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Dive into the research topics where Marie-Christine Combes is active.

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Featured researches published by Marie-Christine Combes.


Molecular Genetics and Genomics | 1999

Molecular characterisation and origin of the Coffea arabica L. genome

Philippe Lashermes; Marie-Christine Combes; J. Robert; Pierre Trouslot; Angélique D'Hont; François Anthony; A. Charrier

Abstract 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.


Theoretical and Applied Genetics | 2002

The origin of cultivated Coffea arabica L. varieties revealed by AFLP and SSR markers

François Anthony; Marie-Christine Combes; Carlos Astorga; Benoît Bertrand; Giorgio Graziosi; Philippe Lashermes

Abstract.Molecular markers were used to assess polymorphism between and within the genetic bases of coffee (i.e. Typica and Bourbon) spread from Yemen since the early 18th century that have given rise to most arabica cultivars grown world-wide. Eleven Coffea arabica accessions derived from the disseminated bases were evaluated by amplified fragment length polymorphism (AFLP) using 37 primer combinations and simple-sequence repeats (SSRs) produced by six microsatellites. Four cultivars growing in Yemen and 11 subspontaneous accessions collected in the primary centre of diversity of the species were included in the study in order to define their relationship with the accessions derived from the genetic bases of cultivars. One hundred and seven AFLP markers were used to calculate genetic distances and construct a dendrogram. The accessions derived from the disseminated bases were grouped separately, according to their genetic origin, and were distinguished from the subspontaneous accessions. The Yemen cultivars were classified with the Typica-derived accessions. Except for one AFLP marker, all AFLP and SSR markers present in the cultivated accessions were also detected in the subspontaneous accessions. Polymorphism among the subspontaneous accessions was much higher than among the cultivated accessions. It was very low within the genetic bases, confirming the historical documentation on their dissemination. The results enabled a discussion of the genetic diversity reductions that successively occurred during the dissemination of C. arabica from its primary centre of diversity.


Euphytica | 1998

Identification and genetic diversity analysis of date palm (Phoenix dactylifera L.) varieties from Morocco using RAPD markers

My Hassan Sedra; Philippe Lashermes; Pierre Trouslot; Marie-Christine Combes

Genetic variation among 43 date palm (Phoenix dactylifera L.) accessions, including 37 accessions from Morocco and 6 cultivars from Iraq and Tunisia, was studied using Random Amplified Polymorphic DNA (RAPD) markers. The pre-screening of 123 primers on four genotypes allowed selection of 19 primers which revealed polymorphism and gave reproducible results. All 43 analysed genotypes were distinguishable by their band patterns. RAPD technology therefore appears very effective for identifying accessions of date palm. RAPD-based genetic distance was used to determine the relationships between the accessions. The grouping-association identified by cluster analysis was rather weak. However, morphologically similar varieties clustered together. A relatively low polymorphism and a lack of evident organisation are observed among the date palm varieties grown in Morocco. This could be related to the mode of introduction and maintenance of the Moroccan date palm germplasm involving limited foundation germplasm, exchange of cultivars between plantations, and periodic development of new recombinant cultivars following sexual reproduction.


Theoretical and Applied Genetics | 1997

Phylogenetic relationships of coffee-tree species ( Coffea L.) as inferred from ITS sequences of nuclear ribosomal DNA

Philippe Lashermes; Marie-Christine Combes; Pierre Trouslot; André Charrier

Abstract Phylogenetic relationships of Coffea species were estimated from the sequences of the internal transcribed spacer (ITS 2) region of nuclear ribosomal DNA. The ITS 2 region of 37 accessions belonging to 26 Coffea taxa and to three Psilanthus species was directly sequenced from polymerase chain reaction (PCR)-amplified DNA fragments. The level of variation was high enough to make the ITS 2 a useful tool for phylogenetic reconstruction. However, an unusual level of intraspecific variation was observed leading to some difficulty in interpreting rDNA sequence divergences. Sequences were analysed using Wagner parsimony as well as the neighbour-joining distance method. Coffea taxa were divided into several major groups which present a strong geographical correspondence (i.e. Madagascar, East Africa, Central Africa and West Africa). This organisation is well supported by cytogenetic evidence. On the other hand, the results were in contradiction with the present classification of coffee-tree taxa into two genera, namely Coffea and Psilanthus. Furthermore, additivity of parental rDNA types was not observed in the allotetraploid species C. arabica.


