共查询到20条相似文献,搜索用时 171 毫秒
1.
Alexis Dereeper Romain Guyot Christine Tranchant-Dubreuil François Anthony Xavier Argout Fabien de Bellis Marie-Christine Combes Frederick Gavory Alexandre de Kochko Dave Kudrna Thierry Leroy Julie Poulain Myriam Rondeau Xiang Song Rod Wing Philippe Lashermes 《Plant molecular biology》2013,83(3):177-189
Coffee is one of the world’s most important agricultural commodities. Coffee belongs to the Rubiaceae family in the euasterid I clade of dicotyledonous plants, to which the Solanaceae family also belongs. Two bacterial artificial chromosome (BAC) libraries of a homozygous doubled haploid plant of Coffea canephora were constructed using two enzymes, HindIII and BstYI. A total of 134,827 high quality BAC-end sequences (BESs) were generated from the 73,728 clones of the two libraries, and 131,412 BESs were conserved for further analysis after elimination of chloroplast and mitochondrial sequences. This corresponded to almost 13 % of the estimated size of the C. canephora genome. 6.7 % of BESs contained simple sequence repeats, the most abundant (47.8 %) being mononucleotide motifs. These sequences allow the development of numerous useful marker sites. Potential transposable elements (TEs) represented 11.9 % of the full length BESs. A difference was observed between the BstYI and HindIII libraries (14.9 vs. 8.8 %). Analysis of BESs against known coding sequences of TEs indicated that 11.9 % of the genome corresponded to known repeat sequences, like for other flowering plants. The number of genes in the coffee genome was estimated at 41,973 which is probably overestimated. Comparative genome mapping revealed that microsynteny was higher between coffee and grapevine than between coffee and tomato or Arabidopsis. BESs constitute valuable resources for the first genome wide survey of coffee and provide new insights into the composition and evolution of the coffee genome. 相似文献
2.
Michelle G. Cotta Leila M. G. Barros Juliana D. de Almeida Fréderic de Lamotte Eder A. Barbosa Natalia G. Vieira Gabriel S. C. Alves Felipe Vinecky Alan C. Andrade Pierre Marraccini 《Plant molecular biology》2014,85(1-2):11-31
The aim of the present study was to perform a genomic analysis of non-specific lipid-transfer proteins (nsLTPs) in coffee. Several nsLTPs-encoding cDNA and gene sequences were cloned from Coffea arabica and Coffea canephora species. In this work, their analyses revealed that coffee nsLTPs belong to Type II LTP characterized under their mature forms by a molecular weight of around 7.3 kDa, a basic isoelectric points of 8.5 and the presence of typical CXC pattern, with X being an hydrophobic residue facing towards the hydrophobic cavity. Even if several single nucleotide polymorphisms were identified in these nsLTP-coding sequences, 3D predictions showed that they do not have a significant impact on protein functions. Northern blot and RT-qPCR experiments revealed specific expression of Type II nsLTPs-encoding genes in coffee fruits, mainly during the early development of endosperm of both C. arabica and C. canephora. As part of our search for tissue-specific promoters in coffee, an nsLTP promoter region of around 1.2 kb was isolated. It contained several DNA repeats including boxes identified as essential for grain specific expression in other plants. The whole fragment, and a series of 5′ deletions, were fused to the reporter gene β-glucuronidase (uidA) and analyzed in transgenic Nicotiana tabacum plants. Histochemical and fluorimetric GUS assays showed that the shorter (345 bp) and medium (827 bp) fragments of nsLTP promoter function as grain-specific promoters in transgenic tobacco plants. 相似文献
3.
