Article

Tracing the native ancestors of the modern Theobroma cacao L. population in Ecuador

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Abstract

The native Theobroma cacao L. population from Ecuador, known as Nacional, is famous for its fine cocoa flavour. From the beginning of the twentieth century, however, it has been subjected to genetic erosion due principally to successive introductions of foreign germplasm whose hybrid descendants gradually replaced the native plantations, implying a decrease in cocoa quality. We attempted to trace this native cacao within a wide pool of modern Ecuadorian cacao population. Three hundred and twenty-two cacao accessions collected from different geographical areas along the pacific coast of Ecuador and maintained in two living collections were analysed using 40 simple-sequence repeat markers. Most of Ecuadorian cacao accessions displayed a high diversity and heterozygosity level. A factorial analysis of correspondence (FAC) showed a continuous variation among them, with a few ones, grouped at an extreme side of the FAC cloud, showing higher levels of homozygosity and lower introgression level by foreign cacaos. A paternity analysis revealed that these highly homozygous individuals are the most probable ancestors of the modern Nacional hybrid pool. These particular accessions studied could represent the native Nacional cacao present in Ecuador before the foreign introductions. Their identification will help to conserve valuable genetic material and to improve cocoa quality in new cacao varieties.

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... Tres principales grupos genéticos de cacao han sido descritos y cultivados tradicionalmente alrededor del mundo: Criollo, Forastero y Trinitario. [4]. El grupo de los Criollos fue originalmente cultivado por los mayas en América Central y representa el primer grupo de cacao domesticado del mundo [5]. ...
... Una significativa cantidad de material genético de cacao Nacional fue recolectada durante varias expediciones realizadas a lo largo de la Región Costera Ecuatoriana en la década de 1940 [4]. Actualmente, este material genético se encuentra almacenado en forma de colecciones ex-situ en los dos principales bancos de germoplasma de Ecuador. ...
... Este alto grado de redundancia no solo dificulta una conservación eficiente de estas accesiones, sino que además obstaculiza su potencial explotación y el mejoramiento genético de los cultivos. Realizar una evaluación exhaustiva de la identidad individual y de la estructura genética de la población es primordial para optimizar programas de mejoramiento genético encaminados a producir nuevas y mejoradas variedades de cacao Nacional para preservar su conocido sabor "arriba" [4]. ...
... Grâce à cette saveur spécifique, le cacao Nacional fut reconnu comme « fino de aroma », c'est-à-dire fin aromatique. Le cacao fin est grandement apprécié des chocolatiers et est uniquement produit en Équateur (Loor S. et al., 2009). Bartley (2005), l'utilisation du nom « Nacional » pour définir ces arbres ancestraux sous-entend qu'il s'agissait d'une seule variété avec un génotype uniforme. ...
... Avant 1920, la diffusion des semences et la culture de cacaoyers étaient faites à partir de fèves issues de croisements incontrôlés. Après la découverte de Moniliophthora perniciosa, le champignon responsable de la maladie du balai de sorcière, et de ses ravages sur les cacaoyers équatoriens, des arbres résistants à la maladie ont été recherchés afin de réduire le niveau de susceptibilité de la population (Bartley, 2005).. Des cacaoyers appelés cultivars Vénézuéliens ont été introduits (Bartley, 2005;Loor S. et al., 2009;Rottiers et al., 2019). L'origine de ces arbres est incertaine. ...
... L'origine de ces arbres est incertaine. Selon Bartley, (2005) et (Loor S. et al., 2009) Loor S. et al., (2009) grâce aux marqueurs moléculaires. La culture généralisée des nouveaux matériels génétiques par les grandes propriétés a contribué à l'accélération du brassage génétique ainsi qu'à la dilution du Nacional ancestral. ...
Thesis
Theobroma cacao est un arbre originaire des régions tropicales humides d’Amérique latine. Il est cultivé pour ses fèves qui permettent la production de chocolat. Le Nacional, originaire d’Equateur, est une variété de cacao fin connue pour ses arômes floraux et épicées, appelée saveur « Arriba ». Les mécanismes de la synthèse de ses arômes restent peu connus. Les travaux de cette thèse ont porté sur l’étude des déterminants génétiques et biochimiques des arômes des cacaos fins équatoriens afin d’initier de contribuer aux connaissances dans ce domaine.Une première partie de l’étude a été réalisée à partir d’une population de cacaoyer de type Nacional moderne, qui est la variété de Nacional actuellement cultivée. Des études d’associations ont été réalisées sur l’ensemble du génome (GWAS) et ont porté sur l’analyse des composés volatils relatifs aux arôme floraux et fruités (fruits frais et fruits secs) contenus dans les fèves, avant et après torréfaction, ainsi que, sur des résultats d’analyses sensorielles de liqueurs. Cette première étude a pu montrer que les arômes floraux du Nacional étaient principalement synthétisés grâce à deux voies de biosynthèse: celle des monoterpènes et la voie de dégradation du L-phénylalanine. Les résultats relatifs aux arômes fruités ont permis de mettre en lumière cinq voies métaboliques majeures: la voie de biosynthèse des monoterpènes, les voies de dégradations du L-phénylalanine, des sucres, des acides gras et des protéines. Des gènes candidats codant pour des enzymes impliqués dans ces voies métaboliques ont été identifiés dans les zones d’associations correspondantes.La variété Nacional moderne est issue de diverses générations de croisements entre des Trinitario (hybrides Amelonado/Criollo) et le Nacional ancestral, mettant ainsi en jeu 3 ancêtres contrastés. L’effet de cette étape de domestication récente sur les arômes de la variété Nacional moderne a été étudié. Grâce aux données de génotypage des trois ancêtres de référence et aux résultats des GWAS portant sur l’ensemble des caractères de qualité (composés volatils et non-volatils, analyses sensorielles), il a été possible de déterminer l’origine des allèles ayant un effet positif sur les arômes dans les différentes zones d’associations. Cette étude a montré que l’ensemble des ancêtres fondateurs ont apporté des allèles favorables à la synthèse d’arômes de qualité (floraux, fruités, …) mais aussi à la synthèse de défauts (amertume, astringence, …). Nous avons pu montrer que les zones d’associations en lien avec les arômes de qualité et celles avec les défauts n’étaient pas liées génétiquement. Il est donc possible de sélectionner les zones d’intérêts pour les arômes tout en contre-sélectionnant les zones apportant des défauts.La deuxième partie de cette étude a porté sur l’analyse des arômes d’une population de cacaoyers natifs d’Amazonie et issus de la zone d’origine de la variété Nacional ancestral. Dans cette étude, des analyses GWAS ont également été effectuées sur l’ensemble des caractères de qualité analysés précédemment. Quatre vingt dix sept gènes candidats sont communs aux deux populations analysées. De nouveaux composés volatils ainsi que de nouvelles zones d’associations ont également été détectées montrant ainsi une plus grande diversité et richesse aromatique de ces nouvelles ressources génétiques et leur intérêt pour la création de nouvelles variétés aromatiques adaptées à l’Amazonie.Enfin, une étude GWAS sur les composés non-volatils, les caractères sensoriels liés à l’amertume et à l’astringence, ainsi que la teneur en matière grasse et en protéines, a également été réalisée sur les deux populations. Des gènes candidats en lien avec la voie de biosynthèse de la caféine et celle des polyphénols, ou en lien avec la voie de biosynthèse des acides gras ont pu être observés dans les zones d’associations.
