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1.
P. Lashermes S. Andrzejewski B. Bertrand M. C. Combes S. Dussert G. Graziosi P. Trouslot F. Anthony 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2000,100(1):139-146
Nineteen arabica coffee introgression lines (BC1F4) and two accessions derived from a spontaneous interspecific cross (i.e. Timor Hybrid) between Coffea arabica (2n=4x=44) and C. canephora (2n=2x=22) were analysed for the introgression of C. canephora genetic material. The Timor Hybrid-derived genotypes were evaluated by AFLP, using 42 different primer combinations, and
compared to 23 accessions of C. arabica and 8 accessions of C. canephora. A total of 1062 polymorphic fragments were scored among the 52 accessions analysed. One hundred and seventy-eight markers
consisting of 109 additional bands (i.e. introgressed markers) and 69 missing bands distinguished the group composed of the
Timor Hybrid-derived genotypes from the accessions of C. arabica. AFLP therefore seemed to be an extremely efficient technique for DNA marker generation in coffee as well as for the detection
of introgression in C. arabica. The genetic diversity observed in the Timor Hybrid-derived genotypes appeared to be approximately double that in C. arabica. Although representing only a small proportion of the genetic diversity available in C. canephora, the Timor Hybrid obviously constitutes a considerable source of genetic diversity for arabica breeding. Analysis of genetic
relationships among the Timor Hybrid-derived genotypes suggested that introgression was not restricted to chromosome substitution
but also involved chromosome recombinations. Furthermore, the Timor Hybrid-derived genotypes varied considerably in the number
of AFLP markers attributable to introgression. In this way, the introgressed markers identified in the analysed arabica coffee
introgressed genotypes were estimated to represent from 9% to 29% of the C. canephora genome. Nevertheless, the amount of alien genetic material in the introgression arabica lines remains substantial and should
justify the development of adapted breeding strategies.
Received: 2 February 1999 / Accepted: 12 May 1999 相似文献
2.
A. Baruah V. Naik P. S. Hendre R. Rajkumar P. Rajendrakumar R. K. Aggarwal 《Molecular ecology resources》2003,3(4):647-650
Genetic improvement of coffee (Coffea arabica L.) is constrained by low genetic diversity and lack of genetic markers, suitable screening tools, information on the genetic make‐up of available gene pool and long generation time. In this context, use of DNA markers such as microsatellites that provide high genetic‐resolution becomes highly desirable. Here, we report the development of nine new microsatellite markers from partial genomic library of an elite variety of Coffea arabica. The developed microsatellites revealed robust cross‐species amplifications in 17 related species of coffee, and their Polymorphic Information Content varied from 0 to 0.6, 0 to 0.78 and 0.67 to 0.90 for the arabica, robusta genotypes and species representatives, respectively. The data thus suggest their potential use as genetic markers for assessment of germplasm diversity and linkage analysis of coffee. 相似文献
3.
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
4.
Gezahegn Berecha Raf Aerts Katrien Vandepitte Sabine Van Glabeke Bart Muys Isabel Roldán‐Ruiz Olivier Honnay 《Biological journal of the Linnean Society. Linnean Society of London》2014,112(1):76-88
Coffea arabica, the wild ancestor of all commercial Arabica coffee cultivars worldwide, is endemic to the montane rainforests of Ethiopia. These forests, which harbour the most important C. arabica gene pool, are threatened by increasing anthropogenic disturbance, potentially altering the mating patterns, pollen dispersal and maintenance of genetic diversity in C. arabica understorey populations. We genotyped 376 adult coffee shrubs and 418 progenies from three natural unmanaged, and three highly managed coffee populations, using 24 microsatellite markers. Mating system analysis of C. arabica yielded an overall multilocus outcrossing rate of 76%, which contrasts with the common knowledge that C. arabica is a predominantly selfing species. In highly managed coffee populations, paternity could be assigned to 78% of the progenies, whereas in the unmanaged natural coffee populations, only 57% of the progenies could be assigned to a father, indicating reduced long‐distance pollen dispersal in managed forests. Furthermore, the fraction of selfed progenies was significantly higher in managed (23%) than unmanaged (10%) coffee forests. Finally, the lack of spatial genetic structure in all studied populations suggests high seed dispersal in unmanaged populations, and intense berry harvesting and coffee planting in the managed populations. Our results imply that in situ conservation of the wild gene pool of C. arabica must focus on limiting intensification of coffee forest management, as decreased pollen dispersal and increased selfing in C. arabica in intensively managed populations may increase the risk of genetic erosion. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112 , 76–88. 相似文献
5.