Marie-Agnès Jacques Nicolas Denancé Bruno Legendre Emmanuelle Morel Martial Briand Stelly Mississipi Karine Durand Valérie Olivier Perrine Portier Fran?oise Poliakoff Dominique Crouzillat 《Applied and environmental microbiology》2016,82(5):1556-1568
Xylella fastidiosa is a xylem-limited phytopathogenic bacterium endemic to the Americas that has recently emerged in Asia and Europe. Although this bacterium is classified as a quarantine organism in the European Union, importation of plant material from contaminated areas and latent infection in asymptomatic plants have engendered its inevitable introduction. In 2012, four coffee plants (Coffea arabica and Coffea canephora) with leaf scorch symptoms growing in a confined greenhouse were detected and intercepted in France. After identification of the causal agent, this outbreak was eradicated. Three X. fastidiosa strains were isolated from these plants, confirming a preliminary identification based on immunology. The strains were characterized by multiplex PCR and by multilocus sequence analysis/typing (MLSA-MLST) based on seven housekeeping genes. One strain, CFBP 8073, isolated from C. canephora imported from Mexico, was assigned to X. fastidiosa subsp. fastidiosa/X. fastidiosa subsp. sandyi. This strain harbors a novel sequence type (ST) with novel alleles at two loci. The two other strains, CFBP 8072 and CFBP 8074, isolated from Coffea arabica imported from Ecuador, were allocated to X. fastidiosa subsp. pauca. These two strains shared a novel ST with novel alleles at two loci. These MLST profiles showed evidence of recombination events. We provide genome sequences for CFBP 8072 and CFBP 8073 strains. Comparative genomic analyses of these two genome sequences with publicly available X. fastidiosa genomes, including the Italian strain CoDiRO, confirmed these phylogenetic positions and provided candidate alleles for coffee plant adaptation. This study demonstrates the global diversity of X. fastidiosa and highlights the diversity of strains isolated from coffee plants. 相似文献
4.
Computational identification of miRNA and targets from expressed sequence tags of coffee (Coffea arabica) 总被引:1,自引:0,他引:1
Arzuba Akter Md. Muzahidul Islam Shakhinur Islam Mondal Zabed Mahmud Nurnabi Azad Jewel Sabiha Ferdous Md. Ruhul Amin Md. Mahfuzur Rahman 《Saudi Journal of Biological Sciences》2014,21(1):3-12
5.
PRASANNA R. BHAT V. KRISHNAKUMAR PRASAD S. HENDRE P. RAJENDRAKUMAR RAJEEV K. VARSHNEY RAMESH K. AGGARWAL 《Molecular ecology resources》2005,5(1):80-83
SSR (simple sequence repeats) markers derived from ESTs (expressed sequence tags), commonly called EST‐SSRs or genic SSRs provide useful genetic markers for crop improvement. These are easy and economical to develop as by‐products of large‐scale EST resources that have become available as part of the functional genomic studies in many plant species. Here, we describe for the first time, nine genic‐SSRs of coffee that are developed from the microsatellite containing ESTs from a cDNA library of moisture‐stressed leaves of coffee variety, ‘CxR’ (a commercial interspecific hybrid between Coffea congensis and Coffea canephora). The markers show considerable allelic diversity with PIC values up to 0.70 and 0.75 for Coffea arabica and Coffea canephora, respectively, and robust cross‐species amplification in 16 other related taxa of coffee. The validation studies thus demonstrate the potential utility of the EST‐SSRs for genetic analysis of coffee germplasm. 相似文献
6.
Thierry Leroy Fabien De Bellis Hyacinthe Legnate Edmund Kananura Gustavo Gonzales Luiz Felipe Pereira Alan Carvalho Andrade Pierre Charmetant Christophe Montagnon Philippe Cubry Pierre Marraccini David Pot Alexandre de Kochko 《Tree Genetics & Genomes》2011,7(4):781-798
Coffea canephora breeding requires combining sustainable productivity with improved technological and cup quality characteristics. Beverage quality is a complex and subjective trait, and breeding for this trait is time consuming and depends on knowledge of the genetics of its components. A highly variable C. canephora progeny resulting from an intraspecific cross was assessed for 63 traits over 5?years. To identify quantitative trait loci (QTLs) controlling agronomic, technological, and quality-related traits, a genetic map comprising 236 molecular markers was constructed, and composite interval mapping was performed. Beverage quality was evaluated in relation to biochemical and cup tasting traits. QTLs were identified for almost half of the traits evaluated, with effects ranging from 6% to 80% of phenotypic variation. Most of them present a consistent detection over years. The strongest QTLs explained a high percentage of the variation for yield in 2006 (34% to 57%), bean size (25% to 35%), content of chlorogenic acids (22% to 35%), sucrose and trigonelline content (29% to 81%), and acidity and bitterness of coffee beverages (30% to 55%). Regions of the C. canephora genome influencing beverage quality were identified. Five QTL zones were co-localized with candidate genes related to the biosynthesis of the analyzed traits: two genes coding for caffeine biosynthesis, one gene implicated in the biosynthesis of chlorogenic acids, and two genes implicated in sugar metabolism. This is one of the first studies on the identification of QTLs combining agronomic and quality traits in coffee. The high variability of quality traits within C. canephora and the presence of consistent QTLs offer breeders a promising tool to improve coffee cup quality. 相似文献
7.
