato (Solanaceae) belong to the Asterid clade, while grapevine (Vitaceae) belongs to the Rosid clade. Coffee and tomato separated from grapevine 125 million years ago, while coffee and tomato diverged 83-89 million years ago. These long periods of divergent evolution should have permitted the genomes to reorganize significantly. So far, very few comparative mappings have been performed between very distantly related species belonging to different clades. We report the first multiple comparison between species from Asterid and Rosid clades, to examine both macro-and microsynteny relationships. RESULTS Thanks to a set of 867 COSII markers, macrosynteny was detected between coffee, tomato and grapevine. While coffee and tomato genomes share 318 orthologous markers and 27 conserved syntenic segments (CSSs), coffee and grapevine also share a similar number of syntenic markers and CSSs: 299 and 29 respectively. Despite large genome macrostructure reorganization, several large chromosome segments showed outstanding macrosynteny shedding new insights into chromosome evolution between Asterids and Rosids. We also analyzed a sequence of 174 kb containing the ovate gene, conserved in a syntenic block between coffee, tomato and grapevine that showed a high-level of microstructure conservation. A higher level of conservation was observed between coffee and grapevine, both woody and long life-cycle plants, than between coffee and tomato. Out of 16 coffee genes of this syntenic segment, 7 and 14 showed complete synteny between coffee and tomato or grapevine, respectively. CONCLUSIONS These results show that significant conservation is found between distantly related species from the Asterid (Coffea canephora and Solanum sp.) and Rosid (Vitis vinifera) clades, at the genome macrostructure and microstructure levels. At the ovate locus, conservation did not decline in relation to increasing phylogenetic distance, suggesting that the time factor alone does not explain divergences. Our results are considerably useful for syntenic studies between supposedly remote species for the isolation of important genes for agronomy.
Collapse
Affiliation(s)
- Romain Guyot
- UMR DIADE, Evolution et Dynamique des Génomes, Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Sathuvalli VR, Mehlenbacher SA. A bacterial artificial chromosome library for 'Jefferson' hazelnut and identification of clones associated with eastern filbert blight resistance and pollen-stigma incompatibility. Genome 2011; 54:862-7. [PMID: 21936690 DOI: 10.1139/g11-048] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
European hazelnut (Corylus avellana L.) is the only economically important nut crop in the family Betulaceae. Because of its small genome size (~385 Mb / 1C), relatively short life cycle, availability of a dense linkage map, and amenability to transformation by Agrobacterium, the European hazelnut could serve as a model plant for the Betulaceae. Here we report the construction of a bacterial artificial chromosome (BAC) library for 'Jefferson' hazelnut using the cloning enzyme MboI and the vector pECBAC1 (BamHI site). The library consists of 39,936 clones arrayed in 104,384-well microtitre plates with a mean insert size of 117 kb. The genomic coverage of the library is estimated to be about 12 genome equivalents. This library provides a valuable resource for the map-based cloning of two important genes, the resistance gene from 'Gasaway' that confers resistance to eastern filbert blight caused by the fungus Anisogramma anomala (Peck) E. Müller and the S locus that controls pollen-stigma incompatibility. Fine-resolution mapping near the two loci was carried out using random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers. Fine mapping at the disease resistance locus showed that markers W07-375 and X01-825 flanked the resistance locus at distances of 0.06 and 0.05 cM, respectively. The S locus is flanked by markers 204-950 and KG819-200 at distances of 0.14 and 0.24 cM, respectively. Assuming that 1 cM corresponds to a physical distance of 430 kb, it will take approximately two to three chromosome walks to assemble BAC contigs that span both loci.
Collapse
|
13
|
Yu Q, Guyot R, de Kochko A, Byers A, Navajas-Pérez R, Langston BJ, Dubreuil-Tranchant C, Paterson AH, Poncet V, Nagai C, Ming R. Micro-collinearity and genome evolution in the vicinity of an ethylene receptor gene of cultivated diploid and allotetraploid coffee species (Coffea). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 67:305-17. [PMID: 21457367 DOI: 10.1111/j.1365-313x.2011.04590.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Arabica coffee (Coffea arabica L.) is a self-compatible perennial allotetraploid species (2n=4x=44), whereas Robusta coffee (C. canephora L.) is a self-incompatible perennial diploid species (2n=2x=22). C. arabica (C(a) C(a) E(a) E(a) ) is derived from a spontaneous hybridization between two closely related diploid coffee species, C. canephora (CC) and C. eugenioides (EE). To investigate the patterns and degree of DNA sequence divergence between the Arabica and Robusta coffee genomes, we identified orthologous bacterial artificial chromosomes (BACs) from C. arabica and C. canephora, and compared their sequences to trace their evolutionary history. Although a high level of sequence similarity was found between BACs from C. arabica and C. canephora, numerous chromosomal rearrangements were detected, including inversions, deletions and insertions. DNA sequence identity between C. arabica and C. canephora orthologous BACs ranged from 93.4% (between E(a) and C(a) ) to 94.6% (between C(a) and C). Analysis of eight orthologous gene pairs resulted in estimated ages of divergence between 0.046 and 0.665 million years, indicating a recent origin of the allotetraploid species C. arabica. Analysis of transposable elements revealed differential insertion events that contributed to the size increase in the C(a) sub-genome compared to its diploid relative. In particular, we showed that insertion of a Ty1-copia LTR retrotransposon occurred specifically in C. arabica, probably shortly after allopolyploid formation. The two sub-genomes of C. arabica, C(a) and E(a) , showed sufficient sequence differences, and a whole-genome shotgun approach could be suitable for sequencing the allotetraploid genome of C. arabica.