... In the past, much debate surrounded cacao's center of origin and domestication. This was due to its unclear distribution and dispersion (human and nature) and because of its long history of cultivation (Cuatrecasas 1964;De la Cruz et al. 1995;Motamayor et al. 2002;Loor et al. 2009). Presently, it is widely accepted that cacao has a South American origin where the headwaters of the Amazon River are described as the primary center of diversity for the species (Wood and Lass 1985;Bartley 2005). ...
... Naturalized Puerto Rican cacao is composed of four genetically distinct groups: Criollo, Trinitario, Amelonado, and UAF hybrids. The Nacional population, studied in detail by Loor et al. (2009), is a unique genetic background not distributed widely out of its native Ecuadorian region. Nacional cacao is known for its sought-after Barriba^strong floral aroma and had fallen out of favor with local farmers for more productive and disease resistant introductions. ...
... Nacional cacao is known for its sought-after Barriba^strong floral aroma and had fallen out of favor with local farmers for more productive and disease resistant introductions. However, more recent efforts have focused on identifying and preserving this unique population in Ecuador due to its value as national patrimony (Loor et al. 2009). Because of its limited distribution, it makes sense that it was not identified among naturalized Puerto Rican cacao. ...
Article
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Identification of genetically diverse cacao with disease resistance, high productivity, and desirable organoleptic traits is vitally important to the agricultural crop’s long-term sustainability. Environmental changes, pests, and diseases as well as nation’s sovereign property rights have led to a decrease in accessibility and exchange of germplasm of interest. Having been introduced during colonial times, naturalized cacao in Puerto Rico could serve as an unexplored source of genetic diversity in improvement programs. An island-wide survey was carried out to identify naturalized trees and to determine their genetic associations to reference cacao accessions. Samples were genotyped with Expressed Sequence Tag-derived single nucleotide polymorphism (SNP) markers. Principal coordinate, cluster, and population structure analysis using the genotype data for both local and reference samples assigned individuals into five distinct genetic backgrounds: Criollo, Trinitario, Amelonado, Upper Amazon Forastero (UAF), and Nacional. Puerto Rican cacao fit into four (Criollo, Trinitario, Amelonado and UAF) of the five genetic backgrounds, being mainly composed of individuals of Criollo ancestry. Based on historical evidence, cacao of Criollo background was probably brought to Puerto Rico from Venezuela and/or Central America during colonial times. Trinitario, Amelonado, and UAF genetic backgrounds are most likely products of more modern introductions. Genotyping cacao in Puerto Rico provides information on the history and possible origin of the naturalized trees on the island. In addition, the assessment has allowed the targeting of material for incorporation and long-term conservation filling gaps in the existing collection and providing new germplasm to be evaluated for agronomic performance.
... In the past, characterization of germplasm collections was based on morphology and agronomic characteristics of individuals (Engels 1983;Bekele and Butler 2000;Iwaro et al. 2003). More recently however, efforts have been underway to assess, describe, and characterize cacao collections based on population structure, genetic diversity, and evolutionary relationships using molecular markers (Zhang et al. 2006a, b;Lerceteau et al. 1997;Johnson et al. 2009;Aikpokpodion et al. 2009;Ventura-López et al. 2006;Motilal et al. 2010;Loor et al. 2009;Motamayor et al. 2002Motamayor et al. , 2003Motamayor et al. , 2008Borrone et al. 2007;Schnell et al. 2005;Irish et al. 2010). Microsatellites or Simple Sequence Repeats (SSRs) and Single Nucleotide Polymorphisms (SNPs) are among the molecular markers being used to characterize cacao germplasm collections (Motilal et al. 2010;Zhang et al. 2006bZhang et al. , 2009Schnell et al. 2005;Motamayor et al. 2008;Lanaud et al. 1999). ...
... Collections in West Africa (12.5 alleles per locus; 144 total alleles; Aikpokpodion et al. 2009) and Cameroon (9.41 alleles per locus; 125 total alleles; Efombagn et al. 2008) are also highly diverse. On the other hand, Loor et al. (2009) reported a low amount of genetic diversity in accessions collected along the Pacific coast of Ecuador (4.22 alleles per locus; 169 total alleles). This report is similar in the number of alleles per locus for a 'Refractario' population in Ecuador but different for the total number of alleles (4.20 alleles per locus; 63 total alleles; Zhang et al. 2008). ...
... Modern Criollo cacao accessions have traditionally been associated with the production of chocolate with milder, fine and nutty flavors (Elwers et al. 2009;Ed Seguine, Mars, Inc., Hackettstown, NJ, personal communication 2011) while the Amelonado types are characterized by more intense cacao flavors (Ed Seguine, Mars, Inc., Hackettstown, NJ, personal communication 2011). The Nacional (Ecuadorian) genetic identities have been linked to chocolate with good organoleptic qualities and fine floral aroma characteristics (Deheuvels et al. 2004;Loor et al. 2009). These organoleptic quality traits, together with the organic production component, are current triggers of competitive international markets (Eskes and Lanaud 1997;Rusconi and Conti 2010). ...
Article
Cacao (Theobroma cacao L.) is a significant agricultural commodity in the Dominican Republic, which ranks 11th in the world for cacao exports. To estimate genetic diversity, determine genetic identity, and identify any labeling errors, 14 SSR markers were employed to fingerprint 955 trees among cacao germplasm accessions and local farmer selections (LFS). Comparisons of homonymous plants across plots revealed a significant misidentification rate estimated to be 40.9 % for germplasm accessions and 17.4 % for LFS. The 14 SSRs amplified a total of 117 alleles with a mean allelic richness of 8.36 alleles per locus and average polymorphism information content (PIC) value of 0.67 for the germplasm collection. Similar levels of variation were detected among the LFS where a total of 113 alleles were amplified with a mean of 8.07 alleles per locus and PIC of 0.57. The observed heterozygosity (Hobs) was 0.67 for the germplasm collection and 0.60 for LFS. Based on population structure analysis 43.9 % of the germplasm accessions and 72.1 % of the LFS are predominantly of the Amelonado ancestry. Among these Amelonado, 51.7 % for the germplasm collection and 50.6 % for LFS corresponded to Trinitario hybrid lineage. Criollo ancestry was found in 7.6 and 9.5 % of the germplasm accessions and LFS, respectively. The Contamana, Nacional, and Iquitos backgrounds were also observed in both populations, but the Curaray background was only detected in the germplasm accessions. No Purús or Guiana ancestry was found in either of the populations. Overall, significant genetic diversity, which could be exploited in the Dominican Republic breeding and selection programs, was identified among the germplasm accessions and LFS.
