Papers by Christophe Montagnon
27th Biennial ASIC Conference, Portland, 16-20 September 2018. Book of abstracts 2019, 2019
RATIONALE While several studies have described the genetic diversity of C.arabica, none has inclu... more RATIONALE While several studies have described the genetic diversity of C.arabica, none has included the whole range of Ethiopian accessions together with a large representation of the varieties cultivated worldwide. None included recently surveyed South Sudanese populations. Over the last years, WCR has built a large database that actually includes all the dimensions of genetic diversity of the species: from Ethiopian, Yemeni and South Sudanese accessions to a large representation of old and new cultivated varieties. The results of the detailed analysis of this database (SSR) are presented here. METHODS The data base represents i) One core collection established in 2014 including mainly Ethiopian accessions (FAO and ORSTOM surveys), ii) Populations of wild arabicas surveyed in South Sudan in 2014 and iii) a large representation of cultivated varieties worldwide. More than 2000 entries of this database were genotyped using a set of9 SSR markers. Multivariate analysis (PCoA) were run in order to decipher the underlying genetic diversity. RESULTS For the first time, wild C. arabica populations of South Sudan are shown to bring new genetic diversity as compared to Ethiopian wild arabicas. A structuration of the Ethiopian accessions surveyed in the 60's (FAO and Orstom) is unraveled. The traditional Bourbon/Typica varieties are genetically related to the Ethiopian cluster east of the Ethiopian coffee area. This study gives a new light on the history of C. arabica movement around the world. While the genetic diversity of cultivated varieties around the world is confirmed to be relatively low, it is still possible to authenticate them through fingerprinting. Most varieties show a residual segregation and not fully fixed homozygous lines. Consequences for varieties authentication are discussed. CONCLUSIONS & PERSPECTIVES This study is the first of its kind with SSR on a wide range of Arabica accessions and varieties. It gives us a new vision of the genetic diversity of the species and history of its movements. As exemplified by the South Sudan Arabica populations, new genetic diversity is to be found in the vast Arabica center of origin covering mainly Ethiopia but also South Sudan. India has been a very important and often overlooked step for the dissemination of genetic diversity out of Ethiopia. As for practical application, opportunities and challenges of varieties authentication through DNA fingerprinting are discussed
Parmi les facteurs qui influencent la durabilite des cultures perennes, l'apport du materiel ... more Parmi les facteurs qui influencent la durabilite des cultures perennes, l'apport du materiel vegetal est envisage dans les cas du cacaoyer, du cafeier et du cocotier. L'apport du materiel vegetal ameliore se situe au niveau de l'aptitude a l'etablissement, de la resistance aux aleas biotiques et abiotiques, du potentiel de production et de la possibilite d'evolution de ce materiel. Ces avantages sont determinants dans le contexte actuel de disparition des fronts pionniers et de la replantation apres jachere. Ils justifient l'investissement de la recherche pour la creation de varietes d'une part et celui des planteurs pour leur acquisition d'autre part. Cependant, l'accessibilite des planteurs a ce materiel devrait etre facilitee. Par ailleurs, les techniques culturales adaptees a ce materiel devraient faire l'objet d'une vulgarisation renforcee. (Resume d'auteur)
Euphytica, 2022
Robusta coffee ( Coffea Canephora ) is an important source of income and employment, contributing... more Robusta coffee ( Coffea Canephora ) is an important source of income and employment, contributing significantly to the economies of many developing countries. This species is split into two genetic groups: Guinean and Congolese. Côte-d’Ivoire is the primary diversification center of the Guinean pool, which offers great potential for genetic improvement. However, genetic erosion of this group is currently a threat in this country because of the massive introduction of Congolese accessions done in the previous decades. In this work, we analyzed the progenies of isolated population of C. canephora composed of a mix of Guinean and Congolese using SNP markers. The analysis is focus on the male parents’ contribution in open pollination. The results show that the introduction of cultivars from the Congolese gene pool threat the genetic integrity of wild populations from the Guinean gene pool. Indeed, this analysis showed that Congolese pollens have more ability to pollinate the Guinean gro...