Tiago Vieira Sousa Eveline Teixeira Caixeta Emilly Ruas Alkimim Antonio Carlos Baião de Oliveira Antonio Alves Pereira Ney Sussumu Sakiyama Marcio Fernando Ribeiro de Resende Júnior Laércio Zambolim 《Tree Genetics & Genomes》2017,13(6):124
The use of single nucleotide polymorphism (SNP) molecular markers has provided advances in selection methodologies used in breeding programs of different crops, reducing cost and time of cultivar release. Despite the great economic and social importance of Coffea arabica, studies with SNP markers are scarce and a small number of SNP are available for this species, when compared with other crops of agronomic importance. Thus, the objective of this study was to identify and validate SNP molecular markers for the species Coffea arabica and to introduce these markers to genetic breeding by means of an accurate analysis of the diversity and genetic structure of breeding populations of this species. After quality filtering, 11,187 SNP markers were selected from the coffee population obtained from crosses between the genotypes Catuaí and Híbrido de Timor. A great number of markers were distributed in the 11 chromosomes, within transcribed regions, and were used to estimate the genetic dissimilarity among the individuals of the breeding population. Dendrogram analysis and a Bayesian approach demonstrated the formation of two groups and the discrimination of all genotypes evaluated. The expressive number of SNP molecular markers distributed throughout C. arabica genome was efficient to discriminate all the accessions evaluated in the experiment, clustering them according to their genealogies. This work identified mixtures within the progenies. The genotyping data also provided detailed information about the parental genotypes and led to the identification of new candidate parents to be introduced to the breeding program. The study discussed population structure and its consequence in obtaining improved varieties of C. arabica. 相似文献
6.
Inter-simple sequence repeat (ISSR) variation in forest coffee trees (Coffea arabica L.) populations from Ethiopia 总被引:1,自引:0,他引:1
Genetic variation of forest coffee trees (Coffea arabica L.) from four regions of Ethiopia was investigated using inter-simple sequence repeat (ISSR) markers. A total of 160 individuals
representing 16 populations were sampled. Eleven ISSR primers amplified a total of 123 fragments of which 31 fragments (25%)
were polymorphic. Estimate of total gene diversity (H
T), and the coefficient of genetic differentiation (G
ST) were 0.37 and 0.81, respectively. This indicates that most of the variability is between populations than within populations.
The partitioning of genetic variation into within and between populations based on Shannon’s information index also revealed
more differentiation between populations (0.80) than within populations (0.20). In the phenogram most of the coffee tree samples
were clustered on the basis of their regions of origin but failed to cluster according to their respective populations, which
could be attributed to the presence of substantial gene flow between adjacent populations in each region assisted by man in
the process of transplantation or by wild animals such as monkeys, which eat the berries and defecate the seeds elsewhere.
On the other hand, the inter-regional clustering of some coffee tree samples from Bale and Jimma regions could be due to the
transport of coffee seeds across regions and their subsequent planting. Although ISSR markers detected lower polymorphic loci
than previously reported results with random amplified polymorphic DNA (RAPD) markers on the same materials, it can be used
as an alternative method for molecular characterization of C. arabica populations. The results may provide information to select sites for in situ conservation. 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.
V. Rani K. P. Singh B. Shiran S. Nandy S. Goel R. M. Devarumath H. L. Sreenath S. N. Raina 《Plant cell reports》2000,19(10):1013-1020
The most important commercial species of coffee, Coffea arabica, which produces 73% of the world's coffee crop and almost all of the coffee in Latin America, is the only tetraploid (allotetraploid,
2n=4x=44) species known in the genus. High-frequency somatic embryogenesis, plant regeneration and plant recovery were achieved
from leaf explants of a mature, elite plant of C. arabica cv. Cauvery (S-4347) using a two-step culture method. To assess the genetic integrity of the nuclear, mitochondrial and chloroplast
genomes among the hardened regenerants, we employed multiple DNA markers (RFLP, RAPD, ISSR) for sampling various regions of
the genome. Although the nuclear and mitochondrial genomes of the mother plant and five ramets derived from the mother ortet
were similar in organization, this was not so in the somatic embryo-derived plants where both nuclear and mitochondrial genomes
changed in different, characteristic ways and produced novel genome organizations. A total of 480 genetic loci, based on the
data obtained from a total of 16 nuclear, mitochondrial and chloroplast gene probes, in combination with nine restriction
enzyme digests, 38 RAPD and 17 SSR primers, were scored in 27 somatic embryo-derived plants and the single control. Among
these, 44 loci were observed to be polymorphic. A relatively low level of polymorphism (4.36%) was found in the nuclear genome,
while polymorphism in the mitochondrial genome (41%) was much higher. No polymorphism was detected in the chloroplast genome.