... In fact, two types are predominantly cultivated in Ecuador, namely the fine Nacional variety and the bulk 'Colecciόn Castro Naranjal 51' (CCN51). First, Nacional, also known as 'Fino de Aroma', is exclusively cultivated in Ecuador and highly appreciated by chocolate manufacturers and consumers, due to its intense floral aroma known as 'Arriba' [4]. The fermented dried beans of traditional Nacional cultivars have a low acidity, bitterness and astringency, and a floral flavor with violet, jasmine, lilac or orange blossom notes [5]. ...
... Nacional cocoa was the only type grown in Coastal Ecuador, until 1890 when the first cocoa pods of the so-called 'Venezuela' cultivar were introduced from Trinidad. These introductions of foreign germplasm progressively increased from 1910 due to the destructive effect of witches' broom and frosty pod rot on the native Nacional plantations [4,6]. The modern Ecuadorian cocoa plantations (≈ 70% of the Ecuadorian cocoa export) are currently a genetic admixture between the traditional Nacional and foreign more productive and disease-resistant cultivars, especially Trinitario types, leading to a dilution of the native Arriba flavor [2,4,7]. ...
... These introductions of foreign germplasm progressively increased from 1910 due to the destructive effect of witches' broom and frosty pod rot on the native Nacional plantations [4,6]. The modern Ecuadorian cocoa plantations (≈ 70% of the Ecuadorian cocoa export) are currently a genetic admixture between the traditional Nacional and foreign more productive and disease-resistant cultivars, especially Trinitario types, leading to a dilution of the native Arriba flavor [2,4,7]. Since 1940, cocoa germplasm was collected in Coastal Ecuador to preserve the Nacional genetic resources [4]. ...
Article
Full-text available
Two cocoa types are predominantly being cultivated in Ecuador, the highly appreciated fine Nacional and the high-yielding and disease-resistant CCN51, classified as bulk. With the introduction of foreign germplasm in Ecuador and the international demand for high-quality Nacional cocoa, the present study aims to characterize and compare the flavor profile of Nacional hybrids (EET103, EET559, EET576 and EET577) and CCN51, and to assess the effect of the genotype. The fermented dried beans were processed into liquor and their sensory properties, volatile composition and odor fingerprint were analyzed by trained panelists, headspace–solid phase microextraction gas chromatography–mass spectrometry (HS–SPME–GC–MS), and GC electronic nose (e-nose), respectively, combined with multivariate statistics. Seventy volatiles were identified and semi-quantified, among them, 16 and 14 volatiles conferring fruity and floral aroma notes, respectively. CCN51 was mainly characterized by undesirable odor-active volatiles, whereas the EET cultivars contained the highest concentration of most fruity and floral volatiles, with differences in between EET cultivars. Sensory data highlighted organoleptic differences between the fine and bulk liquors, i.e. the fruity and acid EET flavor strongly differed from the bitter, astringent and off-flavor attributes of CCN51. Principal component analysis (PCA) discriminated firstly between fine and bulk, and secondly between EET identity. Partial least squares analysis identified possible correlations between sensory attributes and volatile compounds. Besides, e-nose proved its usefulness for rapid assessment of the liquors’ sensory profile. The results provide a foundation for understanding the genotype’s contribution to and the compositional basis of Ecuadorian fine and bulk cocoa flavor.
... Common names: cocoa, cacao, food of the gods present in: South America, Central America, Mexico, West Africa, Southeast Asia harvesting season: year-round, but the main seasons are November-January and May-July harvesting yields: 50-60 fruits per tree per year and 7-9 kg of dried beans per tree per year main use: cocoa solids and butter are used for chocolate production and in the cosmetics industry Substitute: no substitutability Tree density in the forest: high (forming part of the lower forest stratum) harvesting practices: involves knocking the fruit to the ground by climbing or by using long poles handling: the beans are removed from the cocoa fruit, fermented in wooden boxes and dried in the sun Theobroma cacao, a tree species in the Malvaceae family, is native to the Amazon Basin, with the centre of origin in the upper Amazon (Loor et al. 2009). ...
... There are three major morphogenetic groups of domesticated cocoa: criollo, forestero and trinitario. Criollo varieties produce red or purple pods with an uneven surface; they were first cultivated by the Mayans in Central America, and Christopher Columbus collected samples in 1502 (Loor et al. 2009;Lachenaud et al. 2007;Perera and Smith 2013). Today, criollo occurs throughout South America, Central America and southern Mexico, although it is rare because of its susceptibility to disease (CEPLAC undated; Badrie et al. 2015). ...
... Today, criollo occurs throughout South America, Central America and southern Mexico, although it is rare because of its susceptibility to disease (CEPLAC undated; Badrie et al. 2015). Forastero trees, which produce relatively smooth, hard pods, occur mainly in the Amazon, French Guiana, Guyana and Suriname (Loor et al. 2009;Lachenaud et al. 2007). Cocoa-from the forestero subtype amelonado-was introduced to Africa by the Portuguese in 1879 (Pence 1989). ...
... In the past, much debate surrounded cacao's center of origin and domestication. This was due to its unclear distribution and dispersion (human and nature) and because of its long history of cultivation (Cuatrecasas 1964;De la Cruz et al. 1995;Motamayor et al. 2002;Loor et al. 2009). Presently, it is widely accepted that cacao has a South American origin where the headwaters of the Amazon River are described as the primary center of diversity for the species (Wood and Lass 1985;Bartley 2005). ...
... Naturalized Puerto Rican cacao is composed of four genetically distinct groups: Criollo, Trinitario, Amelonado, and UAF hybrids. The Nacional population, studied in detail by Loor et al. (2009), is a unique genetic background not distributed widely out of its native Ecuadorian region. Nacional cacao is known for its sought-after Barriba^strong floral aroma and had fallen out of favor with local farmers for more productive and disease resistant introductions. ...
... Nacional cacao is known for its sought-after Barriba^strong floral aroma and had fallen out of favor with local farmers for more productive and disease resistant introductions. However, more recent efforts have focused on identifying and preserving this unique population in Ecuador due to its value as national patrimony (Loor et al. 2009). Because of its limited distribution, it makes sense that it was not identified among naturalized Puerto Rican cacao. ...