27th Biennial ASIC Conference, Portland, 16-20 September 2018. Book of abstracts 2019, 2019
RATIONALE Access to basic economic information (production costs, losses, etc.) is fundamental to... more RATIONALE Access to basic economic information (production costs, losses, etc.) is fundamental to evaluating and influencing the survival of any business. The coffee industry has a vested interest in ensuring the wellbeing of its smallholder farmers (Ponte, 2002), who tend to be from lower socioeconomic backgrounds (Bacon, 2005) and do not keep records of spending or income. Through focus groups and Monte Carlo simulation techniques (Mun, 2006) we assessed profitability amongst six smallholder Guatemalan coffee farming communities who received the 'Centroamericano' coffee hybrid: a varietal innovation whose impact on profitability has never been studied in this context. METHODS In 2018, using participatory methods (Narayanasamy, 2009), focus groups were held with nearly 200 members of six smallholder coffee farming associations in San Pedro Y epocapa, Guatemala, who received the high-yielding, coffee leaf rust resistant 'Centroamericano' coffee hybrid through a development project implemented by World Coffee Research and Anacafe. Cost of living, cost and income from coffee production, for traditional varieties as well as the hybrid, and business structure at both the household and cooperative levels were identified for the six cooperatives. Qualitative data were analysed by the constant comparative method and net cash farm income was the key output variable used to measure economic feasibility through Monte Carlo simulation. RESULTS We show that profitability of the ' Centroamericano' hybrid in smallholder systems depends on multiple parameters: it exhibits high productivity, resistance to coffee leaf rust and large bean size but requires more inputs to achieve these. Details, including profitability comparisons of the six cooperatives and between traditional varieties and the hybrid will be displayed in stop-light charts. CONCLUSIONS & PERSPECTIVES We conclude that the ' Centroamericano' hybrid can improve profitability for smallholder coffee farmers ifthe productivity potential is met, but higher inputs and technical assistance are required
Le Reseau de recherche sur le cafe (Reca) a ete cree en 1993 par l'Organisation interafricain... more Le Reseau de recherche sur le cafe (Reca) a ete cree en 1993 par l'Organisation interafricaine du cafe. Ce reseau comprend 18 pays membres africains et 5 membres associes. Il est charge de promouvoir des programmes de recherche conjoints destines a accroitre la productivite, reduire les couts de production et ameliorer la qualite du cafe produit. Depuis 1993, le reseau a largement contribue aux echanges scientifiques entre les chercheurs africains Il a permis de lancer divers projets de recherche regionaux visant a lutter contre des maladies ou insectes, mais aussi a ameliorer la qualite du cafe produit. Cet article presente les objectifs, les activites et les acquis du Reca. (Resume d'auteur)
Una de las mayores limitantes para el cultivo del cafeto Coffea canephora en Africa es el bajo in... more Una de las mayores limitantes para el cultivo del cafeto Coffea canephora en Africa es el bajo indice de utilizacion de material vegetal seleccionado. Para Cote d'Ivoire, por ejemplo, este material solo representa aproximadamente el 10% de la superficie
148 varietes d'une collection de C.arabica ont ete evaluees pour 31 criteres botaniques, arch... more 148 varietes d'une collection de C.arabica ont ete evaluees pour 31 criteres botaniques, architecturaux, technologiques, phytopathologique s (resistance aux maladies) et de productivite. Ce travail a permis pour la 1ere fois l'identification de 2 groupes principaux. Le 1er ne contient presque que des genotypes ethiopiens provenant de l'ouest du Rift, alors que le second contient la plupart des varietes cultivees a travers le monde et des genotypes ethiopiens de l'est du Rift. Le groupe 1 ne semble pas avoir participe a la domestication de C. arabica. Les resultats confirment l'interet pour l'enrichissement de la base genetique de l'espece des prospections en Ethiopie a l'ouest de la Rift valley. Une telle prospection, realisee en 1966 par l'IRCC et l'ORSTOM, est a l'origine de 50 des varietes etudiees, parmi lesquelles une structuration phenotypique forte a ete decelee
Cette mission d'appui au programme cafe de l'Irag a permis de dresser un etat des lieux s... more Cette mission d'appui au programme cafe de l'Irag a permis de dresser un etat des lieux sur le dispositif actuel et les axes de recherche cafe a l'Irag. L'examen du programme de selection de clones locaux et introduits ainsi que l'examen du programme sur les techniques culturales ont conduit a presenter des propositions et recommandations sur quatre axes majeurs : les techniques culturales, la selection varietale, les traitements post-recolte et la defense des cultures
