Xavier Argout

• French Agricultural Research Centre for International Development

En este primer capítulo introductorio presentamos los diferentes grupos genéticos que tengan presencia en el Ecuador, sea de origen nativo, o como consecuencia de introducción humana. Consideramos que esta información ayudará a interpretar la composición genética de los diferentes genotipos caracterizados en fincas de agricultores y en colecciones...

Humans have a long history of transporting and trading plants, contributing to the evolution of domesticated plants. Theobroma cacao originated in the Neotropics from South America. However, little is known about its domestication and use in these regions. In this study, ceramic residues from a large sample of pre-Columbian cultures from South and...

Individual Manhattan plots

The Cacao tree ( Theobroma cacao L.) is a major cash crop and an important source of income for millions of farmers across Africa, Asia and Latin America. However, cacao farmers and producing countries are facing multiple challenges including pest and disease management, sustainable production under threat of climate changes and diversification of...

A genome-wide association study (GWAS) was undertaken to unravel marker-trait associations (MTAs) between SNP markers and phenotypic traits. It involved a subset of 421 cacao accessions from the large and diverse collection conserved ex situ at the International Cocoa Genebank Trinidad. A Mixed Linear Model (MLM) in TASSEL was used for the GWAS and...

S9 Table contains Predictive values (GEBV) of phenotypic traits associated with SNPS. (Labelled S 6 in error)

Cocoa (Theobroma cacao L.) is the only tree that can produce cocoa. Cocoa beans are highly sought after by chocolate makers to produce chocolate. Cocoa can be fine aromatic, characterized by floral and fruity notes, or it can be described as standard cocoa with a more pronounced cocoa aroma and bitterness. In this study, the genetic and biochemical...

Societal Impact Statement Recent surveys conducted on Amazonian cocoa trees in their home range are a unique opportunity to assess the aromas, diversity and potential of the Ecuadorian Amazon to create new aromatic cocoa varieties. Our results reveal informations about the diversity and genesis of aromas in Ecuadorian fine cocoa. The great aromatic...

Societal Impact Statement “Fine flavor” cocoa, known for its superior flavor and aroma, commands a higher price for farmers than “bulk” cocoa produced for market. These fine flavor cocoa varieties make an important contribution to the agricultural sector in Ecuador. However, cocoa diversity is threatened by deforestation. The effective preservation...

The witches’ broom (Moniliophthora perniciosa) is considered as one of the main threats for cacao production and, consequently, for chocolate production worldwide.. In this work, the genetic diversity and population structure of M. perniciosa were analyzed for 59 isolates collected in five departments of Colombia and using 10 microsatellite markers...

A genome-wide association study was undertaken to unravel marker-trait associations (MTAs) between SNP markers and yield-related traits. It involved a subset of 421 cacao accessions from the large and diverse collection conserved ex situ at the International Cocoa Genebank Trinidad. An average linkage disequilibrium (r 2 ) of 0.10 at 5.2 Mb was fou...

Nacional is a variety of cocoa tree known for its "Arriba" aroma characterised mainly by fruity, floral, and spicy aromatic notes. In this study, the genetic basis of the fruity aroma of modern Nacional cocoa was investigated. GWAS studies have been conducted on biochemical and sensorial fruity traits and allowed to identify a large number of assoc...

Theobroma cacao is the only source that allows the production of chocolate. It is of major economic importance for producing countries such as Ecuador, which is the third-largest cocoa producer in the world. Cocoa is classified into two groups: bulk cocoa and aromatic fine flavour cocoa. In contrast to bulk cocoa, fine flavour cocoa is characterise...

The establishment of cocoa (Theobroma cacao L.) in Martinique is an old story. Some authors believe that the first cocoa trees were planted there by the native Caribbean people, while others indicate that cocoa was introduced in the seventeenth century. Since then, the history of cocoa farming in Martinique has been punctuated by different waves of...