Conference Paper
Full-text available
Native to the headwaters of the Amazon River, cacao (Theobroma cacao L.) is an important agricultural tree crop produced in tropical regions around the world. Its raw product, the seed or ‘beans’, is the source for the multi-billion dollar chocolate industry. The USDA-ARS Tropical Agriculture Research Station in Mayaguez, PR maintains a diverse, replicated field cacao collection consisting of close to 200 clonally propagated accessions. Although no large scale commercial production exists on the island today, Puerto Rico has a long history of cacao introduction and production. Based on anecdotal information, on historical publications and data presented here, ‘old’ (>100 years) naturalized cacao trees can be found throughout the island. In addition, and based on preliminary evidence, many of the cacao trees appeared to belong to the ‘Criollo’ genetic background with unique morphological pod features and characteristic white colored beans. To confirm preliminary findings and in order to asses genetic relationships between naturalized trees and existing cacao in the TARS collection, a collection leaf samples from close to 160 trees from diverse regions on the island was carried out. DNAs from collected leaves were screened with 48 EST-derived SNP markers which had been previously assessed for their allelic range and informativeness in assessing genetic diversity in cacao germplasm. Analysis of the SNP data supported initial findings and showed that a large number of trees sampled indeed belonged to the ‘Criollo’ genetic background. In addition, other unique genetic backgrounds including trees belonging to Upper Amazon populations, Amelonado, Trinitario and hybrids among these germplasm groups were identified. The results revealed a high level of allelic and genotype diversity in the cacao samples collected from Puerto Rico. Furthermore, during sample collecting trips several trees with important agronomic traits (e.g., large pods with many large seed) were located. A subset of Criollo-background trees, as well as those with agronomic potential, are being collected and propagated to fill gaps in genetic diversity coverage in the existing TARS collection and for further evaluation.
... Analogous values of genetic diversity have been reported by Loor et al. (2009), who analyzed 322 plants of 'Nacional' cocoa collected in different geographic zones along the Ecuadorian coast. These authors determined that the genetic structure of modern populations of the 'Nacional' cocoa is characterized by high levels of heterozygosity and genetic diversity. ...
... This could also indicate that they have a similar origin but there is variability among them, which indicated that they are the product of clonal multiplication. is the result of the double hybridization of 'Trinitario' and 'Forastero' genetic material of an Amazon origin and is recognized as having a yield potential and carrying resistance to common fungal diseases (Amores et al., 2009). This clone was grouped with the recently introduced materials of the Tumaco zone, suggesting that these materials could have a hybrid origin, like CCN 51 and TSH 561. ...
Article
Full-text available
Random amplified microsatellite (RAMs) markers six were used to characterize 93 genotypes of cocoa in Tumaco (Colombia). Hundred twenty seven bands were generated. The number of polymorphic loci varied between 11 and 25 for the AG and TG primers, respectively. This study differentiated the 93 genotypes into six groups with a 0.53 similarity, 0.28 mean heterozygosity (He) for the population, and 0.12±0.02 genetic differentiation coefficient or Fst. A significant level of genetic diversity was evident in the T. cacao genotypes. This resource would benefit selection programs of individual trees or plant breeding programs. The genotypes clustered in a large proportion in accordance with the collection zone. This characteristic was associated with collection zones and along the rivers in the municipality of Tumaco. The RAM technique proved to be a useful tool for the determination of genetic diversity in Theobroma species.
... Criollo cacaos, the first to be domesticated, were originally cultivated by the Mayas in Central America from Mexico to Costa Rica. A fine chocolate of excellent quality and taste can be produced from the seeds of this group (Motamayor et al. 2002;Sereno et al. 2006;Bhattacharjee and Kumar 2007;Loor et al. 2009;Monteiro et al. 2009). The fruits are rugose and oblong with an attenuate or acute apex. ...
... Having inherited the morphological traits of both parental groups, these hybrids vary widely in morphological traits such as immature fruit color, fruit mesocarp thickness, number of seeds, and seed and fruit size. Trinitario is thus a very heterogeneous group that displays extreme diversity (Días 2001;Bekele et al. 2006;Loor et al. 2009;Monteiro et al. 2009). Motamayor et al. (2008) proposed a new classification for the species T. cacao based on the genotyping of 1241 accessions from a large geographical sampling in Central and South America using 106 microsatellite markers. ...
Article
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Plantations of cacao (Theobroma cacao L.) more than 60 years old still exist in Cuba and are probably quite similar to the original introductions. We studied the phenotypic diversity of a representative sample of 537 traditional Cuban cacao plants and 165 reference plants from the different T. cacao genetic groups, using 33 morphological descriptors. The results were compared with the previously determined allelic compositions at 15 simple sequence repeat (SSR) loci designated as international standards. Most morphological traits showed high variation, with all but one found to be polymorphic. The most frequent character states were (1) in the seeds: flat transversal sections, intensely violet color and slightly acidic flavor, (2) in the fruit: yellow color at maturity with no anthocyanin, ten ridges distributed in five pairs, medium-depth furrows, intermediate rugosity and hard mesocarp and (3) in the flower: divergent, intensely purple staminodes, white horizontal sepals, intense yellow petals, white stamen filaments, light purple peduncles and white closed flowers. By comparison with reference plants, the traditional Cuban cacao samples were classified as Trinitario group members using cluster and multiple correspondence analyses. We found associations among several fruit color states and allelic forms at mTcCIR12, a locus probably related to anthocyanin pigmentation. Other fruit morphological trait states were related to one another and were correlated with 10 SSR markers, reflecting the complex genetic basis of T. cacao fruit morphology. Cotyledon color was associated with the mTcCIR18 locus in linkage group 4, and thus most likely near loci coding for this trait.
... Molecular markers such as simple sequence repeat (SSR) and single nucleotide polymorphism are used to study genetic identity and evolutionary relationships in germplasm collections. In cacao, these markers have been used for establishing genotype identities, genetic relationships, identification of genetic gaps, and in marker-assisted selection in both national and international cacao breeding and selection programs (Boza et al., 2013;Irish et al., 2010;Loor et al., 2009;Motamayor et al., 2002Motamayor et al., , 2003Motamayor et al., , 2008Schnell et al., 2005Schnell et al., , 2007Zhang et al., 2006aZhang et al., , 2006b. A study by Motamayor et al. (2008) used SSR markers to improve the understanding of the origin, classification, and population differentiation within T. cacao. ...
... Although fine flavor is known to be largely influenced by the fermentation process, great effort has been made over the past few years to improve the selection and breeding programs for this trait in Ecuador. However, this specific characteristic may have been eroded by successive introductions of foreign germplasm whose hybrid descendants have gradually replaced native plantations (Loor et al., 2009). The structure analysis results indicate that the origin of 'CCN 51' is based on its hybridization, suggesting the IMC type as the primary genetic source followed by Criollo and Amelonado ancestries. ...