2 essais d'hybridation avec 20 a 100 cafeiers par descendance sont analyses en comparant les ... more 2 essais d'hybridation avec 20 a 100 cafeiers par descendance sont analyses en comparant les hybrides intergroupes (Congolais x Guineen) a des clones temoins haut-producteurs. Le diametre du tronc a 30 mois et la productivite (3 ans de recolte) sont analyses statistiquement. Les descendances controlees sont obtenues par pollinisation manuelle. Les meilleures descendances sont equivalentes au temoin le plus productif (clone 461). 84 cafeiers de 16 descendances hybrides produisent individuellement plus que la production moyenne du clone 461. En tenant compte d'autres caracteres selectionnes, 61 cafeiers ont ete retenus pour des essais clonaux
Canephora coffee is an important source of income and employment, contributing significantly to t... more Canephora coffee is an important source of income and employment, contributing significantly to the economies of many developing countries. This species is split into two genetic groups: Guinean and Congolese. Côte-d’Ivoire is the primary diversification center of the Guinean pool, which offers great potential for genetic improvement. However, genetic erosion of this group is currently a threat in this country because of the massive introduction of Congolese accessions in the previous decades. In this work, we analyzed the progenies of isolated population of C. canephora composed of a mix of Guinean and Congolese using SNP markers. The analysis is focus on the male parents’ contribution on open pollination progenies. The result shows that the introduction of cultivars from the Congolese gene pool threat the genetic integrity of wild populations of the Guinean gene pool. We recommend that a conservation program be put in place to ensure the entegrity of wild population of C. canephor...
L'objet de la mission etait d'une part l'appui au projet RC'2 et a l'IRAG en ... more L'objet de la mission etait d'une part l'appui au projet RC'2 et a l'IRAG en agronomie, selection clonale et production de materiel vegetal, d'autre part la definition d'un programme de recherchedevelop pement pour l'expert cafe affecte a l'IRAG. Dans une premiere partie, sont donnes les resultats concernant la production de materiel vegetal : etat et conduite des parcs a bois, preparation des boutures feuilles et substrat de bouturage, bacs et ombrieres, sortie des boutures et devenir des boutures racinees. La seconde partie est consacree au programme de RechercheDeveloppement : Description du dispositif actuel de la RechercheDeeloppement en Guinee; Remarques d'ordre general sur l'environnement des essais en station et des points d'essais, et sur l'UEP et les demonstrations; Presentation des axes du Programme; Protection des cultures; Strategie qualite; Cas du Fouta Djallon
Frontiers in Sustainable Food Systems, 2021
Cultivated Arabica coffee outside Ethiopia is plagued by low genetic diversity, compromising dise... more Cultivated Arabica coffee outside Ethiopia is plagued by low genetic diversity, compromising disease resistance, climate resiliency and sensory potential. Access to the wider genetic diversity of this species may circumvent some of these problems. In addition to Ethiopia, South Sudan has been postulated as a center of origin for Arabica coffee, but this has never been genetically confirmed. We used simple sequence repeat (SSR) markers to assess the genetic diversity of wild and cultivated populations of Arabica coffee from the Boma Plateau in South Sudan, against farmed accessions (of wild origin) from Ethiopia, Yemen, and global cultivars. Our results not only validate Boma Plateau as part of the natural distribution and as a center of origin for Arabica coffee but also indicate that wild populations in South Sudan are genetically distinct from Ethiopian Arabica. This newly identified genetic diversity within Arabica could have the potential for crop improvement through selection a...
A method developed in coffee tree breeding to assess family competition effects (partner effects)... more A method developed in coffee tree breeding to assess family competition effects (partner effects) in comparative variety trials was applied to the cocoa tree (Theobroma cacao L.). The study was conducted in a hybrid comparative trial planted in French Guiana, involving twelve families of 50 trees in a totally randomized single-tree plot design, at a density of 1,667 trees per hectare. The trial was thinned at 10 years, at a rate of two out of four rows. Competition was studied with reference to juvenile and adult vegetative vigour, and to periodic and cumulative yields (number of pods, potential weight, average weight of one pod, and the production: vigour ratio). At the end of the trial, after thirteen years of monitoring, competition effects were revealed which explained 8 to 10% of the residual variance after removal of the hybrid and micro-environment effects. These effects, which were detected as early as 18 months, occurred earlier than generally acknowledged. Under the trial conditions, the families could be classed as aggressive, stimulating or passive for their neighbours. Vegetative vigour (trunk cross-section) explained 34% of the competition effects (partner effects), which, with hindsight, vindicated the use of the production : vigour ratio as the main selection criterion in cocoa breeding. The partner effects noted on the production variables were never explained by any production variable, hence non-aggressive high-yielding families can be selected.