Collapse
Affiliation(s)
- Qingyi Yu
- Hawaii Agriculture Research Center, Waipahu, HI 96797, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Marraccini P, Freire LP, Alves GSC, Vieira NG, Vinecky F, Elbelt S, Ramos HJO, Montagnon C, Vieira LGE, Leroy T, Pot D, Silva VA, Rodrigues GC, Andrade AC. RBCS1 expression in coffee: Coffea orthologs, Coffea arabica homeologs, and expression variability between genotypes and under drought stress. BMC PLANT BIOLOGY 2011; 11:85. [PMID: 21575242 PMCID: PMC3121667 DOI: 10.1186/1471-2229-11-85] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 05/16/2011] [Indexed: 05/08/2023]
Abstract
BACKGROUND In higher plants, the inhibition of photosynthetic capacity under drought is attributable to stomatal and non-stomatal (i.e., photochemical and biochemical) effects. In particular, a disruption of photosynthetic metabolism and Rubisco regulation can be observed. Several studies reported reduced expression of the RBCS genes, which encode the Rubisco small subunit, under water stress. RESULTS Expression of the RBCS1 gene was analysed in the allopolyploid context of C. arabica, which originates from a natural cross between the C. canephora and C. eugenioides species. Our study revealed the existence of two homeologous RBCS1 genes in C. arabica: one carried by the C. canephora sub-genome (called CaCc) and the other carried by the C. eugenioides sub-genome (called CaCe). Using specific primer pairs for each homeolog, expression studies revealed that CaCe was expressed in C. eugenioides and C. arabica but was undetectable in C. canephora. On the other hand, CaCc was expressed in C. canephora but almost completely silenced in non-introgressed ("pure") genotypes of C. arabica. However, enhanced CaCc expression was observed in most C. arabica cultivars with introgressed C. canephora genome. In addition, total RBCS1 expression was higher for C. arabica cultivars that had recently introgressed C. canephora genome than for "pure" cultivars. For both species, water stress led to an important decrease in the abundance of RBCS1 transcripts. This was observed for plants grown in either greenhouse or field conditions under severe or moderate drought. However, this reduction of RBCS1 gene expression was not accompanied by a decrease in the corresponding protein in the leaves of C. canephora subjected to water withdrawal. In that case, the amount of RBCS1 was even higher under drought than under unstressed (irrigated) conditions, which suggests great stability of RBCS1 under adverse water conditions. On the other hand, for C. arabica, high nocturnal expression of RBCS1 could also explain the accumulation of the RBCS1 protein under water stress. Altogether, the results presented here suggest that the content of RBCS was not responsible for the loss of photosynthetic capacity that is commonly observed in water-stressed coffee plants. CONCLUSION We showed that the CaCe homeolog was expressed in C. eugenioides and non-introgressed ("pure") genotypes of C. arabica but that it was undetectable in C. canephora. On the other hand, the CaCc homeolog was expressed in C. canephora but highly repressed in C. arabica. Expression of the CaCc homeolog was enhanced in C. arabica cultivars that experienced recent introgression with C. canephora. For both C. canephora and C. arabica species, total RBCS1 gene expression was highly reduced with WS. Unexpectedly, the accumulation of RBCS1 protein was observed in the leaves of C. canephora under WS, possibly coming from nocturnal RBCS1 expression. These results suggest that the increase in the amount of RBCS1 protein could contribute to the antioxidative function of photorespiration in water-stressed coffee plants.
Collapse
Affiliation(s)
- Pierre Marraccini
- Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917 Brasilia, Distrito Federal, Brazil
- CIRAD UMR AGAP, 34398 Montpellier Cedex 5, France
| | - Luciana P Freire
- Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917 Brasilia, Distrito Federal, Brazil
| | - Gabriel SC Alves
- Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917 Brasilia, Distrito Federal, Brazil
| | - Natalia G Vieira
- Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917 Brasilia, Distrito Federal, Brazil
| | - Felipe Vinecky
- Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917 Brasilia, Distrito Federal, Brazil
| | - Sonia Elbelt
- Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917 Brasilia, Distrito Federal, Brazil
| | - Humberto JO Ramos
- Instituto Agronômico do Paraná (IAPAR/LBI-AMG), Rodovia Celso Garcia Cid, Km 375, CP 481, 86001-970 Londrina, Paraná, Brazil
- Universidade Federal de Viçosa (UFV), PH Rolfs S/A, 36570-000 Viçosa, Minas Gerais, Brazil
| | | | - Luiz GE Vieira
- Instituto Agronômico do Paraná (IAPAR/LBI-AMG), Rodovia Celso Garcia Cid, Km 375, CP 481, 86001-970 Londrina, Paraná, Brazil
| | | | - David Pot
- CIRAD UMR AGAP, 34398 Montpellier Cedex 5, France
| | - Vânia A Silva
- EPAMIG/URESM, Rodovia Lavras/IJACI, Km 02, CP 176, 37200-000 Lavras, Minas Gerais, Brazil
| | - Gustavo C Rodrigues
- Embrapa Cerrados, BR 020 Km18, CP 08223, 73310-970 Planaltina, Distrito Federal, Brazil
| | - Alan C Andrade
- Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917 Brasilia, Distrito Federal, Brazil
| |
Collapse
|
15
|
Two novel Ty1-copia retrotransposons isolated from coffee trees can effectively reveal evolutionary relationships in the Coffea genus (Rubiaceae). Mol Genet Genomics 2011; 285:447-60. [PMID: 21505885 DOI: 10.1007/s00438-011-0617-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 03/29/2011] [Indexed: 12/14/2022]
Abstract
In the study, we developed new markers for phylogenetic relationships and intraspecies differentiation in Coffea. Nana and Divo, two novel Ty1-copia LTR-retrotransposon families, were isolated through C. canephora BAC clone sequencing. Nana- and Divo-based markers were used to test their: (1) ability to resolve recent phylogenetic relationships; (2) efficiency in detecting intra-species differentiation. Sequence-specific amplification polymorphism (SSAP), retrotransposon-microsatellite amplified polymorphism (REMAP) and retrotransposon-based insertion polymorphism (RBIP) approaches were applied to 182 accessions (31 Coffea species and one Psilanthus accession). Nana- and Divo-based markers revealed contrasted transpositional histories. At the BAC clone locus, RBIP results on C. canephora demonstrated that Nana insertion took place prior to C. canephora differentiation, while Divo insertion occurred after differentiation. Combined SSAP and REMAP data showed that Nana could resolve Coffea lineages, while Divo was efficient at a lower taxonomic level. The combined results indicated that the retrotransposon-based markers were useful in highlighting Coffea genetic diversity and the chronological pattern of speciation/differentiation events. Ongoing complete sequencing of the C. canephora genome will soon enable exhaustive identification of LTR-RTN families, as well as more precise in-depth analyses on contributions to genome size variation and Coffea evolution.