Cacao (Theobroma cacao L.) is considered a key crop in Colombian social programs aiming at alleviating rural poverty, promoting peace in post-conflict regions and, replacing crops used for illicit purposes. Colombia is thought to be part of the center of origin of cacao; several germplasm collecting expeditions have been implemented, dating back to...

The archaeological site of Santa Ana-La Florida (SALF), located in the Ecuadorian upper Amazon, is in the region of Theobroma spp. greatest genetic diversity, thus making it ideal to investigate the origins of domestication of this enigmatic tree. We present research showing that the residents of SALF were involved in the domestication of cacao, tr...

Cacao (Theobroma cacao L.) is an important economic crop, yet studies of its domestication history and early uses are limited. Traditionally, cacao is thought to have been first domesticated in Mesoamerica. However, genomic research shows that T. cacao’s greatest diversity is in the upper Amazon region of northwest South America, pointing to this r...

Resistance to Cocoa Swollen Shoot Virus disease (CSSVD) is becoming an increasingly important criterion for selection of new cocoa cultivars in Côte-d’Ivoire, where the disease resurfaced since 2003. This virus can seriously affect the yield of trees with a loss of 25%, 1 year after infection, to around 100% 3 years after. In order to find tolerant...

Since 1985, CIRAD has been involved in surveying, collecting, studying and conserving ex situ wild cacao trees of French Guiana. Around 225 accessions of this genetic material (open progenies and clones), derived from 18 demes (sub-populations), are currently conserved in a collection at the Perennial Plants Biological Resource Centre (CRB-PPG) in...

Background There is great potential for the genetic improvement of oil palm yield. Traditional progeny tests allow accurate selection but limit the number of individuals evaluated. Genomic selection (GS) could overcome this constraint. We estimated the accuracy of GS prediction of seven oil yield components using A × B hybrid progeny tests with alm...

Cocoa self-compatibility is an important yield factor and has been described as being controlled by a late gameto-sporophytic system expressed only at the level of the embryo sac. It results in gametic non-fusion and involves several loci. In this work, we identified two loci, located on chromosomes 1 and 4 (CH1 and CH4), involved in cocoa self-inc...

Background Theobroma cacao L., native to the Amazonian basin of South America, is an economically important fruit tree crop for tropical countries as a source of chocolate. The first draft genome of the species, from a Criollo cultivar, was published in 2011. Although a useful resource, some improvements are possible, including identifying misassem...

Depuis plusieurs années, les programmes de recherche chez le cacaoyer ont mis l'accent sur l'étude des bases génétiques des caractères agronomiques d'intérêt, notamment concernant la résistance aux maladies et la qualité des fèves de cacao, qui représentent deux attributs importants pour la cacaoculture et la production de chocolat. Ce travail prés...

Sexual compatibility limits the production of cacao plantations, being an important selection criterion in breeding programs. However, the current method for characterizing compatibility, based on the frequency of flower setting after controlled pollination, is time consuming, requiring a long time to identify self-compatible individuals. The ident...

Premise of the study: We developed microsatellite (simple sequence repeat [SSR]) markers in the Neotropical tree Handroanthus billbergii (Bignoniaceae), to be applied in assessment of genetic diversity in this species as a reference for inferring the impact of dry forest fragmentation in Ecuador. Methods and Results: Using next-generation sequenci...

Traditional cocoa plantations in Ecuador are mostly composed of a complex mix of highly variable hybrid progenies, which has greatly reduced the population of native trees of the “Nacional” variety, to such a point that they are considered today as heading for extinction, which is increasingly worrying the international chocolate industry. Some yea...

There are two categories of quality recognized by the world market of cocoa beans: the “standard quality cocoa”, which corresponds to 95% of the total market; and the “fine flavored cocoa” which is mainly produced by the Criollo and Nacional varieties, and brings a higher price in the market. Ecuador’s fine-flavored cacao or “Nacional cacao” is a n...

Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanacea...