H. Etienne F. Anthony S. Dussert D. Fernandez P. Lashermes B. Bertrand 《In vitro cellular & developmental biology. Plant》2002,38(2):129-138
Summary The important advances in coffee biotechnological techniques which have been made particularly during the last 10yr could
benefit the coffee breeder in practice and open new perspectives for the development of new varieties. The molecular phylogeny
of Coffea species has been established using DNA sequence data. The molecular markers have revealed an extremely reduced genetic diversity
in Coffea arabica L. in comparison to C. canephora. However, wild accessions collected in the Ethiopian highlands appeared to constitute a valuable gene reservoir. A complete
genetic linkage map of C. canephora was reported and additional ones are being constructed, particularly on C. arabica. The integration of Molecular Assisted Selection in coffee breeding promises to drastically increase the efficiency of breeding
programs. Economically important genes of the caffeine biosynthetic pathway or genes encoding for seed storage proteins have
been isolated. The high performance already achieved in the in vitro propagation process by somatic embryogenesis offers the possibility to mass propagate superior hybrids in different countries
of both C. arabica (selected F1 hybrids) and C. canephora (rootstock variety). Pilot productions by somatic embryogenesis currently permit preparation for commercial application.
Somaclonal variation was observed. The percentage of the off-types can vary between 3 and 10% depending on the genotype. Seed
cryopreservation enables a routine use for long-term conservation of coffee genetic resources. Transgenic plants have been
obtained for the C. arabica and C. canephora cultivated species through Agrobacterium-mediated transformation which constitutes the technique now currently used to transfer directly genes in coffee plants. 相似文献
8.
Paola Crisafulli Luciano Navarini Fabio Silizio Alberto Pallavicini Anna Illy 《Tropical plant biology》2014,7(1):1-12
In the coffee seed, the lipid component known as coffee oil is stored in the endosperm tissue as an energy reserve for germination and post-germination growth. This coffee constituent is present in the form of subcellular spherical oil bodies (“oleosomes”) in a typical size range of 0.2–2.5 μm. These particles are filled with an osmiophilic matrix of triglycerides, delimited by a single protein membrane, typical of oleaginous plant tissues. The object of this study is to characterize the morphology and distribution of oil bodies in different coffee species. In particular, we studied Indian samples of Coffea arabica, C. canephora, C. liberica, C. stenophylla and C. salvatrix. After appropriate fixation and preparation, the samples were examined and oil bodies characterized by optical microscopy and transmission electron microscopy. Oil bodies morphology, tissue distribution and size distribution were determined and several features of these subcellular structures were observed and discussed for the first time in the framework of a coffee inter-species comparative study. 相似文献
9.
R.L.R. Canche-Moo A. Ku-Gonzalez C. Burgeff V.M. Loyola-Vargas L.C. Rodríguez-Zapata E. Castaño 《Plant Cell, Tissue and Organ Culture》2006,84(3):373-377
Agrobacterium-mediated plant transformation protocol was evaluated as a fast method to obtain genetically modified Coffea canephora plantlets. Leaf explants were used as source material for Agrobacterium tumefaciens-mediated transformation involving a vacuum infiltration protocol, followed by a step of somatic embryogenesis induction and
a final selection of the transformed plants. A. tumefaciens strain C58CI containing the binary vector pER10W-35SRed was used. PCR amplification of DsRFP gene and visual detection of
the red fluorescent protein demonstrated 33% transformed embryos. The protocol presented here produces reliable transgenic
coffee embryos in two months. 相似文献
10.
11.