Euphytica | 1996

Genetic diversity for RAPD markers between cultivated and wild accessions of Coffea arabica

Philippe Lashermes; Pierre Trouslot; François Anthony; Marie-Christine Combes; André Charrier

SummaryRandom amplified polymorphic DNA (RAPD) markers have been successfully employed to analyse the genetic diversity among cultivated and subspontaneous accessions of Coffea arabica. The narrow genetic base of commercial cultivars was confirmed. On the other hand, a relatively large genetic diversity was observed within the germplasm collection demonstrating the importance of collecting missions. Results suggested an East-West differentiation in Ethiopia, the primary centre of diversification of C. arabica. The large heterosis effect reported in intergroup hybrids could be related to such genetic differentiation. RAPD method appeared to be effective in resolving genetic variations and in grouping germplasm in C. arabica.


Theoretical and Applied Genetics | 2000

Molecular analysis of introgressive breeding in coffee (Coffea arabica L.).

Philippe Lashermes; Sandra Andrzejewski; Benoît Bertrand; Marie-Christine Combes; Stéphane Dussert; Giorgio Graziosi; Pierre Trouslot; François Anthony

Abstract 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.


Euphytica | 1997

Identification of RAPD markers for resistance to coffee berry disease, Colletotrichum kahawae, in arabica coffee

Charles O. Agwanda; Philippe Lashermes; Pierre Trouslot; Marie-Christine Combes; A. Charrier

Resistance to Coffee Berry Disease (CBD) in Arabica coffee is controlled by at least three genes which are present in the varieties Hibrido de Timor (T gene), Catimor (T gene), Rume Sudan (R and k genes) and K7 (k gene). Hibrido de Timor, Catimor and Rume Sudan are genetically distant from most of the commercial cultivars, and the utilisation of molecular markers would greatly improve the efficiency of breeding programmes concerned with CBD resistance. The objectives of the present work were therefore: (1) to identify random amplified polymorphic DNA (RAPD) markers associated with CBD resistance and (2) to identify markers which could be used to select against the genetic background of the resistance donors. Identification of RAPD markers was carried out in three steps. The first step involved the comparison of the RAPD profiles between the susceptible cultivars and the resistant donors. This was followed by comparison of the RAPD profiles between resistant and susceptible types of each donor variety. The final step involved assay of the resistance markers in the first and the second backcrosses between these donors and the recurrent parent. High genetic variability was demonstrated in Catimor, and to some extent in Rume Sudan. Three RAPD markers were shown to be closely associated to the T gene. Attempts to identify markers associated with the R and k genes were less rewarding. The implications of the current observations in relation to breeding for CBD resistance in Arabica coffee are discussed.


Theoretical and Applied Genetics | 1996

Inheritance and restriction fragment length polymorphism of chloroplast DNA in the.genus Coffea L.

Philippe Lashermes; Joëlle Cros; Marie-Christine Combes; Pierre Trouslot; François Anthony; Serge Hamon; André Charrier

CpDNA variation among 52 tree samples belonging to 25 different taxa of Coffea and two species of Psilanthus was assessed by RFLP analysis on both the total chloroplast genome and the atpB-rbcL intergenic region. Twelve variable characters were distinguished allowing the identification of 12 different plastomes. The low sequence divergence observed might suggest that Coffea is a young genus. The results were in contradiction with the present classification into two genera. Additionally, cpDNA inheritance was studied in interspecific hybrids between C. arabica and C. canephora, and in an intraspecific progeny of C. canephora, using PCR-based markers. Both studies showed exclusively maternal inheritance of cpDNA.