Natural rubber is harvested by tapping Hevea brasiliensis (Willd. ex A. Juss.) Müll. Arg. Harvesting stress can lead to tapping panel dryness (TPD). MicroRNAs (miRNAs) are induced by abiotic stress and regulate gene expression by targeting the cleavage or translational inhibition of target messenger RNAs. This study set out to sequence miRNAs expre...

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,...

[This corrects the article on p. e48438 in vol. 7.].

Background: Rubber tree (Hevea brasiliensis) laticifers are the source of natural rubber. Rubber production depends on endogenous and exogenous ethylene (ethephon). AP2/ERF transcription factors, and especially Ethylene-Response Factors, play a crucial role in plant development and response to biotic and abiotic stresses. This study set out to seq...

Banana is one of the world’s favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyled...

Ecuador's economic history has been closely linked to Theobroma cacao L cultivation, and specifically to the native fine flavour Nacional cocoa variety. The original Nacional cocoa trees are presently in danger of extinction due to foreign germplasm introductions. In a previous work, a few non-introgressed Nacional types were identified as potentia...

Origin, collection, % heterozygosity and status of the 176 T. cacao accessions analysed in the present study. CATIE: Centro Agronomico Tropical de Investigación y Ensenanza (Costa Rica); CIC: Centro de Investigación Caribia (Colombia); CIRAD/Mpl: Centre de Coopération internationale en recherche agronomique pour le développement (France)/Montpellie...

Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries. The Musa domesticatio...

Plants respond to external stimuli through fine regulation of gene expression partially ensured by small RNAs. Of these, microRNAs (miRNAs) play a crucial role. They negatively regulate gene expression by targeting the cleavage or translational inhibition of target messenger RNAs (mRNAs). In Hevea brasiliensis, environmental and harvesting stresses...

Three types of roots (taproots, first order laterals and second order laterals) were functionally characterized on 7-month-old in vitro plantlets regenerated by somatic embryogenesis in Hevea brasiliensis. A histological analysis revealed different levels of differentiation depending on root diameter. A primary structure was found in first and seco...

Theobroma cacao is an economically important tree of several tropical countries. Its genetic improvement is essential to provide protection against major diseases and improve chocolate quality. We discovered and mapped new expressed sequence tag-single nucleotide polymorphism (EST-SNP) and simple sequence repeat (SSR) markers and constructed a high...

Theobroma cacao L. is a major cash crop for tropical countries, providing incomes for 14 million small farmers. Establishing sustainable disease resistance and maintaining cocoa qualities are among the major objectives of breeding programs. To enrich the high-density genetic map, useful for all cocoa genetic studies, with gene-based markers, a rece...

Fruit provide essential nutrients and vitamins for the human diet. Not only is the lipid-rich fleshy mesocarp tissue of the oil palm (Elaeis guineensis) fruit the main source of edible oil for the world, but it is also the richest dietary source of provitamin A. This study examines the transcriptional basis of these two outstanding metabolic charac...

We sequenced and assembled the draft genome of Theobroma cacao, an economically important tropical-fruit tree crop that is the source of chocolate. This assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of these genes anchored on the 10 T. cacao chromosomes. Analysis of this sequen...

We sequenced and assembled the draft genome of Theobroma cacao, an economically important tropical-fruit tree crop that is the source of chocolate. This assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of these genes anchored on the 10 T. cacao chromosomes. Analysis of this sequen...

We sequenced and assembled the genome of Theobroma cacao, an economically important tropical fruit tree crop that is the source of chocolate. The assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of them anchored on the 10 T. cacao chromosomes. Analysis of this sequence information...

Theobroma cacao L., is a diploid tree fruit species (2n = 2x = 20), originated from the South American rainforests. A criollo genotype, providing a high quality chocolate and highly homozygous, has been choosing by the ICGS to sequence the cocoa genome. A combination of Sanger and NGS technologies was chosen for sequencing the criollo genotype, wit...