The polymorphism in the mitochondrial genome was found in only 4 plants. Such selective polymorphism was not true for the
nuclear genome. Thus, this in-depth and comprehensive study demonstrates, for the first time, the presence of subtle genetic
variability and novel genome organizations in the commercially well-established somatic embryogenesis-derived plants of this
important coffee species.
Received: 2 July 1999 / Revision received: 1 February 2000 / Accepted: 17 February 2000 相似文献
9.
Lucas Fidelis Pereira Elaine Aparecida de Souza Fernanda Aparecida Castro Pereira Flvia Maria Avelar Gonalves 《Journal of Phytopathology》2019,167(11-12):645-654
Coffee blister spot has been associated with species from the Colletotrichum genus, but there is no information on the variability of isolates present on leaf lesions. This study evaluated a population of Colletotrichum gloeosporioides strains from blister spot lesions in Coffea arabica. Colletotrichum spp. isolates were collected from blister spot lesions on leaves of coffee trees from Catuaí and Topázio cultivars (Coffea arabica). Monosporic cultures were obtained from colonies with sporulation. A pathogenicity test was carried out by inoculation of pathogens on the leaves of young coffee plants. C. gloeosporioides strains were characterized by morphologial, cytological and physiological analyses. The molecular analysis was carried out using Inter‐Retrotransposon Amplified Polymorphism (IRAP) markers. C. gloeosporioides strains showed no pathogenicity on coffee plants and presented a wide variability in all traits evaluated. The presence of sexual strains, formation of CATs (conidial anastomosis tubes) among conidial strains and high mycelial compatibility among strains observed suggest the occurrence of sexual and asexual recombination. The role of these C. gloeosporioides strains on the lesions of coffee plant leaves is unclear. 相似文献
10.
Virginie Merot‐L'anthoene Rmi Tournebize Olivier Darracq Vimel Rattina Maud Lepelley Laurence Bellanger Christine Tranchant‐Dubreuil Manon Coule Marie Pgard Sylviane Metairon Coralie Fournier Piet Stoffelen Steven B. Janssens Catherine Kiwuka Pascal Musoli Ucu Sumirat Hyacinthe Legnat Jean‐Lon Kambale Joo Ferreira da Costa Neto Clara Revel Alexandre de Kochko Patrick Descombes Dominique Crouzillat Valrie Poncet 《Plant biotechnology journal》2019,17(7):1418-1430
Coffee species such as Coffea canephora P. (Robusta) and C. arabica L. (Arabica) are important cash crops in tropical regions around the world. C. arabica is an allotetraploid (2n = 4x = 44) originating from a hybridization event of the two diploid species C. canephora and C. eugenioides (2n = 2x = 22). Interestingly, these progenitor species harbour a greater level of genetic variability and are an important source of genes to broaden the narrow Arabica genetic base. Here, we describe the development, evaluation and use of a single‐nucleotide polymorphism (SNP) array for coffee trees. A total of 8580 unique and informative SNPs were selected from C. canephora and C. arabica sequencing data, with 40% of the SNP located in annotated genes. In particular, this array contains 227 markers associated to 149 genes and traits of agronomic importance. Among these, 7065 SNPs (~82.3%) were scorable and evenly distributed over the genome with a mean distance of 54.4 Kb between markers. With this array, we improved the Robusta high‐density genetic map by adding 1307 SNP markers, whereas 945 SNPs were found segregating in the Arabica mapping progeny. A panel of C. canephora accessions was successfully discriminated and over 70% of the SNP markers were transferable across the three species. Furthermore, the canephora‐derived subgenome of C. arabica was shown to be more closely related to C. canephora accessions from northern Uganda than to other current populations. These validated SNP markers and high‐density genetic maps will be useful to molecular genetics and for innovative approaches in coffee breeding. 相似文献
11.