Conference Paper
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Cacao (Theobroma cacao L.) is an important cash crop in several growing regions of the world and particularly for small cacao farmers. Cacao production in the Americas constitutes ~13.0% of global production. Ecuador is among the higher producers in South America and its cacao beans are well known for fine flavors, aroma, and fat content. CCN-51 is one of the most planted varieties in Ecuador; its pedigree is complex and sometimes mistaken for the Nacional type. Seventy simple sequence repeat (SSR) loci were used to determine the genetic identity of CCN-51; in which 80% (56) were heterozygous and 20% (14) were homozygous. This finding of high heterozygocity for CCN-51 is not consistent with that of a Nacional type clone. No Nacional specific alleles were found. Comparison of agronomic characteristics between CCN-51 and several Nacional clones indicated significant differences in cacao dry bean weight, yield potential, production efficiency, healthy pods, and witches' broom disease reaction. Additionally, physical, chemical, and organoleptic characteristics suggest that CCN-51 is different from those of Nacional lineage. Based on population structure analysis, the predominant ancestries for CCN-51 are Iquitos (45.4%), Criollo (22.2%), and Amelonado (21.5%). Moreover, results of parentage and phylogenetic analyses using neighbor joining and unweighted pair group method with arithmetic mean (UPGMA) yielding high bootstrap values strongly support the relatedness of CCN-51 with Iquitos, Criollo and Amelonado. CCN-51 constitutes a valuable genetic resource that is currently used not only in its country of origin, but also in many other national breeding and selection programs worldwide.
... Ecuador is the leading exporter of fine cocoa. Next to Nacional, i.e. the indigenous variety of Ecuador recognized for its intense floral aroma ('Arriba'), many Trinitario types or hybrids are also currently being cultivated in Ecuador [5]. In addition to variety and origin, post-harvest processes influence the final flavor quality [6]. ...
... PC1, accounting for 55.97% of total variance, discriminated between fermentation times, 0 h, 18/24 h and 48/66 h. The samples in the former group (negative axis), collected before fermentation (0 h), were mainly characterized by high concentrations of His, Trp, sucrose, 2-methyl-3-buten-2-ol (23), and fruity fatty acid-derived volatiles 2-pentanone (3), 2-hexanol (6), 2-pentanol (4), 2-heptanol (7) and 2-heptanone (5). The middle group combined the samples after 18-24 h fermentation, and were highly influenced by Gln, Arg, the floral terpenes ocimene (19), β-myrcene (18) and linalool (22), the fruity compounds isoamyl alcohol (1), isobutyl acetate (11), 2-pentyl acetate (12), ethyl acetate (10), 2-nonanone (8) and 2-nonanol (9), and the offflavor 2-methyl-1-propanol (41). ...
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Fine flavor cocoa is worldwide renowned to produce origin chocolates with special aromas, e.g. fruity or floral, in addition to its chocolate aroma. This research aims to elucidate fine flavor dynamics during fermentation by analyzing the sugar, free amino acid (FAA) and volatile profile. Ecuadorian Trinitario beans (Sacha Gold) were sampled after 0, 18, 24, 48 and 66 h of spontaneous fermentation. The unfermented beans contained significant sucrose, glutamic acid and asparagine amounts while the fermented beans (66 h) contained more flavor precursors, e.g. glucose, fructose, hydrophobic and other FAA. Forty-one volatiles were identified, including 13 fruity- and 12 floral-like, derived from various metabolic pathways. Whereas the level of fatty acid-derived fruity volatiles decreased, the amount of amino acid-derived fruity and floral volatiles increased and floral terpenes remained stable. Some fine volatiles were assumed to be pulp-derived (e.g. linalool, β-myrcene, 2-heptyl acetate) or intrinsic to the bean (e.g. 2-heptanol, 2-heptanone, 2-pentanol), while others were generated during fermentation by microbial synthesis (e.g. 2-phenylethanol, isoamyl alcohol). Multivariate analysis clustered samples according to fermentation time and quality. These findings demonstrate that cocoa fermentation is essential for the formation of flavor precursors and the development or preservation of important fine aroma compounds. Trinitario (or hybrids), one of the cocoa varieties with fine flavor potential, is cultivated all over the world and hence, care should be taken during post-harvest to fully exploit this fine flavor character and deliver high-quality cocoa beans with fine sensory characteristics.
... At the moment, 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 (Loor et al. 2009), which is increasingly worrying the international chocolate industry. ...
... In this context, genetic molecular markers have been used to identify trees considered to be relics of the ancient original population of the "Nacional" variety (Loor et al. 2009). After analysis of wild material collected in Amazonia by Allen and Lass (1983), some wild trees were identified as highly related to the "Nacional" variety in a particular region of the southern Ecuadorian Amazon, considered now as its potential region of origin and domestication (Loor et al. 2012). ...
Article
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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 years ago, we used genetic molecular markers to identify trees considered to be relics of the ancient original population of the “Nacional” variety, and some wild cocoa trees in a particular region of the southern Ecuadorian Amazon were identified as highly related to the “Nacional” variety. This paper presents the results of two surveys carried out in the southern Ecuadorian Amazon, in the Zamora-Chinchipe Province, in 2010 and 2013. The objective of these surveys was to search for, identify and rescue cocoa trees that might be the wild ancestors of the “Nacional” variety. In 2010, 83 mother trees were collected (budwood, pods and leaves) and 48 in 2013. They were preserved at the Granja Domono experimental farm, near Macas (Morona-Santiago province) and at the Tropical Experimental station Pichilingue, near Quevedo. The trees collected are currently being characterized for their genetic diversity, using molecular markers, and for the biochemical diversity of their beans.
... Molecular markers such as simple sequence repeat (SSR) and single nucleotide polymorphism are used to study genetic identity and evolutionary relationships in germplasm collections. In cacao, these markers have been used for establishing genotype identities, genetic relationships, identification of genetic gaps, and in marker-assisted selection in both national and international cacao breeding and selection programs (Boza et al., 2013;Irish et al., 2010;Loor et al., 2009;Motamayor et al., 2002Motamayor et al., , 2003Motamayor et al., , 2008Schnell et al., 2005Schnell et al., , 2007Zhang et al., 2006aZhang et al., , 2006b. A study by Motamayor et al. (2008) used SSR markers to improve the understanding of the origin, classification, and population differentiation within T. cacao. ...
... Although fine flavor is known to be largely influenced by the fermentation process, great effort has been made over the past few years to improve the selection and breeding programs for this trait in Ecuador. However, this specific characteristic may have been eroded by successive introductions of foreign germplasm whose hybrid descendants have gradually replaced native plantations (Loor et al., 2009). The structure analysis results indicate that the origin of 'CCN 51' is based on its hybridization, suggesting the IMC type as the primary genetic source followed by Criollo and Amelonado ancestries. ...