Collapse
|
16
|
Paiva JAP, Prat E, Vautrin S, Santos MD, San-Clemente H, Brommonschenkel S, Fonseca PGS, Grattapaglia D, Song X, Ammiraju JSS, Kudrna D, Wing RA, Freitas AT, Bergès H, Grima-Pettenati J. Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries. BMC Genomics 2011; 12:137. [PMID: 21375742 PMCID: PMC3060884 DOI: 10.1186/1471-2164-12-137] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 03/04/2011] [Indexed: 11/10/2022] Open
Abstract
Background Eucalyptus species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding practice will be increasingly important in the decades to come. Bacterial artificial chromosome (BAC) libraries are key genomic tools that enable positional cloning of important traits, synteny evaluation, and the development of genome framework physical maps for genetic linkage and genome sequencing. Results We describe the construction and characterization of two deep-coverage BAC libraries EG_Ba and EG_Bb obtained from nuclear DNA fragments of E. grandis (clone BRASUZ1) digested with HindIII and BstYI, respectively. Genome coverages of 17 and 15 haploid genome equivalents were estimated for EG_Ba and EG_Bb, respectively. Both libraries contained large inserts, with average sizes ranging from 135 Kb (Eg_Bb) to 157 Kb (Eg_Ba), very low extra-nuclear genome contamination providing a probability of finding a single copy gene ≥ 99.99%. Libraries were screened for the presence of several genes of interest via hybridizations to high-density BAC filters followed by PCR validation. Five selected BAC clones were sequenced and assembled using the Roche GS FLX technology providing the whole sequence of the E. grandis chloroplast genome, and complete genomic sequences of important lignin biosynthesis genes. Conclusions The two E. grandis BAC libraries described in this study represent an important milestone for the advancement of Eucalyptus genomics and forest tree research. These BAC resources have a highly redundant genome coverage (> 15×), contain large average inserts and have a very low percentage of clones with organellar DNA or empty vectors. These publicly available BAC libraries are thus suitable for a broad range of applications in genetic and genomic research in Eucalyptus and possibly in related species of Myrtaceae, including genome sequencing, gene isolation, functional and comparative genomics. Because they have been constructed using the same tree (E. grandis BRASUZ1) whose full genome is being sequenced, they should prove instrumental for assembly and gap filling of the upcoming Eucalyptus reference genome sequence.
Collapse
Affiliation(s)
- Jorge A P Paiva
- Instituto de Investigação Científica Tropical, Centro de Florestas e dos Produtos Florestais, Tapada da Ajuda, 1349-018 Lisboa, Portugal.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Mondego JMC, Vidal RO, Carazzolle MF, Tokuda EK, Parizzi LP, Costa GGL, Pereira LFP, Andrade AC, Colombo CA, Vieira LGE, Pereira GAG. An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora. BMC PLANT BIOLOGY 2011; 11:30. [PMID: 21303543 PMCID: PMC3045888 DOI: 10.1186/1471-2229-11-30] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2010] [Accepted: 02/08/2011] [Indexed: 05/10/2023]
Abstract
BACKGROUND Coffee is one of the world's most important crops; it is consumed worldwide and plays a significant role in the economy of producing countries. Coffea arabica and C. canephora are responsible for 70 and 30% of commercial production, respectively. C. arabica is an allotetraploid from a recent hybridization of the diploid species, C. canephora and C. eugenioides. C. arabica has lower genetic diversity and results in a higher quality beverage than C. canephora. Research initiatives have been launched to produce genomic and transcriptomic data about Coffea spp. as a strategy to improve breeding efficiency. RESULTS Assembling the expressed sequence tags (ESTs) of C. arabica and C. canephora produced by the Brazilian Coffee Genome Project and the Nestlé-Cornell Consortium revealed 32,007 clusters of C. arabica and 16,665 clusters of C. canephora. We detected different GC3 profiles between these species that are related to their genome structure and mating system. BLAST analysis revealed similarities between coffee and grape (Vitis vinifera) genes. Using KA/KS analysis, we identified coffee genes under purifying and positive selection. Protein domain and gene ontology analyses suggested differences between Coffea spp. data, mainly in relation to complex sugar synthases and nucleotide binding proteins. OrthoMCL was used to identify specific and prevalent coffee protein families when compared to five other plant species. Among the interesting families annotated are new cystatins, glycine-rich proteins and RALF-like peptides. Hierarchical clustering was used to independently group C. arabica and C. canephora expression clusters according to expression data extracted from EST libraries, resulting in the identification of differentially expressed genes. Based on these results, we emphasize gene annotation and discuss plant defenses, abiotic stress and cup quality-related functional categories. CONCLUSION We present the first comprehensive genome-wide transcript profile study of C. arabica and C. canephora, which can be freely assessed by the scientific community at http://www.lge.ibi.unicamp.br/coffea. Our data reveal the presence of species-specific/prevalent genes in coffee that may help to explain particular characteristics of these two crops. The identification of differentially expressed transcripts offers a starting point for the correlation between gene expression profiles and Coffea spp. developmental traits, providing valuable insights for coffee breeding and biotechnology, especially concerning sugar metabolism and stress tolerance.