Erika V. S. Albuquerque Welcimar G. Cunha Aulus E. A. D. Barbosa Poliene M. Costa João B. Teixeira Giovanni R. Vianna Glaucia B. Cabral Diana Fernandez Maria F. Grossi-de-Sa 《In vitro cellular & developmental biology. Plant》2009,45(5):532-539
The genetic modification of Coffea arabica fruits is an important tool for the investigation of physiological characteristics and functional validation of genes related
to coffee bean quality traits. In this work, plants of C. arabica cultivar Catuaí Vermelho were successfully genetically modified by bombardment of embryogenic calli. Calli were obtained
from 90% of the leaf explants cultivated in a callogenesis-inducing medium modified with 20 μM 2,4-dichlorophenoxyacetic acid
(2,4-D). The resulting calli were bombarded with the pBI426 vector containing a uidA and nptII gene fusion that was driven by the double CaMV35s promoter. Kanamycin-selected embryos were positive for β-glucuronidase
(GUS) activity in histochemical assays and for target gene amplification by polymerase chain reaction. Integration of the
nptII gene was confirmed by Southern blot and showed a low copy number (one to three) of insertions. Transformed plants showed
normal development and settled fruits. GUS expression was assessed in the flower and fruit organs demonstrating the capacity
of the double CaMV35s promoter to drive long-term stable expression of uidA in C. arabica fruit tissues. Moreover, we obtained a T1 progeny presenting 3:1 Mendelian segregation of the uidA gene. This investigation is the first to report exogenous gene expression in coffee fruits and transgenic inheritance in
C. arabica plants. 相似文献
12.
Emilly Ruas Alkimim Eveline Teixeira Caixeta Tiago Vieira Sousa Antônio Alves Pereira Antonio Carlos Baião de Oliveira Laércio Zambolim Ney Sussumu Sakiyama 《Molecular breeding : new strategies in plant improvement》2017,37(1):6
Selecting superior genotypes is facilitated by marker-assisted selection (MAS), which is particularly suitable for transferring disease resistance alleles because it nullifies environmental effects and allows selection of resistant individuals in the absence of the pathogen or race, enabling preventive breeding. Molecular markers linked to two major genes (SH3 and SH?), conferring resistance to coffee rust, and those linked to the Ck-1 gene, conferring resistance to coffee berry disease (CBD), have previously been identified. These markers were validated and used in a progeny of crosses between Indian selections with Coffea arabica cultivars. Eleven resistant individuals homozygous for SH3 were identified by MAS. Of these, seven carry SH? from Híbrido de Timor and the gene introduced from Coffea liberica (SH3). SH? was characterized as derived from Coffea canephora. Thus, it was possible to identify C. arabica genotypes carrying important genes for rust resistance introgressed from other coffee species. MAS also allowed identification of sources of CBD resistance for use in preventive breeding for resistance to this serious disease. Using two validated molecular markers, two coffee plants carrying Ck-1 were identified: the UFV 328-60 genotype (F2) was resistant and homozygous based on both molecular markers but exhibited no markers related to SH3 and SH?, and the UFV 317-12 genotype (F1) was resistant and homozygous but resistant and heterozygous based on CBD-Sat207 and CBD-Sat235, respectively. Along with possessing Ck-1, the latter carries SH?. Overall, plants carrying different genes for resistance to rust and CBD were identified. These plants are important sources for gene pyramiding in breeding programs aimed at multiple and durable resistance. 相似文献
13.
N. E. Nyange B. Williamson G. D. Lyon R. J. McNicol T. Connolly 《Plant cell reports》1997,16(11):763-769
Hypocotyl-derived calli of genotypes and segregating populations of Coffea arabica, differing in susceptibility to Colletotrichum kahawae, were used to produce cell suspensions and protoplasts which were exposed to partially purified culture filtrates (PPCFs)
prepared from the pathogen. The growth and viability of PPCF-treated cells and protoplasts were measured using packed cell
volume, fluorescein diacetate staining and a colorimetric assay involving the tetrazolium salt MTT. Differential responses
of cells and protoplasts were influenced by genotype, time of exposure and PPCF concentration. Protoplasts of resistant genotypes
responded differentially from more susceptible genotypes as early as 4 h after challenge with the phytotoxin, suggesting that
they were more sensitive than cell suspensions to the treatments. Protoplasts exposed to PPCFs from C. kahawae may therefore be used to screen and select genotypes resistant to, or tolerant of, coffee berry disease.
Received: 10 April 1996 / Revision received: 25 August 1996 / Accepted: 15 September 1996 相似文献
14.