Le colatier Cola nitida (Vent.) Schott et Endl. est une plante originaire de l'Afrique de l&#... more Le colatier Cola nitida (Vent.) Schott et Endl. est une plante originaire de l'Afrique de l'Ouest. Elle produit des fruits dont les graines appelees encore noix de cola (figure) sont employees en Afrique occidentale et centrale pour des usages traditionnels (mariages, funerailles, gages d'amitie, sacrifices rituels, etc.). Elles inter-viennent dans l'industrie pharmaceutique et alimentaire pour la fabrication de stimulants cardiaques, laxatifs, sedatifs et boissons gazeuses. Malgre son importance socio-economique, cette espece est menacee de disparition a cause de l'abattage des arbres lors de l'etablissement de grandes exploitations agricoles (cacaoyers, cafeiers, palmiers a huile, heveas, etc.). Cela a conduit a la collecte de genotypes par bouturage a travers trois pays d'Afrique (Cote d'Ivoire, Nigeria, Guinee) et a la mise en place d'une collection en Cote d'Ivoire au Centre national de recherche agronomique. La caracterisation par marqueurs biochimiques (enzymatiques) et une etude de diversite genetique ont ete entreprises pour une bonne gestion des ressources genetiques de l'espece C. nitida. Nos travaux ont mis en evidence trois groupes genetiques, A, B e t C, avec respectivement 49, 20 et 10 genotypes. Le groupe minoritaire C est le plus eloigne genetiquement des deux autres. La differenciation entre ces groupes se situe essentiellement au niveau de l'enzyme PGI et de l'allele f du locus Pgi-2 et des alleles e, f et g de Pgi-3. La repartition des genotypes dans ces trois groupes est independante de leurs provenances geographiques. Cela indique que ces aires de collecte ne constituent pas des centres de dispersion independants de cette plante. Elle met en evidence une dispersion humaine recente de cette culture. Il existe une importante diversification genetique intergroupe (Fst = + 0,20). La structuration presente dans la collection pourrait etre utilisee dans une strategie de selection comme la selection recurrente pour ameliorer le colatier. II existe un deficit d'heterozygotie intra-groupe eleve (Fis = - 0,15). Cela suggere de nouvelles prospections dans des aires plus diversifiees, ce qui permettra d'augmenter la diversite genetique de la collection. (Texte integral)
Agronomy
While Ethiopia and South Sudan are the native habitats for Coffea arabica, Yemen is considered an... more While Ethiopia and South Sudan are the native habitats for Coffea arabica, Yemen is considered an important domestication center for this coffee species as most Arabica coffee grown around the world can be traced back to Yemen. Furthermore, climatic conditions in Yemen are hot and extremely dry. As such, Yemeni coffee trees likely have genetic merits with respect to climate resilience. However, until recently, very little was known about the genetic landscape of Yemeni coffee. The Yemeni coffee sector identifies coffee trees according to numerous vernacular names such as Udaini, Tufahi or Dawairi. However, the geographical landscape of these names and their correlation with the genetic background of the coffee trees have never been explored. In this study, we investigated the geographic occurrence of vernacular names in 148 coffee farms across the main coffee areas of Yemen. Then, we used microsatellite markers to genotype 88 coffee trees whose vernacular name was ascertained by far...