Collapse
Affiliation(s)
- Jorge MC Mondego
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico de Campinas, CP 28, 13001-970, Campinas-SP, Brazil
| | - Ramon O Vidal
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, 13083-970, Campinas-SP, Brazil
- Laboratório Nacional de Biociências (LNBio), CP 6192, 13083-970, Campinas-SP, Brazil
| | - Marcelo F Carazzolle
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, 13083-970, Campinas-SP, Brazil
- Centro Nacional de Processamento de Alto Desempenho em São Paulo, Universidade Estadual de Campinas, CP 6141, 13083-970, Campinas, SP, Brazil
| | - Eric K Tokuda
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, 13083-970, Campinas-SP, Brazil
| | - Lucas P Parizzi
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, 13083-970, Campinas-SP, Brazil
| | - Gustavo GL Costa
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, 13083-970, Campinas-SP, Brazil
| | - Luiz FP Pereira
- Embrapa Café - Instituto Agronômico do Paraná, Laboratório de Biotecnologia Vegetal, CP 481, 86001-970, Londrina-PR, Brazil
| | - Alan C Andrade
- Núcleo de Biotecnologia-NTBio, Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP 02372, 70770-900, Brasília-DF, Brazil
| | - Carlos A Colombo
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico de Campinas, CP 28, 13001-970, Campinas-SP, Brazil
| | - Luiz GE Vieira
- Instituto Agronômico do Paraná, Laboratório de Biotecnologia Vegetal, CP 481, CEP 86001-970, Londrina-PR, Brazil
| | - Gonçalo AG Pereira
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, 13083-970, Campinas-SP, Brazil
| |
Collapse
|
18
|
Cenci A, Combes MC, Lashermes P. Comparative sequence analyses indicate that Coffea (Asterids) and Vitis (Rosids) derive from the same paleo-hexaploid ancestral genome. Mol Genet Genomics 2010; 283:493-501. [PMID: 20361338 DOI: 10.1007/s00438-010-0534-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Accepted: 03/16/2010] [Indexed: 11/30/2022]
Abstract
The complete sequence of Vitis vinifera revealed that the rosid clade derives from a hexaploid ancestor. At present, no analysis of complete genome sequence is available for an asterid, the other large eudicot clade, which includes the economically important species potato, tomato and coffee. To elucidate the genomic history of asterids, we compared the sequence of an 800 kb region of diploid Coffea genome to the orthologous regions of V. vinifera, Populus trichocarpa and Arabidopsis thaliana. We found a very high level of collinearity between around 80 genes of the three rosid species and Coffea. Collinearity comparisons between orthologous and paralogous regions indicates that (1) the Coffea (and consequently all asterids) and rosids share the same hexaploid ancestor; (2) the diploidization process (loss of duplicated and redundant copies from the whole genome duplication) was very advanced in the most recent common ancestor of rosids and asterids. Finally, no additional polyploidization events were detected in the Coffea lineage. Differences in gene loss rates were detected among the three rosid species and linked to the divergence in protein sequences.
Collapse
Affiliation(s)
- Alberto Cenci
- IRD, Institut de Recherche pour le Développement, UMR RPB (CIRAD, IRD Université Montpellier II), BP 64501, 34394, Montpellier Cedex 5, France.
| | | | | |
Collapse
|
19
|
Musoli P, Cubry P, Aluka P, Billot C, Dufour M, De Bellis F, Pot D, Bieysse D, Charrier A, Leroy T. Genetic differentiation of wild and cultivated populations: diversity of Coffea canephora Pierre in Uganda. Genome 2010; 52:634-46. [PMID: 19767894 DOI: 10.1139/g09-037] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Coffea canephora Pierre ex Frohener is a perennial plant originated from Africa. Two main groups, Guinean and Congolese, have already been identified within this species. They correspond to main refugia in western and central Africa. In this paper we present the analysis of a region that has not yet been studied, Uganda. Two wild, one feral (once cultivated but abandoned for many years), and two cultivated populations of C. canephora from Uganda were evaluated using 24 microsatellite markers. Basic diversity, dissimilarity and genetic distances between individuals, genetic differentiation between populations, and structure within populations were analysed. Expected heterozygosity was high for wild compartments (0.48 to 0.54) and for cultivated and feral ones (0.57 to 0.59), with the number of private alleles ranging from 12 for cultivated genotypes to 37 for a wild compartment. The Ugandan samples show significant population structuring. We compared the Ugandan populations with a representative sample of known genetic diversity groups within the species using 18 markers. Coffea canephora of Ugandan origin was found to be genetically different from previously identified diversity groups, implying that it forms another diversity group within the species. Given its large distribution and extremely recent domestication, C. canephora can be used to understand the effect of refugia colonization on genetic diversity.
Collapse
Affiliation(s)
- P Musoli
- Coffee Research Institute, P.O. Box 185, Mukono, Uganda
| | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Plechakova O, Tranchant-Dubreuil C, Benedet F, Couderc M, Tinaut A, Viader V, De Block P, Hamon P, Campa C, de Kochko A, Hamon S, Poncet V. MoccaDB - an integrative database for functional, comparative and diversity studies in the Rubiaceae family. BMC PLANT BIOLOGY 2009; 9:123. [PMID: 19788737 PMCID: PMC2760556 DOI: 10.1186/1471-2229-9-123] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Accepted: 09/29/2009] [Indexed: 05/08/2023]
Abstract
BACKGROUND In the past few years, functional genomics information has been rapidly accumulating on Rubiaceae species and especially on those belonging to the Coffea genus (coffee trees). An increasing number of expressed sequence tag (EST) data and EST- or genomic-derived microsatellite markers have been generated, together with Conserved Ortholog Set (COS) markers. This considerably facilitates comparative genomics or map-based genetic studies through the common use of orthologous loci across different species. Similar genomic information is available for e.g. tomato or potato, members of the Solanaceae family. Since both Rubiaceae and Solanaceae belong to the Euasterids I (lamiids) integration of information on genetic markers would be possible and lead to more efficient analyses and discovery of key loci involved in important traits such as fruit development, quality, and maturation, or adaptation. Our goal was to develop a comprehensive web data source for integrated information on validated orthologous markers in Rubiaceae. DESCRIPTION MoccaDB is an online MySQL-PHP driven relational database that houses annotated and/or mapped microsatellite markers in Rubiaceae. In its current release, the database stores 638 markers that have been defined on 259 ESTs and 379 genomic sequences. Marker information was retrieved from 11 published works, and completed with original data on 132 microsatellite markers validated in our laboratory. DNA sequences were derived from three Coffea species/hybrids. Microsatellite markers were checked for similarity, in vitro tested for cross-amplification and diversity/polymorphism status in up to 38 Rubiaceae species belonging to the Cinchonoideae and Rubioideae subfamilies. Functional annotation was provided and some markers associated with described metabolic pathways were also integrated. Users can search the database for marker, sequence, map or diversity information through multi-option query forms. The retrieved data can be browsed and downloaded, along with protocols used, using a standard web browser. MoccaDB also integrates bioinformatics tools (CMap viewer and local BLAST) and hyperlinks to related external data sources (NCBI GenBank and PubMed, SOL Genomic Network database). CONCLUSION We believe that MoccaDB will be extremely useful for all researchers working in the areas of comparative and functional genomics and molecular evolution, in general, and population analysis and association mapping of Rubiaceae and Solanaceae species, in particular.