Laetitia Mahé Marie-Christine Combes Vitor M. P. Várzea Claire Guilhaumon Philippe Lashermes 《Molecular breeding : new strategies in plant improvement》2008,21(1):105-113
Coffee leaf rust due to Hemileia vastatrix is one of the most serious diseases in Arabica coffee (Coffea arabica). A resistance gene (SH3) has been transferred from C. liberica into C. arabica. The present work aimed at developing sequence-characterized genetic markers for leaf rust resistance. Linkage between markers
and leaf rust resistance was tested by analysing two segregating populations, one F2 population of 101 individuals and one backcross (BC2) population of 43 individuals, derived from a cross between a susceptible and a SH3-introgressed resistant genotype. A total
of ten sequence-characterized genetic markers closely associated with the SH3 leaf rust resistance gene were generated. These included simple sequence repeats (SSR) markers, sequence-characterised amplified
regions (SCAR) markers resulting from the conversion of amplified fragment length polymorphism (AFLP) markers previously identified
and SCAR markers derived from end-sequences of bacterial artificial chromosome (BAC) clones. Those BAC clones were identified
by screening of C. arabica genomic BAC library using a cloned AFLP-marker as probe. The markers we developed are easy and inexpensive to run, requiring
one PCR step followed by gel separation. While three markers were linked in repulsion with the SH3 gene, seven markers were clustered in coupling around the SH3 gene. Notably, two markers appeared to co-segregate perfectly with the SH3 gene in the two plant populations analyzed. These markers are suitable for marker-assisted selection for leaf rust resistance
and to facilitate pyramiding of the SH3 gene with other leaf rust resistance genes. 相似文献
15.
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
16.
Kassahun Tesfaye Kim Govers Endashaw Bekele Thomas Borsch 《Plant Systematics and Evolution》2014,300(5):881-897
Forests of SW Ethiopia constitute the native habitat of Coffea arabica and also the place where domestication of Arabica coffee started. Selection from wild populations has led to numerous landraces (farmer’s varieties) and cultivars. Inter-simple sequence repeats (ISSRs) were generated from a representative set of forest coffee populations and landraces across Ethiopia. For the broad diversity assessment, nine di- and tri-nucleotide ISSR primers were applied, as chosen from a total of 102 primers tested initially. Tetranucleotide ISSR primers differed in amplifying fingerprints that could hardly be analysed due to excessive variation. Tree building analysis (NJ, UPGMA) of 84 polymorphic loci amplified for 125 C. arabica individuals provided evidence for several groups of related genotypes occurring in certain geographical areas of Ethiopia and underscored the existence of wild coffee distinct from landraces. Landraces seem to have originated in different geographical areas of Ethiopia in a stepwise domestication process. While the overall geographical signal in the dataset was weak, analysis in a Bayesian framework using the admixture model with geographical priors in STRUCTURE recovered some genetic clustering. Based on Shannon’s diversity index, populations from Yayu (0.47) and Bonga (0.46) showed highest diversity, followed by individuals from Berhane Kontir (0.41). A likely scenario for the differentiation of C. arabica after an allopolyploidization event is that the hierarchical-geographical patterning of wild Coffea genotypes expected from stepwise range extension was obscured by recent or ancient gene flow. The diversity and geographical distribution of autochthonous C. arabica genotypes indicates the need for a multi-site in situ conservation approach. 相似文献
17.
Lin Zhou Fernando E. Vega Huawei Tan Aixa E. Ramírez Lluch Lyndel W. Meinhardt Wanping Fang Sue Mischke Brian Irish Dapeng Zhang 《Tropical plant biology》2016,9(2):82-95
Coffee is one of the most widely consumed beverages and represents a multibillion-dollar global industry. Accurate identification of coffee cultivars is essential for efficient management, exchange, and use of coffee genetic resources. To date, a universal platform that can allow data comparison across different laboratories and genotyping platforms has not been developed by the coffee research community. Using expressed sequence tags (EST) of Coffea arabica, C. canephora and C. racemosa from public databases, we developed 7538 single nucleotide polymorphism (SNP) markers and selected 180 for validation using 25 C. arabica and C. canephora accessions from Puerto Rico. Based on the validation result, we designated a panel of 55 SNP markers that are polymorphic across the two species. The average minor allele frequency and information index of this SNP panel are 0.281 and 0.690, respectively. This panel enabled the differentiation of all tested accessions of C. canephora, which accounts for 79.2 % of the total polymorphism in the samples. Only 21.8 % of the polymorphic SNPs were detected in the 12 C. arabica cultivars, which, nonetheless, were able to unambiguously differentiate the 12 Arabica cultivars into ten unique genotypes, including two synonymous groups. Several local Puerto Rican cultivars with partial Timor pedigree, including Limaní, Frontón, and TARS 18087, showed substantial genetic difference from the other common Arabica cultivars, such as Catuai, Borbón, and Mundo Nuevo. This coffee SNP panel provides robust and universally comparable DNA fingerprints, thus can serve as a genotyping tool to assist coffee germplasm management, propagation of planting material, and coffee cultivar authentication. 相似文献
18.