Article
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Cacao (Theobroma cacao L.) is an important cash crop in tropical growing regions of the world and particularly for small cacao farmers. Over the past two decades, 'CCN 51' has become one of the most planted cultivars in Ecuador, mainly as a result of its high productivity and disease resistance. Intermixing of Nacional fine flavor Ecuadorian beans with beans of 'CCN 51' has become common practice, reducing overall bean quality and decreasing value. The primary goals of this study were to determine the genetic identity, structure, and allelic richness of 'CCN 51', its maternal origin and to compare 'CCN 51's' agronomic characteristics against a composite group of Nacional cultivars. To investigate the complex genetic background of this cultivar, 70 simple sequence repeat loci were used. The high heterozygosity observed (56 of 70 loci) for 'CCN 51' is not characteristic of traditional Nacional cultivars. Comparison of agronomic characteristics between 'CCN 51' and several Nacional cultivars indicates significant differences in cacao dry bean weight, yield potential, production efficiency, percent healthy pods, and witches' broom [Moniliophthora perniciosa (Stahel) Aime & Phillips-Mora] disease incidence. Additionally, physical, chemical, and organoleptic characteristics suggest that 'CCN 51' is different from those of Nacional lineage. Based on population structure analysis, the predominant ancestries for 'CCN 51' are Iquitos (45.4%), Criollo (22.2%), and Amelonado (21.5%) genetic groups. A lesser proportion of its genome was accounted for by genetic groups Contamana (3.9%), Purús (2.5%), Marañ on (2.1%), and Nacional (1.1%) admixtures. Results of phylogenetic analyses using the unweighted pair group method with arithmetic mean yielding high bootstrap values strongly support the relatedness of 'CCN 51' with Iquitos, Criollo, and Amelonado genetic groups. Moreover, seven mitochondrial simple sequence repeat loci revealed that 'CCN 51' maternally inherited the 'IMC 67' cytotype. 'CCN 51' constitutes a valuable cacao genetic resource that is currently used not only in its country of origin, but also in many other national breeding and selection programs worldwide.
... The aroma of the modern Nacional probably contains floral and fruity aromas that could be the legacy of crossbreeding with Trinitarios (hybrid trees between Criollo and Amelonado) (Loor S. et al., 2009;Rottiers et al., 2019). Loor et al. (2009) (Loor S. et al., 2009), have demonstrated this hybrid nature using molecular markers. This genetic mixing has led to a dilution of the Arriba flavour (Beckett et al., 2017;Boza et al., 2014;Loor S. et al., 2009). ...
... The genetic diversity of the population and its structure has been described by Loor et al. (2009) (Loor S. et al., 2009) using SSR markers and by Colonges et al. (2021) (Colonges et al., 2021) using SNP markers. The population has a high rate of heterozygosity. ...
Article
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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 association zones. These areas are linked to both the volatile compounds known to provide fruity flavours and present in the beans before and after roasting, and to the fruity notes detected by sensorial analysis. Five main metabolic pathways were identified as involved in the fruity traits of the Nacional population: the protein degradation pathway, the sugar degradation pathway, the fatty acid degradation pathway, the monoterpene pathway, and the L-phenylalanine pathway. Candidate genes involved in the biosynthetic pathways of volatile compounds identified in association areas were detected for a large number of associations.
... Amongst all the cacao groups, Trinitario, Forastero, Criollo and Nacional are the most commercialized worldwide [5]. Nacional cacao is mostly produced in Ecuador and has been categorized as fine-flavor, but few materials of this genetic group are currently available [5,6], as hybrids between Nacional and Trinitario have become predominant in Ecuador. Nacional × Trinitario cacao beans are also regarded as fine-flavor because of their distinctive organoleptic characteristics [4,6]. ...
... Nacional cacao is mostly produced in Ecuador and has been categorized as fine-flavor, but few materials of this genetic group are currently available [5,6], as hybrids between Nacional and Trinitario have become predominant in Ecuador. Nacional × Trinitario cacao beans are also regarded as fine-flavor because of their distinctive organoleptic characteristics [4,6]. From a global market perspective, huge opportunities and more monetary benefits are offered for fineflavor cacao beans compared to those proffered in the bulk cacao market [7,8]. ...
Article
Cacao demand is continuously increasing, and variations in cacao prices have been associated with the aroma of fermented cacao beans. However, the role of microorganisms in the formation of volatile-aroma compounds during fermentation remains unclear. Microbial diversity in Nacional × Trinitario cacao was characterized during spontaneous fermentation by using culture-based methods and next-generation sequencing (NGS) of DNA amplicons. Cacao beans that were spontaneously fermented for 0, 24, 48, 72 and 96 h were UV-sterilized prior to the inoculation of the microbial isolates obtained by the culture-based methods. The volatile formation in inoculated cacao beans was evaluated by GC-MS. The species isolated during fermentation included yeast, such as Saccharomyces cerevisiae and Candida metapsilosis; lactic acid bacteria (LAB), such as Limosilactobacillus fermentum and Liquorilactobacillus nagelii; acetic acid bacteria (AAB), such as Acetobacter pasteurianus, Acetobacter ghanensis and Acetobacter syzygii, as well as other species, such as Bacillus subtilis and Bacillus amyloliquefaciens. Additionally, NGS revealed an abundance of environmental microorganisms, including Escherichia spp., Pantoea spp., Staphylococcus spp., Botrytis spp., Tetrapisispora spp. and Pichia spp., among others. During the lab-scale fermentation, the inoculation of S. cerevisiae mostly yielded alcohols, while LAB and AAB produced volatiles associated with floral, almond and fruity notes throughout the fermentation, but AAB also produced acetic acid with a sour aroma. Similarly, the inoculation of C. metapsilosis and Bacillus spp. in 96 h fermented cacao beans yielded esters with floral aromas. This is the first report describing the role of microorganisms in volatile formation during fine-flavor cacao fermentation.
... Past studies have shown the hybrid nature of most of the modern Nacional cacao. Loor et al. (2009) studied 322 accessions of cacao collected in the coastal region of Ecuador. A group of ancient highly homozygous cacao HoN which could be the ancestors of the high quality cacao Nacional was identified. ...
... Two serious plagues decimated the production in the XXth century: the Witches Broom (Moniliophthora perniciosa) in the 1920s and the Monilla (Moniliophthora roreri) in the 1940s. This encouraged the introduction of foreign germoplasm (Loor et al., 2009) and, in this way, the origin of CCN-51. ...
Article
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Geographical Indications (GIs) are names of regions, specific places or, in exceptional cases, countries, used to describe an agricultural product or a foodstuff (EC 510/2006, Art. 2). They have received much attention in recent years not only at the European level, where they stem from, but also at different international forums such as at the World Trade Organization (wto). Being a particular form of intellectual property, these certification schemes have the potential to be applied also to non-agrifood commodities or even services. Furthermore, due to the grave menace of biodiversity loss caused by globalization, GIs could serve as a tool to promote biodiversity if linked to plant varieties or animal species in danger of disappearance. It seems that at European level these issues are gathering momentum. For this reason, the purpose of this paper is to support new interpretations regarding GI legislation. In the remainder of this paper, the authors will present a short description of GIs as they have been discussed at different international forums. Also, the innovative implementation of GIs in Ecuador will be illustrated by means of two examples: the Sombrero of Montecristi and the cacao Nacional Arriba. Based on these examples we trace possible scenarios of GI implementation in a particular type of service economy such as food tourism. In the final part, some conclusions will be presented.
... enzymes) properties are frequently used (Dostert et al., 2012). Of all the varieties cultivated in Ecuador, the 'Nacional fino de aroma' and CCN-51 are the most appreciated on the international market Loor et al., 2009). ...