Collapse
Affiliation(s)
- Olga Plechakova
- UMR DIAPC, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | | | - Fabrice Benedet
- UMR DIAPC, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
- CIRAD TA C 37/D, Campus International de Baillarguet 34398 Montpellier Cedex 5, France
| | - Marie Couderc
- UMR DIAPC, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Alexandra Tinaut
- UMR DIAPC, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Véronique Viader
- UMR DIAPC, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
- UMR DIAPC, INRA, Domaine de MelgueiI, Chemin de Mézouls, 34130 Mauguio, France
| | - Petra De Block
- National Botanic Garden of Belgium, Domein van Bouchout, 1860 Meise, Belgium
| | - Perla Hamon
- UMR DIAPC, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Claudine Campa
- UMR DIAPC, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Alexandre de Kochko
- UMR DIAPC, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Serge Hamon
- UMR DIAPC, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Valérie Poncet
- UMR DIAPC, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| |
Collapse
|
21
|
Guyot R, de la Mare M, Viader V, Hamon P, Coriton O, Bustamante-Porras J, Poncet V, Campa C, Hamon S, de Kochko A. Microcollinearity in an ethylene receptor coding gene region of the Coffea canephora genome is extensively conserved with Vitis vinifera and other distant dicotyledonous sequenced genomes. BMC PLANT BIOLOGY 2009; 9:22. [PMID: 19243618 PMCID: PMC2656508 DOI: 10.1186/1471-2229-9-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Accepted: 02/25/2009] [Indexed: 05/11/2023]
Abstract
BACKGROUND Coffea canephora, also called Robusta, belongs to the Rubiaceae, the fourth largest angiosperm family. This diploid species (2x = 2n = 22) has a fairly small genome size of approximately 690 Mb and despite its extreme economic importance, particularly for developing countries, knowledge on the genome composition, structure and evolution remain very limited. Here, we report the 160 kb of the first C. canephora Bacterial Artificial Chromosome (BAC) clone ever sequenced and its fine analysis. RESULTS This clone contains the CcEIN4 gene, encoding an ethylene receptor, and twenty other predicted genes showing a high gene density of one gene per 7.8 kb. Most of them display perfect matches with C. canephora expressed sequence tags or show transcriptional activities through PCR amplifications on cDNA libraries. Twenty-three transposable elements, mainly Class II transposon derivatives, were identified at this locus. Most of these Class II elements are Miniature Inverted-repeat Transposable Elements (MITE) known to be closely associated with plant genes. This BAC composition gives a pattern similar to those found in gene rich regions of Solanum lycopersicum and Medicago truncatula genomes indicating that the CcEIN4 regions may belong to a gene rich region in the C. canephora genome. Comparative sequence analysis indicated an extensive conservation between C. canephora and most of the reference dicotyledonous genomes studied in this work, such as tomato (S. lycopersicum), grapevine (V. vinifera), barrel medic M. truncatula, black cottonwood (Populus trichocarpa) and Arabidopsis thaliana. The higher degree of microcollinearity was found between C. canephora and V. vinifera, which belong respectively to the Asterids and Rosids, two clades that diverged more than 114 million years ago. CONCLUSION This study provides a first glimpse of C. canephora genome composition and evolution. Our data revealed a remarkable conservation of the microcollinearity between C. canephora and V. vinifera and a high conservation with other distant dicotyledonous reference genomes. Altogether, these results provide valuable information to identify candidate genes in C. canephora genome and serve as a foundation to establish strategies for whole genome sequencing. Future large-scale sequence comparison between C. canephora and reference sequenced genomes will help in understanding the evolutionary history of dicotyledonous plants.
Collapse
Affiliation(s)
- Romain Guyot
- UMR GDP, IRD BP 64501, Centre IRD de Montpellier, BP 64501, Montpellier Cedex 5, France
| | - Marion de la Mare
- UMR DIA-PC, IRD Génomique Comparative et Fonctionnelle de l'Adaptation, Centre IRD de Montpellier, BP 64501, Montpellier Cedex 5, France
| | - Véronique Viader
- UMR DIA-PC, IRD Génomique Comparative et Fonctionnelle de l'Adaptation, Centre IRD de Montpellier, BP 64501, Montpellier Cedex 5, France
| | - Perla Hamon
- UMR DIA-PC, IRD Génomique Comparative et Fonctionnelle de l'Adaptation, Centre IRD de Montpellier, BP 64501, Montpellier Cedex 5, France
| | - Olivier Coriton
- UMR 118, INRA Agrocampus Rennes Amélioration des Plantes, Domaine de la Motte – BP 35327, 35650 Le Rheu cedex, France
| | - José Bustamante-Porras
- UMR DIA-PC, IRD Génomique Comparative et Fonctionnelle de l'Adaptation, Centre IRD de Montpellier, BP 64501, Montpellier Cedex 5, France
| | - Valérie Poncet
- UMR DIA-PC, IRD Génomique Comparative et Fonctionnelle de l'Adaptation, Centre IRD de Montpellier, BP 64501, Montpellier Cedex 5, France
| | - Claudine Campa
- UMR DIA-PC, IRD Génomique Comparative et Fonctionnelle de l'Adaptation, Centre IRD de Montpellier, BP 64501, Montpellier Cedex 5, France
| | - Serge Hamon
- UMR DIA-PC, IRD Génomique Comparative et Fonctionnelle de l'Adaptation, Centre IRD de Montpellier, BP 64501, Montpellier Cedex 5, France
| | - Alexandre de Kochko
- UMR DIA-PC, IRD Génomique Comparative et Fonctionnelle de l'Adaptation, Centre IRD de Montpellier, BP 64501, Montpellier Cedex 5, France
| |
Collapse
|
22
|
Cavagnaro PF, Chung SM, Szklarczyk M, Grzebelus D, Senalik D, Atkins AE, Simon PW. Characterization of a deep-coverage carrot (Daucus carota L.) BAC library and initial analysis of BAC-end sequences. Mol Genet Genomics 2008; 281:273-88. [PMID: 19104839 DOI: 10.1007/s00438-008-0411-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Accepted: 11/29/2008] [Indexed: 11/29/2022]
Abstract
Carrot is the most economically important member of the Apiaceae family and a major source of provitamin A carotenoids in the human diet. However, carrot molecular resources are relatively underdeveloped, hampering a number of genetic studies. Here, we report on the synthesis and characterization of a bacterial artificial chromosome (BAC) library of carrot. The library is 17.3-fold redundant and consists of 92,160 clones with an average insert size of 121 kb. To provide an overview of the composition and organization of the carrot nuclear genome we generated and analyzed 2,696 BAC-end sequences (BES) from nearly 2,000 BACs, totaling 1.74 Mb of BES. This analysis revealed that 14% of the BES consists of known repetitive elements, with transposable elements representing more than 80% of this fraction. Eleven novel carrot repetitive elements were identified, covering 8.5% of the BES. Analysis of microsatellites showed a comparably low frequency for these elements in the carrot BES. Comparisons of the translated BES with protein databases indicated that approximately 10% of the carrot genome represents coding sequences. Moreover, among eight dicot species used for comparison purposes, carrot BES had highest homology to protein-coding sequences from tomato. This deep-coverage library will aid carrot breeding and genetics.