Jean-Christophe Breitler Eveline Dechamp Claudine Campa Leonardo Augusto Zebral Rodrigues Romain Guyot Pierre Marraccini Hervé Etienne 《Plant Cell, Tissue and Organ Culture》2018,134(3):383-394
Genome editing, which is an unprecedented technological breakthrough, has provided a valuable means of creating targeted mutations in plant genomes. In this study, we developed a genomic web tool to identify all gRNA target sequences in the coffee genome, along with potential off-targets. In all, 8,145,748 CRISPR guides were identified in the draft genome of Coffea canephora corresponding to 5,338,568 different sequences and, of these, 4,655,458 were single, and 514,591 were covering exons. The proof of concept was established by targeting the phytoene desaturase gene (CcPDS) using the Agrobacterium tumefaciens transformation technique and somatic embryogenesis as the plant regeneration method. An analysis of the RNA-guided genome-editing events showed that 22.8% of the regenerated plants were heterozygous mutants and 7.6% were homozygous mutants. Mutation efficiency at the target site was estimated to be 30.4%. We demonstrated that genome editing by the CRISPR/Cas9 method is an efficient and reliable way of knocking out genes of agronomic interest in the coffee tree, opening up the way for coffee molecular breeding. Our results also showed that the use of somatic embryogenesis, as the method for regenerating genome-edited plants, could restrict the choice of targeted genes to those that are not essential to the embryo development and germination steps. 相似文献
12.
While the conservation impacts of invasive plant species on tropical biodiversity is widely recognised, little is known of
the potential for cultivated crops turning invasive in tropical forest regions. In the Western Ghats biodiversity hotspot,
India, fragmented rainforests often adjoin coffee plantations. This study in the Anamalai hills assessed the effects of distance
from edges and forest structure on the occurrence and abundance of shade-tolerant coffee (Arabica Coffea arabica and Robusta C. canephora) in four fragments (32–200 ha) using replicate line transects laid from the edges into the interiors. The coffee species
cultivated in adjoining plantations was more abundant than the other coffee species inside study fragments, showing a clear
decline in stem density from edge (0 m) to interior (250 m), suggesting the influence of propagule pressure of adjoining plantations,
coupled with edge effects and seed dispersal by animals. Significant positive correlations of coffee density with canopy cover
indicate the potential threat of coffee invasion even in closed canopy rainforests. Stem density of Coffea arabica (150–1,825 stems/ha) was higher in more disturbed fragments, whereas Coffea canephora had spread in disturbed and undisturbed sites achieving much higher densities (6.3–11,486 stems/ha). In addition, a negative
relationship between C. canephora and native shrub density indicates its potential detrimental effects on native plants. 相似文献
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15.
Simkin AJ Moreau H Kuntz M Pagny G Lin C Tanksley S McCarthy J 《Journal of plant physiology》2008,165(10):1087-1106
16.
Leroy T Marraccini P Dufour M Montagnon C Lashermes P Sabau X Ferreira LP Jourdan I Pot D Andrade AC Glaszmann JC Vieira LG Piffanelli P 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2005,111(6):1032-1041
The first bacterial artificial chromosome (BAC) library of Robusta coffee (Coffea canephora) was constructed, with the aim of developing molecular resources to study the genome structure and evolution of this perennial crop. Clone 126, which is highly productive and confers good technological and organoleptic qualities of beverage, was chosen for development of this library. The BAC library contains 55,296 clones, with an average insert size of 135 Kb per plasmid, therefore representing theoretically nine haploid genome equivalents of C. canephora. Its validation was achieved with a set of 13 genetically anchored single-copy and 4 duplicated RFLP probes and yielded on average 9 BAC clones per probe. Screening of this BAC library was also carried out with partial cDNA probes coding for enzymes of sugar metabolism like invertases and sucrose synthase, with the aim of characterizing the organization and promoter structure of this important class of genes. It was shown that genes for both cell wall and vacuolar forms of invertases were probably unique in the Robusta genome whereas sucrose synthase was encoded by at least two genes. One of them (CcSUS1) was cloned and sequenced, showing that our BAC library is a valuable tool to rapidly identify genes of agronomic interest or linked to cup quality in C. canephora. 相似文献
17.