Euphytica | 2002

AFLP analysis of introgression in coffee cultivars (Coffea arabica L.) derived from a natural interspecific hybrid

N.S. Prakash; Marie-Christine Combes; Naveen Somanna; Philippe Lashermes

S.288 an offspring of a putative spontaneous interspecific hybrid between tetraploid Coffea Arabica (2n = 4x = 44) and diploid C. liberica(2n = 2x = 22) and 17 arabica coffee introgression lines (representing F2 and F4) derived from the cross S.288 x Kent arabica were evaluated for introgression of C. liberica genetic material. In all, 36 AFLP primer combinations were used in the analysis. The AFLP profiles of introgressed lines were compared to five accessions each of C. arabica and C. liberica. A total of 137 polymorphic bands were scored among the 29 accessions analysed. The introgressed genotypes exhibited 102 marker bands consisting of 65 additional bands and 37missing bands associated with introgression of C. liberica genetic material. C. liberica accessions of EA group (C. liberica var liberica of Guinean origin) seemed to be the likely progenitor in the origin of natural hybrid. Analysis of genetic relationships in the introgressed lines suggested that introgression was limited to few fragments. Segregation and wide variation in number of marker fragments in the F2 and F4progenies were attributed to chromosome recombinations. The differences in the level of introgression between introgressed parent, F2 and F4 groups was not pronounced. Therefore the alien genetic material appeared to be fixed and there was no elimination or counter-selection over generations, from introgressed parent to F4.In C. arabica accessions, only 35 polymorphic bands were seen confirming the low genetic diversity. On the contrary, although representing a small amount of alien genome introgression, the Liberica-introgressed genotypes provided notable genetic diversity. Considering the fact that the diploid species of Coffea constitute a valuable source of genetic diversity, the potential implications of variability generated by Liberica-introgressed genotypes in C. arabica breeding are discussed.


BMC Plant Biology | 2011

Agrobacterium-mediated genetic transformation of Coffea arabica (L.) is greatly enhanced by using established embryogenic callus cultures

Alessandra F Ribas; Eveline Dechamp; Anthony Champion; Benoît Bertrand; Marie-Christine Combes; Jean-Luc Verdeil; Fabienne Lapeyre; Philippe Lashermes; Hervé Etienne

BackgroundFollowing genome sequencing of crop plants, one of the main challenges today is determining the function of all the predicted genes. When gene validation approaches are used for woody species, the main obstacle is the low recovery rate of transgenic plants from elite or commercial cultivars. Embryogenic calli have frequently been the target tissue for transformation, but the difficulty in producing or maintaining embryogenic tissues is one of the main problems encountered in genetic transformation of many woody plants, including Coffea arabica.ResultsWe identified the conditions required for successful long-term proliferation of embryogenic cultures in C. arabica and designed a highly efficient and reliable Agrobacterium tumefaciens-mediated transformation method based on these conditions. The transformation protocol with LBA1119 harboring pBin 35S GFP was established by evaluating the effect of different parameters on transformation efficiency by GFP detection. Using embryogenic callus cultures, co-cultivation with LBA1119 OD600 = 0.6 for five days at 20 °C enabled reproducible transformation. The maintenance conditions for the embryogenic callus cultures, particularly a high auxin to cytokinin ratio, the age of the culture (optimum for 7-10 months of proliferation) and the use of a yellow callus phenotype, were the most important factors for achieving highly efficient transformation (> 90%). At the histological level, successful transformation was related to the number of proembryogenic masses present. All the selected plants were proved to be transformed by PCR and Southern blot hybridization.ConclusionMost progress in increasing transformation efficiency in coffee has been achieved by optimizing the production conditions of embryogenic cultures used as target tissues for transformation. This is the first time that a strong positive effect of the age of the culture on transformation efficiency was demonstrated. Our results make Agrobacterium-mediated transformation of embryogenic cultures a viable and useful tool both for coffee breeding and for the functional analysis of agronomically important genes.

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Philippe Lashermes

Institut de recherche pour le développement

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François Anthony

Institut de recherche pour le développement

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Alberto Cenci

Institut de recherche pour le développement

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Hervé Etienne

Centre de coopération internationale en recherche agronomique pour le développement

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Alexis Dereeper

Institut de recherche pour le développement

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Stéphane Dussert

Institut de recherche pour le développement

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Laetitia Mahé

Institut de recherche pour le développement

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