Collapse
Affiliation(s)
- Pablo F Cavagnaro
- Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA
| | | | | | | | | | | | | |
Collapse
|
23
|
Geromel C, Ferreira LP, Davrieux F, Guyot B, Ribeyre F, Brígida dos Santos Scholz M, Protasio Pereira LF, Vaast P, Pot D, Leroy T, Androcioli Filho A, Esteves Vieira LG, Mazzafera P, Marraccini P. Effects of shade on the development and sugar metabolism of coffee (Coffea arabica L.) fruits. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2008; 46:569-79. [PMID: 18420417 DOI: 10.1016/j.plaphy.2008.02.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Indexed: 05/11/2023]
Abstract
Coffee fruits grown in shade are characterized by larger bean size than those grown under full-sun conditions. The present study assessed the effects of shade on bean characteristics and sugar metabolism by analyzing tissue development, sugar contents, activities of sucrose metabolizing enzymes and expression of sucrose synthase-encoding genes in fruits of coffee (Coffea arabica L.) plants submitted to full-sun (FS) and shade (SH) conditions. Evolution of tissue fresh weights measured in fruits collected regularly from flowering to maturation indicated that this increase is due to greater development of the perisperm tissue in the shade. The effects of light regime on sucrose and reducing sugar (glucose and fructose) contents were studied in fresh and dry coffee beans. Shade led to a significant reduction in sucrose content and to an increase in reducing sugars. In pericarp and perisperm tissues, higher activities of sucrose synthase (EC 2.4.1.13) and sucrose-phosphate synthase (SPS: EC 2.4.1.14) were detected at maturation in the shade compared with full sun. These two enzymes also had higher peaks of activities in developing endosperm under shade than in full sun. It was also noted that shade modified the expression of SUS-encoding genes in coffee beans; CaSUS2 gene transcripts levels were higher in SH than in FS. As no sucrose increase accompanied these changes, this suggests that sucrose metabolism was redirected to other metabolic pathways that need to be identified.
Collapse
Affiliation(s)
- Clara Geromel
- Departamento de Fisiologia Vegetal-IB, UNICAMP, CP 6109, 13083-970 Campinas, SP, Brazil
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Cubry P, Musoli P, Legnaté H, Pot D, de Bellis F, Poncet V, Anthony F, Dufour M, Leroy T. Diversity in coffee assessed with SSR markers: structure of the genus Coffea and perspectives for breeding. Genome 2008; 51:50-63. [PMID: 18356939 DOI: 10.1139/g07-096] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The present study shows transferability of microsatellite markers developed in the two cultivated coffee species (Coffea arabica L. and C. canephora Pierre ex Froehn.) to 15 species representing the previously identified main groups of the genus Coffea. Evaluation of the genetic diversity and available resources within Coffea and development of molecular markers transferable across species are important steps for breeding of the two cultivated species. We worked on 15 species with 60 microsatellite markers developed using different strategies (SSR-enriched libraries, BAC libraries, gene sequences). We focused our analysis on 4 species used for commercial or breeding purposes. Our results establish the high transferability of microsatellite markers within Coffea. We show the large amount of diversity available within wild species for breeding applications. Finally we discuss the consequences for future comparative mapping studies and breeding of the two cultivated species.
Collapse
Affiliation(s)
- Philippe Cubry
- CIRAD, UMR DAP, TA A-96/03, avenue Agropolis, 34398 Montpellier Cedex 5, France.
| | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Privat I, Foucrier S, Prins A, Epalle T, Eychenne M, Kandalaft L, Caillet V, Lin C, Tanksley S, Foyer C, Mccarthy J. Differential regulation of grain sucrose accumulation and metabolism in Coffea arabica (Arabica) and Coffea canephora (Robusta) revealed through gene expression and enzyme activity analysis. THE NEW PHYTOLOGIST 2008; 178:781-797. [PMID: 18384509 DOI: 10.1111/j.1469-8137.2008.02425.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
* Coffea arabica (Arabica) and Coffea canephora (Robusta) are the two main cultivated species used for coffee bean production. Arabica genotypes generally produce a higher coffee quality than Robusta genotypes. Understanding the genetic basis for sucrose accumulation during coffee grain maturation is an important goal because sucrose is an important coffee flavor precursor. * Nine new Coffea genes encoding sucrose metabolism enzymes have been identified: sucrose phosphate synthase (CcSPS1, CcSPS2), sucrose phosphate phosphatase (CcSP1), cytoplasmic (CaInv3) and cell wall (CcInv4) invertases and four invertase inhibitors (CcInvI1, 2, 3, 4). * Activities and mRNA abundance of the sucrose metabolism enzymes were compared at different developmental stages in Arabica and Robusta grains, characterized by different sucrose contents in mature grain. * It is concluded that Robusta accumulates less sucrose than Arabica for two reasons: Robusta has higher sucrose synthase and acid invertase activities early in grain development - the expression of CcSS1 and CcInv2 appears to be crucial at this stage and Robusta has a lower SPS activity and low CcSPS1 expression at the final stages of grain development and hence has less capacity for sucrose re-synthesis. Regulation of vacuolar invertase CcInv2 activity by invertase inhibitors CcInvI2 and/or CcInvI3 during Arabica grain development is considered.