The cuticular waxes of leaves of Coffea arabica cv. ‘Catuaí Vermelho’, C. arabica cv. ‘Obatã’, Coffea canephora cv. ‘Apoatã’, Coffea racemosa and two hybrids between C. arabica and C. racemosa were extracted by rapid washing of the surface with chloroform. The waxes were fractionated by thin layer chromatography over silicagel. The fractions of the constituent classes were characterized by infrared spectroscopy and the distribution of the homologs of the n-alkanes and n-primary alcohols was determined by GC/MS and GC/FID. Among the samples analyzed, leaves of C. racemosa have the highest content of foliar wax (22.9 μg cm−2). Most samples contain either n-alkanes (C. canephora and C. racemosa) or n-primary alcohols (C. arabica) as predominant wax constituents. The distribution of n-alkanes allowed the distinction of C. racemosa from the other samples; the distribution of alcohols allowed the distinction of the three species. The two hybrids have waxes similar to the wax of C. arabica. 相似文献
18.
Priyono Bruno Florin Michel Rigoreau Jean-Paul Ducos Ucu Sumirat Surip Mawardi Charles Lambot Pierre Broun Vincent Pétiard Teguh Wahyudi Dominique Crouzillat 《Plant cell reports》2010,29(4):343-357
The purpose of the study was to evaluate the possible genetic effect on vegetative propagation of Coffea canephora. Diversity for somatic embryogenesis (SE) ability was observed not only among two groups of C. canephora Pierre (Congolese and Guinean), but also within these different genetic groups. The results therefore showed that, under given experimental conditions, SE ability is depending on genotype. Furthermore the detection of quantitative trait loci (QTLs) controlling the SE and cutting abilities of C. canephora was performed on a large number of clones including accessions from a core collection, three parental clones and their segregating progenies. On the one hand we detected eight QTLs determining SE. Six positive QTLs for SE ability, whatever the criteria used to quantify this ability, were localized on one single chromosome region of the consensus genetic map. Two negative QTLs for SE ability (frequency of micro calli without somatic embryo) were detected on another linkage group. Deep analysis of the six QTLs detected for SE ability came to the conclusion that they can be assimilated to one single QTL explaining 8.6–12.2% of the observed variation. On the other hand, two QTLs for average length of roots and length of the longest sprouts of cuttings were detected in two linkage groups. These QTLs detected for cutting ability are explaining 12–27% of the observed variation. These observations led to conclude that SE and cutting abilities of C. canephora Pierre appeared to be genetic dependent but through independent mechanisms. 相似文献
19.
Herrera JC Combes MC Anthony F Charrier A Lashermes P 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2002,104(4):661-668
Transfer of desired characters from the diploid relative species such as Coffea canephora into the cultivated allotetraploid coffee species (Coffea arabica L.) is essential to the continued improvement of varieties. Behaviour of the C. canephora genome and its interaction with the C. arabica genome were investigated in tetraploid interspecific hybrids (C. arabica×C. canephora 4x) resulting from a cross between an accession of C. arabica and a tetraploid plant of C. canephora obtained following colchicine treatment. Segregation and co-segregation of restriction fragment length polymorphism (RFLP)
and microsatellite loci-markers were studied in two BC1 populations. These two populations of 28 and 45 individuals, respectively, resulted from the backcross of two tetraploid
F1 plants to C. arabica. The presence in BC1 plants of specific C. canephora markers was scored for 24 loci (11 RFLP and 13 microsatellites) distributed on at least 7 of the 11 linkage groups identified
in C. canephora. At almost all loci analysed, the segregation of C. canephora alleles transmitted by the (C. arabica×C. canephora 4x) hybrids conformed to the expected ratio assuming random chromosome segregation and the absence of selection. The recombination
fractions of C. canephora chromosome segments were estimated for seven marker intervals, and compared with the recombination fractions previously observed
in C. canephora for the equivalent marker intervals. The recombination frequencies estimated in both plant materials were rather similar,
suggesting that recombination in the (C. arabica×C. canephora 4x) hybrid is not significantly restricted by the genetic differentiation between chromosomes belonging to the different genomes.
The hybrid (C. arabica×C. canephora 4x) therefore appeared particularly favourable to intergenomic recombination events and gene introgressions.
Received: 26 March 2001 / Accepted: 29 June 2001 相似文献