... Besides color diversity, Graziani de Fariñas et al. (2002), in Venezuela, found contrasting physical characteristics of the fruits of criollo, trinitario, and other external types from the town of Cumboto. These findings were reported as well by Loor et al. (2009) in Ecuador. ...
Article
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The cacao has become an essential part of the fight against the effects of illegal crops and rural poverty in Colombia. Because of their bromatological characteristics, cocoa beans are preferred in markets. However, there are few studies on the variability of the regional genotypes. The goal of this study was to characterize the cacao trees in Tumaco, Nariño (Colombia) and establish their morpho-agronomic variability. Plant collections were conducted in five production zones of the municipality between 0 to 270 m. On each farm, the productivity and plant health variables were recorded for the outstanding plants. The characterization was carried out using a Principal Component Analysis (PCA), Multiple Correspondence Analysis (MCA) and Cluster analysis. In the PCA, the first five components explained 70.2% of the variation. The first three components were characterized by productivity, while the last two components showed a low pod and grain index. In the MCA, the first three factors expressed 39.5% of the variation. The first three corresponded to the cundeamor cacao, acute pod apex, absence of anthocyanin in ripe fruits, without notable pulvinus, staminodes without anthocyanins, and moderately susceptible to Moniliophthora perniciosa. The last two components reported tolerance to M. roreriand Crinnipellis perniciosa, intense anthocyanin pigmentation on the floral buttons and Angoleta-shaped fruit. The selected genotypes showed important characteristics that must be analyzed with molecular and sensorial analyses.
... This was similar to on-farm cacao in Dominica (H e = 0.320; Gopaulchan et al., 2020), in Honduras and Nicaragua (H e = 0.367; Lukman et al., 2014), and Uganda (H e = 0.332; Gopaulchan et al., 2019) but higher than in Colombia (H e = 0.28; Yacenia Morillo et al., 2014), Ghana (H e = 0.245; Padi et al., 2015), and Chuncho cacao from the La Convención province in south Peru (H e = 0.230; Céspedes-Del Pozo et al., 2018). The H e of cacao in north Peru was lower than that reported in Bolivia (H e = 0.56; Zhang et al., 2012), Cameroon (H e = 0.50; Efombagn et al., 2008), of the Juanjui province of San Martin in north Peru (H e = 0.741; Zhang et al., 2011) and that of Ecuador (H e = 0.496; Loor Solorzano et al., 2009). The moderate H e observed in this study is probably reflective of the lack of imported varieties to give rise to differential hybrid material. ...
Article
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Cacao (Theobroma cacao L.) is the basis of the lucrative confectionery industry with “fine or flavour” cocoa attracting higher prices due to desired sensory and quality profiles. The Amazonas Region (north Peru) has a designation of origin, Fine Aroma Cacao, based on sensory quality, productivity and morphological descriptors but its genetic structure and ancestry is underexplored. We genotyped 143 Fine Aroma Cacao trees from northern Peru (Bagua, Condorcanqui, Jaén, Mariscal Cáceres, and Utcubamba; mainly Amazonas Region), using 192 single nucleotide polymorphic markers. Identity, group, principal coordinate, phylogenetic and ancestry analyses were conducted. There were nine pairs of matched trees giving 134 unique samples. The only match within 1,838 reference cacao profiles was to a putative CCN 51 by a Condorcanqui sample. The “Peru Uniques” group was closest to Nacional and Amelonado-Nacional genetic clusters based on FST analysis. The provinces of Bagua and Utcubamba were genetically identical (Dest = 0.001; P = 0.285) but differed from Condorcanqui (Dest = 0.016–0.026; P = 0.001–0.006). Sixty-five (49%) and 39 (29%) of the Peru Uniques were mixed from three and four genetic clusters, respectively. There was a common and strong Nacional background with 104 individuals having at least 30% Nacional ancestry. The fine aroma of cacao from Northern Peru is likely due to the prevalent Nacional background with some contribution from Criollo. A core set of 53 trees was identified. These findings are used to support the continuance of the fine or flavour industry in Peru.
... Other traditional varieties, such as Criollo and Nacional, also possess low genetic diversity [37][38][39]. These clones shared a similar domestication process marked by genetic bottlenecks caused by humans demand for the nutritional benefits of cacao [40]. ...
Article
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Bahia is the most important cacao-producing state in Brazil, which is currently the sixth-largest country worldwide to produce cacao seeds. In the eighteenth century, the Comum, Pará and Maranhão varieties of cacao were introduced into southern Bahia, and their descendants, which are called 'Bahian cacao' or local Bahian varieties, have been cultivated for over 200 years. Comum plants have been used to start plantations in African countries and extended as far as countries in South Asia and Oceania. In Brazil, two sets of clones selected from Bahian varieties and their mutants, the Agronomic Institute of East (SIAL) and Bahian Cacao Institute (SIC) series, represent the diversity of Bahian cacao in germplasm banks. Because the genetic diversity of Bahian varieties, which is essential for breeding programs, remains unknown, the objective of this work was to assess the genetic structure and diversity of local Bahian varieties collected from farms and germplasm banks. To this end, 30 simple sequence repeat (SSR) markers were used to genotype 279 cacao plants from germplasm and local farms. The results facilitated the identification of 219 cacao plants of Bahian origin, and 51 of these were SIAL or SIC clones. Bahian cacao showed low genetic diversity. It could be verified that SIC and SIAL clones do not represent the true diversity of Bahian cacao, with the greatest amount of diversity found in cacao trees on the farms. Thus, a core collection to aid in prioritizing the plants to be sampled for Bahian cacao diversity is suggested. These results provide information that can be used to conserve Bahian cacao plants and applied in breeding programs to obtain more productive Bahian cacao with superior quality and tolerance to major diseases in tropical cacao plantations worldwide.
... Cacao produced in Ecuador and other South America countries has favorable quality for making fine chocolate (Loor et al., 2009). However, concentrations of heavy metals (including Cd and Pb) above a critical level (0.6 mg kg −1 for Cd), established by European Union, has raised concerns of safety in the consumption of cacao-based chocolate (dark chocolate) (Mounicou et al., 2003;Zarcinas et al., 2004;Dahiya et al., 2005). ...