27th Biennial ASIC Conference, Portland, 16-20 September 2018. Book of abstracts 2019, 2019
RATIONALE Male sterility and tree size are two major traits for breeders. Male sterility enables ... more RATIONALE Male sterility and tree size are two major traits for breeders. Male sterility enables to decrease the mass multiplication costs of FI hybrids. Indeed, two types of Arabica varieties can be produced: fixed lines or FI hybrids. FI hybrids are more vigorous, resilient and less affected by diseases than fixed lines. However, it is more difficult to reproduce them making the cost of mass production higher. Producing FI hybrid seems to be a good alternative to face the ongoing climate change and the rust crisis and using male sterility could enable limiting the costs. Breeding for dwarf leads to production of coffee trees well adapted to mechanization. The objective of this study was to find markers associated to dwarf and male sterility in order to set up marker assisted breeding and to speed up varietal creation. METHODS A F2 population has been created by crossing the dwarf sarchimor IAPAR59 and a tall male sterile coffee tree. 277 coffee progeny as well as the FI and two parents were genotyped using GBS and the restriction enzyme Pstl for complexity reduction. DNA from the coffee samples was restricted with PstI and a 12 bp unique barcode identifier was ligated to the cut-site prior to pooling for Illumina template preparation. 150 bp single end reads were collected on an Illumina HiSeq 2500. Seventy-two barcoded samples were pooled per lane on the Illumina flow cell and 150 bp single-end reads were collected. An average of 2.8M reads per sample was obtained for the 277 progenies. The two parents were blasted against the C. canephora genome to identify sequence polymorphisms between them. 871 markers were identified. The association between dwarf trait, male sterility and SNPs markers was tested by a Chi-squared test. RESULTS A region containing 100 markers situated on the scaffold 612 on the chromosome 7 has been identified in association with male sterility. A PCoA performed on those markers showed a good discrimination between male sterile and male fertile genotypes. A selection based on those markers will enable to be more efficient through an early selection of male sterile plants in a segregating population. A SNP marker of dwarfism has been identified on chromosome 3. One version of this SNP is totally absent in tall genotypes. CONCLUSIONS & PERSPECTIVES An association has been found between a chromosom 7 region and male sterility. It could help breeder to enrich their working population with male sterile and then to reduce hybrid F 1 production cost. A more precise study of this region has to be performed. A marker of dwarfism which could be usefull to breed for mechanization adapted coffee trees has been discovered
List of plants evaluated with DarTseq markers. Table S2. List of DArTseq markers and used in the ... more List of plants evaluated with DarTseq markers. Table S2. List of DArTseq markers and used in the analysis. Table S3. Structural SNPs contributing to the population structure in C. canephora. Table S4. Putative outlier marker loci identified by the Fst outlier method implemented in Lositan. (XLSX 457Â kb)
28 populations sylvestres et origines cultivees couvrant l'aire de repartition de Coffea cane... more 28 populations sylvestres et origines cultivees couvrant l'aire de repartition de Coffea canephora sont etudiees. L'analyse globale de la diversite genotypique evaluee par marqueur enzymatique (6 systemes enzymatiques etudies par electrophorese permettent l'observation de 9 loci) et de la diversite phenotypique evaluee par une etude botanique en collection et une etude architecturale en essai de geniteurs, permet de mettre en evidence 2 sous-groupes dans le groupe genetique congolais. Ce sont 2 sous-groupes phenotypiques dont la separation genetique demande a etre confirmee. Le sous-groupe 1 a des caracteristiques morphologiques proches des guineens (petites feuilles, grand nombre d'entre-noeuds, bonne ramification, port buissonnant). Le sous-groupe 2 correspond a la description classique des congolais (grandes feuilles, faible nombre d'entre-noeuds, faible ramification)
Plusieurs annees de recherche permettent de tirer un premier bilan sur l'efficacite de la sel... more Plusieurs annees de recherche permettent de tirer un premier bilan sur l'efficacite de la selection de geniteurs et tetes de clone pour l'amelioration de #Coffea canephora# en Cote d'Ivoire. Les correlations entre la production des tetes de clone et celles des clones correspondant, calculees pour deux experimentations distinctes, s'elevent a 0,75 et 0,47, traduisant l'efficacite de la selection des tetes de clone. La correlation entre la performance des geniteurs testes sur deux testeurs de la population reciproque est de 0,79 dans le cas des geniteurs congolais et de 0,68 dans le cas des geniteurs guineens. En revanche, les correlations entre les performances des geniteurs guineens testes en inter et en intragroupe sont faibles. Les consequences pour la selection sont discutees. (Resume d'auteur)
Uploads
Papers by Christophe Montagnon