German López-Gartner Hernando Cortina Susan R. McCouch Maria Del Pilar Moncada 《Tree Genetics & Genomes》2009,5(3):435-446
The knowledge of population structure is important to determine the degree of linkage disequilibrium, which allows the selection
of genotypes for association mapping. Using 47 SSR markers, the genetic variability and population structure of 68 accessions
of C. arabica (wild and cultivated) and of three diploid species used as reference were evaluated. The analysis was done with the distance
method and the structure model. The structure analysis inferred nine subpopulations (k = 9), for which the greatest values of probability were obtained. Three of the groups corresponded to the three diploid species
as expected. There were six groups identified within C. arabica. The genetic subdivisions within C. arabica were based on geographical origin, degree of domestication, and dispersal history of coffee. One group consisted entirely
of cultivated genotypes, where intense population bottleneck were associated with a founder effect. This was the most homogeneous
group, as demonstrated by the reduced distance between cultivars in the dendrogram. Three of the cultivated genotypes, originating
from Sudan, were separated into an independent group, presumably due to selective adaptation to a different set of environmental
conditions. Another group consisted of genotypes of the type “ennarea” that were grown and cultivated in isolation on the
shores of the Tana lake. The semi-wild genotypes clustered into three different groups. This type of analysis provides a strong
evidence of population structure in C. arabica. Based on these findings, it is possible to better identify a balanced sample of diverse plants in germplasm. 相似文献
19.
N E. Nyange B. Williamson R J. McNicol G D. Lyon Christine A. Hackett 《The Annals of applied biology》1995,127(3):425-439
Calli derived from hypocotyl explants of a susceptible and resistant genotype of Coffea arabica were evaluated for their response to different concentrations of partially purified culture filtrates (PPCFs) produced by Colletotrichum kahawae which are phytotoxic. The size of calli was measured non-destructively by automated image analysis. Differential responses of calli ranged from complete necrosis or reduced growth in the susceptible genotype (N39) to an absence of necrosis and rapid growth in the resistant genotype (cv. Hybrido de Timor). Subsequently, one selection cycle in the presence of PPCF was devised and applied to calli of nine C. arabica genotypes. Normal plants were regenerated through somatic embryogenesis of callus lines that survived the phytotoxin treatment and in vitro and in vivo testing of these plants against the PPCF showed that increased resistance to the toxin had been obtained. These studies suggest that in vitro selection of calli may be a feasible approach to acquiring germplasm with improved resistance to coffee berry disease. 相似文献
20.
Lashermes P Combes MC Robert J Trouslot P D'Hont A Anthony F Charrier A 《Molecular & general genetics : MGG》1999,261(2):259-266
Restriction fragment length polymorphism (RFLP) markers were used in combination with genomic in situ hybridisation (GISH)
to investigate the origin of the allotetraploid species Coffea arabica (2n = 44). By comparing the RFLP patterns of potential diploid progenitor species with those of C. arabica, the sources of the two sets of chromosomes, or genomes, combined in C. arabica were identified. The genome organisation of C. arabica was confirmed by GISH using simultaneously labelled total genomic DNA from the two putative genome donor species as probes.
These results clearly suggest that C. arabica is an amphidiploid formed by hybridisation between C. eugenioides and C. canephora, or ecotypes related to these diploid species. Our results also indicate low divergence between the two constituent genomes
of C. arabica and those of its progenitor species, suggesting that the speciation of C. arabica took place relatively recently. Precise localisation in Central Africa of the site of the speciation of C. arabica, based on the present distribution of the coffee species, appears difficult, since the constitution and extent of tropical
forest has varied considerably during the late Quaternary period.
Received: 6 June 1998 / Accepted: 10 November 1998 相似文献