Collapse
Affiliation(s)
- Isabelle Privat
- Centre de Recherche Nestlé, 101 Av. Gustave Eiffel, Notre Dame d'Oé, BP 49716-37097 Tours, France
| | - Séverine Foucrier
- Centre de Recherche Nestlé, 101 Av. Gustave Eiffel, Notre Dame d'Oé, BP 49716-37097 Tours, France
| | - Anneke Prins
- School of Agriculture, Food and Rural Development, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Thibaut Epalle
- Centre de Recherche Nestlé, 101 Av. Gustave Eiffel, Notre Dame d'Oé, BP 49716-37097 Tours, France
| | - Magali Eychenne
- Centre de Recherche Nestlé, 101 Av. Gustave Eiffel, Notre Dame d'Oé, BP 49716-37097 Tours, France
| | - Laurianne Kandalaft
- Centre de Recherche Nestlé, 101 Av. Gustave Eiffel, Notre Dame d'Oé, BP 49716-37097 Tours, France
| | - Victoria Caillet
- Centre de Recherche Nestlé, 101 Av. Gustave Eiffel, Notre Dame d'Oé, BP 49716-37097 Tours, France
| | - Chenwei Lin
- Department of Plant Breeding, 248 Emerson, Cornell University, Ithaca, NY 14853, USA
| | - Steve Tanksley
- Department of Plant Breeding, 248 Emerson, Cornell University, Ithaca, NY 14853, USA
| | - Christine Foyer
- School of Agriculture, Food and Rural Development, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - James Mccarthy
- Centre de Recherche Nestlé, 101 Av. Gustave Eiffel, Notre Dame d'Oé, BP 49716-37097 Tours, France
| |
Collapse
|
26
|
Salmona J, Dussert S, Descroix F, de Kochko A, Bertrand B, Joët T. Deciphering transcriptional networks that govern Coffea arabica seed development using combined cDNA array and real-time RT-PCR approaches. PLANT MOLECULAR BIOLOGY 2008; 66:105-24. [PMID: 18026845 DOI: 10.1007/s11103-007-9256-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2007] [Accepted: 10/27/2007] [Indexed: 05/04/2023]
Abstract
Due to its economic importance, Coffea arabica is becoming the subject of increasing genomic research and, in particular, the genes involved in the final chemical composition of the bean and the sensorial quality of the coffee beverage. The aim of the present study was to decipher the transcriptional networks that govern the development of the C. arabica seed, a model for non-orthodox albuminous seeds of tropical origin. For this purpose, we developed a transcriptomic approach combining two techniques: targeted cDNA arrays, containing 266 selected candidate gene sequences, and real-time RT-PCR on a large subset of 111 genes. The combination of the two techniques allowed us to limit detection of false positives and to reveal the advantages of using large real-time RT-PCR screening. Multivariate analysis was conducted on both datasets and results were broadly convergent. First, principle component analysis (PCA) revealed a dramatic re-programming of the transcriptional machinery between early cell division and elongation, storage and maturation phases. Second, hierarchical clustering analysis (HCA) led to the identification of 11 distinct patterns of gene expression during seed development as well as to the detection of genes expressed at specific developmental stages that can be used as functional markers of phenological changes. In addition, this study led to the description of gene expression profiles for quality-related genes, most of them formerly uncharacterised in Coffea. Their involvement in storage compound synthesis and accumulation during endosperm development and final metabolic re-adjustments during maturation is discussed.
Collapse
Affiliation(s)
- Jordi Salmona
- IRD, UMR DIAPC, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, ligne Paradis, 97410 Saint Pierre, France
| | | | | | | | | | | |
Collapse
|
27
|
Bustamante-Porras J, Campa C, Poncet V, Noirot M, Leroy T, Hamon S, de Kochko A. Molecular characterization of an ethylene receptor gene (CcETR1) in coffee trees, its relationship with fruit development and caffeine content. Mol Genet Genomics 2007; 277:701-12. [PMID: 17318584 DOI: 10.1007/s00438-007-0219-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2006] [Accepted: 02/01/2007] [Indexed: 11/30/2022]
Abstract
To understand the importance of ethylene receptor genes in the quality of coffee berries three full-length cDNAs corresponding to a putative ethylene receptor gene (ETR1) were isolated from Coffea canephora cDNA libraries. They differed by their 3'UTR and contained a main ORF and a 5'UTR short ORF putatively encoding a small polypeptide. The CcETR1 gene, present as a single copy in the C. canephora genome, contained five introns in the coding region and one in its 5'UTR. Alternative splicing can occur in C. canephora and C. pseudozanguebariae, leading to a truncated polypeptide. C. pseudozanguebariae ETR1 transcripts showed various forms of splicing alterations. This gene was equally expressed at all stages of fruit development. A segregation study on an inter-specific progeny showed that ETR1 is related to the fructification time, the caffeine content of the green beans, and seed weight. Arabidopsis transformed etiolated seedlings, which over-expressed CcETR1, displayed highly reduced gravitropism, but the triple response was observed in an ethylene enriched environment. These plants behaved like a low-concentration ethylene-insensitive mutant thus confirming the receptor function of the encoded protein. This gene showed no induction during the climacteric crisis but some linkage with traits related to quality.
Collapse
|
28
|
De Castro RD, Marraccini P. Cytology, biochemistry and molecular changes during coffee fruit development. ACTA ACUST UNITED AC 2006. [DOI: 10.1590/s1677-04202006000100013] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In commercial coffee species (Coffea arabica and Coffea canephora), fruit development is a lengthy process, characterized by tissue changes and evolutions. For example, soon after fecundation and up to mid development, the fruit is mainly constituted of the pericarp and perisperm tissue. Thereafter, the perisperm gradually disappears and is progressively replaced by the endosperm (true seed). Initially present in a "liquid" state, the endosperm hardens as it ripens during the maturation phase, as a result of accumulation of storage proteins, sucrose and complex polysaccharides representing the main reserves of the seed. The last step of maturation is characterized by the dehydration of the endosperm and the color change of the pericarp. Important quantitative and qualitative changes accompany fruit growth, highlighting the importance of its study to better understand the final characteristics of coffee beans. Following a description of the coffee fruit tissues, this review presents some data concerning biochemical, enzymatic and gene expression variations observed during the coffee fruit development. The latter will also be analyzed in the light of recent data (electronic expression profiles) arising from the Brazilian Coffee Genome Project.