Unlabelled: Premise of the study: Large-scale population genetics studies are required to investigate the dispersal processes underlying the emergence of Mycosphaerella fijiensis, a fungal pathogen of banana. To this end, we have developed an optimized genotyping procedure combining novel microsatellite markers and a modified DNA extraction prot...

Background The genus Musa is a large species complex which includes cultivars at diploid and triploid levels. These sterile and vegetatively propagated cultivars are based on the A genome from Musa acuminata, exclusively for sweet bananas such as Cavendish, or associated with the B genome (Musa balbisiana) in cooking bananas such as Plantain variet...

Pisang Lilin genetic map built at LOD 5. Molecular marker names are on the right side of each linkage group whereas genetic distances are on the left (cM; Kosambi mapping function). Loci labeled with asterisks showed distorted segregation (1* P < 0.05, 2* P < 0.01, 3* P < 0.005, 4* P < 0.001, 5* P < 0.0005, 6* P < 0.0001, 7* P < 0.00005). Anchor ma...

Borneo genetic map built at LOD 3.5. Molecular marker names are on the right side of each linkage group whereas genetic distances are on the left (cM; Kosambi mapping function). Loci labeled with asterisks showed distorted segregation (1* P < 0.05, 2* P < 0.01, 3* P < 0.005, 4* P < 0.001, 5* P < 0.0005, 6* P < 0.0001, 7* P < 0.00005). Anchor marker...

Neighbor-joining tree designed from linkage group 6+8 of Borneo defined at LOD 3.5; Markers in grey are DArTs markers, those in black SSR markers.

Among the various PCR-based techniques, the simple sequence repeats (SSRs) or microsatellites are characterized by the co-dominant mode of inheritance which permits easy transfer of markers between genetic maps of different crosses in contrast to dominant PCR markers types such as RAPD or AFLP. Microsatellites detect multiple alleles at a single lo...

The development and application of molecular genetic markers provide the opportunity to establish and evaluate measures for the quality of genetic resources collections. In particular, DNA-based polymorphisms are a powerful tool for the assessment of genetic diversity. Among the various molecular markers, RFLPs were the first to be used for plant g...

Theobroma cacao, is a tropical understorey tree that is a major economic resource to several tropical countries. However, the crop is under increased threat from several diseases that are responsible for 30% loss of harvest globally. Although QTL data related to the genetic determinism of disease resistance exist in cocoa, QTL mapping experiments a...

Theobroma cacao L., is a tree originated from the tropical rainforest of South America. It is one of the major cash crops for many tropical countries. T. cacao is mainly produced on smallholdings, providing resources for 14 million farmers. Disease resistance and T. cacao quality improvement are two important challenges for all actors of cocoa and...

During the last decade, numerous microsatellite markers were developed for genotyping and to identify closely related plant genotypes. In citrus, previously developed microsatellite markers were arisen from genomic libraries and more often located in non coding DNA sequences. To optimize the use of these EST-SSRs as genetic markers in genome mappin...

Simple Sequence Repeats (SSRs), or microsatellites, are among the most powerful genetic markers known. A common method for the development of SSR markers is the construction of genomic DNA libraries enriched for SSR sequences, followed by DNA sequencing. However, designing optimal SSR markers from bulk sequence data is a laborious and time-consumin...

Improvement of Citrus, the most economically important fruit crop in the world, is extremely slow and inherently costly because of the long-term nature of tree breeding and an unusual combination of reproductive characteristics. Aside from disease resistance, major commercial traits in Citrus are improved fruit quality, higher yield and tolerance t...

Putative gene duplications in Citrus. The table contains the A. thaliana loci that have been foun duplicated in Citrus.

The present study aimed to identify and assess the frequency and tissue specificity of plant genes in the actinorhizal Casuarina glauca-Frankia symbiosis through expressed sequence tag (EST) analysis. Using a custom analysis pipeline for raw sequences of C. glauca uninfected roots and nodules, we obtained an EST databank web interface. Gene express...