Collapse
|
29
|
Vieira LGE, Andrade AC, Colombo CA, Moraes AHDA, Metha Â, Oliveira ACD, Labate CA, Marino CL, Monteiro-Vitorello CDB, Monte DDC, Giglioti É, Kimura ET, Romano E, Kuramae EE, Lemos EGM, Almeida ERPD, Jorge ÉC, Albuquerque ÉVS, Silva FRD, Vinecky F, Sawazaki HE, Dorry HFA, Carrer H, Abreu IN, Batista JAN, Teixeira JB, Kitajima JP, Xavier KG, Lima LMD, Camargo LEAD, Pereira LFP, Coutinho LL, Lemos MVF, Romano MR, Machado MA, Costa MMDC, Sá MFGD, Goldman MHS, Ferro MIT, Tinoco MLP, Oliveira MC, Van Sluys MA, Shimizu MM, Maluf MP, Eira MTSD, Guerreiro Filho O, Arruda P, Mazzafera P, Mariani PDSC, Oliveira RLD, Harakava R, Balbao SF, Tsai SM, Mauro SMZD, Santos SN, Siqueira WJ, Costa GGL, Formighieri EF, Carazzolle MF, Pereira GAG. Brazilian coffee genome project: an EST-based genomic resource. ACTA ACUST UNITED AC 2006. [DOI: 10.1590/s1677-04202006000100008] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Coffee is one of the most valuable agricultural commodities and ranks second on international trade exchanges. The genus Coffea belongs to the Rubiaceae family which includes other important plants. The genus contains about 100 species but commercial production is based only on two species, Coffea arabica and Coffea canephora that represent about 70 % and 30 % of the total coffee market, respectively. The Brazilian Coffee Genome Project was designed with the objective of making modern genomics resources available to the coffee scientific community, working on different aspects of the coffee production chain. We have single-pass sequenced a total of 214,964 randomly picked clones from 37 cDNA libraries of C. arabica, C. canephora and C. racemosa, representing specific stages of cells and plant development that after trimming resulted in 130,792, 12,381 and 10,566 sequences for each species, respectively. The ESTs clustered into 17,982 clusters and 32,155 singletons. Blast analysis of these sequences revealed that 22 % had no significant matches to sequences in the National Center for Biotechnology Information database (of known or unknown function). The generated coffee EST database resulted in the identification of close to 33,000 different unigenes. Annotated sequencing results have been stored in an online database at <A HREF="http://www.lge.ibi.unicamp.br/cafe">http://www.lge.ibi.unicamp.br/cafe</A>. Resources developed in this project provide genetic and genomic tools that may hold the key to the sustainability, competitiveness and future viability of the coffee industry in local and international markets.
Collapse
Affiliation(s)
| | | | | | | | - Ângela Metha
- Embrapa Recursos Genéticos e Biotecnologia, Brazil
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Leroy T, Ribeyre F, Bertrand B, Charmetant P, Dufour M, Montagnon C, Marraccini P, Pot D. Genetics of coffee quality. ACTA ACUST UNITED AC 2006. [DOI: 10.1590/s1677-04202006000100016] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coffee quality, in the present context of overproduction worldwide, has to be considered as a main selection criterion for coffee improvement. After a definition of quality, and an overview of the non genetic factors affecting its variation, this review focuses on the genetic factors involved in the control of coffee quality variation. Regarding the complexity of this trait, the different types of quality are first presented. Then, the great variation within and between coffee species is underlined, mainly for biochemical compounds related to quality (caffeine, sugars, chlorogenic acids, lipids). The ways for breeding quality traits for cultivated species, Coffea arabica and Coffea canephora are discussed, with specific challenges for each species. For C. arabica, maintaining a good quality in F1 intraspecific hybrids, introgressed lines from Timor hybrid, and grafted varieties are the main challenges. For C. canephora, the improvement is mainly based on intraspecific and interspecific hybrids, using the whole genetic variability available within this species. An improvement is obtained for bean size, with significant genetic gains in current breeding programmes. The content in biochemical compounds related to cup quality is another way to improve Robusta quality. Finally, ongoing programmes towards the understanding of the molecular determinism of coffee quality, particularly using coffee ESTs, are presented.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - David Pot
- CIRAD, France; Instituto Agronômico do Paraná, Brazil
| |
Collapse
|
31
|
Marraccini P, Rogers WJ, Caillet V, Deshayes A, Granato D, Lausanne F, Lechat S, Pridmore D, Pétiard V. Biochemical and molecular characterization of alpha-D-galactosidase from coffee beans. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2005; 43:909-20. [PMID: 16310367 DOI: 10.1016/j.plaphy.2005.08.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2005] [Revised: 06/20/2005] [Accepted: 08/18/2005] [Indexed: 05/05/2023]
Abstract
Alpha-D-Galactosidase (alpha-Gal; EC 3.2.1.22) is one of three principal enzymes involved in the modification or degradation of plant cell wall galactomannans. In the present paper it is shown that alpha-galactosidase activities in field-grown coffee beans are variable amongst cultivars of the two species investigated (Coffea arabica and C. canephora var. Robusta). Higher activities were found in Arabica cultivars. Using beans from greenhouse-cultivated C. arabica as a model, we showed that alpha-Gal activity was undetectable in the bean perispem tissue, but increased gradually during the endosperm development, to reach a peak at approximately 30 weeks after flowering (WAF) which coincided with the hardening of the endosperm. Alpha-Gal-specific transcripts detected at 22 and 27 WAF accompanied the peak of alpha-Gal activity, but were reduced to be undetectable in mature beans at 30 WAF, while alpha-Gal activity still persisted. Two isoforms were distinguished in 2-DE profiles of crude protein extracts by N-terminal sequencing analysis. Analysis of two-dimensional gel electrophoresis profiles demonstrated that both isoforms accumulated in a linear fashion throughout grain maturation. Alpha-Gal activity was also observed to increase to high levels during in vitro germination of coffee beans suggesting an important function of this enzyme in this process. Alpha-Gal cDNA sequences from Arabica and Robusta were sequenced and their deduced proteins appeared to be very similar, differing by only eight amino acids. Southern-blot analysis suggests that the enzyme was encoded by at least two genes in C. arabica that could explain the existence of the two isoforms identified in 2-DE profiles.
Collapse
Affiliation(s)
- Pierre Marraccini
- Nestlé Research Center, 101, avenue Gustave Eiffel, B.P. 9716, 37097 Tours cedex 2, France
| | | | | | | | | | | | | | | | | |
Collapse
|