Conference Paper
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The determination of bioavailable pools for emerging contaminants in soils and the factors controlling their bioavailability is a continuous effort in scientific community worldwide. Cacao (Theobroma cacao L.), and more specifically cacao bean, has been reported to accumulate high levels of cadmium (Cd), which may enhance the risk of Cd exposure in cacao-based products. The concern of Cd in cacao beans was also reported in some South America countries including Ecuador. The objectives of this study were: a) to understand the accumulation of Cd in cacao beans relative to soil Cd availability, and b) to determine chemical speciation and other factors that may control plant-available Cd in soils. Nineteen cacao farms were sampled; leaves, cacao pods and soils were collected; soils were sampled at 0-5 and 5-15 cm (depths 1 and 2) to pinpoint vertical distribution of available Cd. Cacao tissue and beans were pulverized and digested with concentrated HNO3. Single extractions using 1 M NH4OAc, 0.1 M HCl, or Mehlich 3 extractants, and soil Cd fractionation with a sequential extraction method (Tessier et al, 1979) were performed. Plant analysis showed low concentration of Cd in leaves but much higher in beans, which ranged from 0 to 2.9 mg kg-1, twelve out of nineteen sites surpassed the critical level of 0.5 mg kg-1. The analysis of variance (ANOVA) showed a significant difference (P< 0.001) among the single extraction methods, with extractable Cd decreasing in the order of 0.1 M HCl > Mehlich 3 >> 1 M NH4OAc. Available Cd estimated with single extraction varied significantly with depth of soil, higher in depth 1 than depth 2 (P<0.01); however there was no significant interactions between methods and depths. Bean Cd concentration was significantly correlated with both total recoverable Cd and extractable Cd in soil, but more closely related to extractable Cd, r = 0.77, 0.79 and 0.40 (P< 0.0001, < 0.0001, and < 0.0002), respectively for 0.1 M HCl, Mehlich 3 and 1 M NH4OAc. Soil Cd fractionation showed that organically bound Cd is the dominant fraction of the total recoverable Cd, which is significantly correlated with available Cd estimated by chemical extraction. The results from this study indicate that the high concentrations of Cd in cacao bean are related to Cd accumulation in soil. The constant litter accumulation and decomposition in cacao plantations and other potential anthropogenic activities such as irrigation may have contributed to Cd accumulation in the soils, which tends to decrease with soil depth. Extractable Cd estimated by Mehlich 3 or 0.1 M HCl appears to be a good indicator of available Cd in the soils. The high percentage of organically bound Cd in the soils merits further study for improving soil remediation management.
... Cacao produced in Ecuador and other South America countries has favorable quality for making fine chocolate (Loor et al., 2009). However, concentrations of heavy metals (including Cd and Pb) above a critical level (0.6 mg kg −1 for Cd), established by European Union, has raised concerns of safety in the consumption of cacao-based chocolate (dark chocolate) (Mounicou et al., 2003;Zarcinas et al., 2004;Dahiya et al., 2005). ...
... The second cluster is the SCA group, which is comprised of wild Peruvian trees mainly from the Ucayali population and includes SCA 6 and SCA 24. The third cluster comprised of the Nacional accessions, which are not widely distributed and produce a unique BArriba^flavour distinct to Ecuador cacao beans (Loor et al. 2009). The fourth cluster is a combination of genetic groups NA and PA which are a part of the Pound collection of natural populations originally collected from the Marañon river basin in Peru (Bartley 2005;Zhang et al. 2009). ...
Article
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Cacao is an economically important commodity in Jamaica. Knowledge of the genetic diversity of Jamaican cacao germplasm is essential for their conservation and management. In spite of cacao’s economic importance in Jamaica, the crop is under studied, therefore limiting sound decisions toward improving productivity. Assessment of germplasm and on-farm genetic diversity is required to assist selecting superior genotypes to propagate and distribute across the island, as well as to use them as parental clones in breeding programs. Using 94 single nucleotide polymorphism (SNP) markers, 140 Jamaican cacao samples from two germplasm collections and a farmer’s estate along with 150 reference samples were analyzed. The principal coordinate analysis demonstrated that the majority of the Jamaican cacao selections were hybrids derived from five original germplasm groups, including Criollo, Amelonado and three Upper Amazon Forastero groups. Among the Upper Amazon groups, the Bayesian clustering analysis revealed that the Parinari (PA) ancestral lineage contributed the most (29.9%) to the Jamaican cacao germplasm. The germplasm collections showed greater diversity in terms of ancestral contributions compared to the farmer’s estate. However, the genetic differentiation between the three collecting sites was small (Fst = 0.036), indicating that samples collected from the three sites were derived from a common pool of germplasm. The current study supports the historical records and clarified the ancestry of Jamaican cacao. Although the majority of the cacao genetic groups were observed in the Jamaican cacao collections, several diversity gaps were found in both germplasm collections and in the farmer’s estate, especially germplasm with disease resistance to cacao frosty pod rot that was recently found in Jamaica.
... The samples from the EET hybrid population are the products of relatively few generations of humanmediated crosses made within the last century. These crosses were attempts by breeders to introgress disease resistance phenotypes from wild Upper Amazon clones into local, high yielding breeding stock with a Trinitario genetic background (Loor et al. 2009). It is difficult to make any generalizations about association analyses using the EET population as the number of samples was very small (Table 1). ...
Article
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Linkage disequilibrium (LD) measured over the genomes of a species can provide important indications for how future association analyses should proceed. This information can be advantageous especially for slow-growing, perennial crops such as Theobroma cacao, where experimental crosses are inherently time-consuming and logistically expensive. While LD has been evaluated in cacao, previous work has been focused on relatively narrow genetic bases. We use microsatellite marker data collected from a uniquely diverse sample of individuals broadly covering both wild and cultivated varieties to gauge the LD present in the different cacao diversity groups and populations. We find that genome-wide LD decays far more rapidly in the wild and primitive diversity groups of cacao as compared to those representing cultivated varieties. The impact that such differences can have on association analyses is demonstrated using phenotypic data on pod color and genotypic data from two cacao populations with contrasting patterns of LD decay. Our results indicate that the more rapid LD decay in wild and primitive germplasm can lead to higher-resolution mapping intervals when compared to results from cultivated germplasm. Through simulations, we demonstrate how future association mapping analyses, comprising of cacao samples with a wild or primitive background, will likely exhibit lower LD and would be more suitable for fine-scale association mapping analyses. As many traits targeted by cacao breeders are found exclusively in wild and primitive germplasm, association mapping in wild cacao populations holds significant promise for cacao improvement through marker-assisted breeding and emphasize the need to further explore the natural diversity of Amazonian cacao.
... Cacao produced in Ecuador and other South America countries has favorable quality for making fine chocolate (Loor et al., 2009). However, concentrations of heavy metals (including Cd and Pb) above a critical level (0.6 mg kg −1 for Cd), established by European Union, has raised concerns of safety in the consumption of cacao-based chocolate (dark chocolate) (Mounicou et al., 2003;Zarcinas et al., 2004;Dahiya et al., 2005). ...
... However, the original Nacional cocoa trees are currently in danger of extinction due to the introduction of an external unrelated germplasm (Solorzano et al., 2012). A large genetic admixture between native Nacional cocoa and foreign germplasm is currently found in modern Ecuador plantations (Solorzano et al., 2009), thus reducing the fine-flavoured cocoa aroma. Currently, pure Nacional cocoa varieties are rare and there is an increasing demand for fine flavour cocoa although Ecuador still represents 6.8% of the supply of 'arriba' flavoured cocoa in the world market (ICCO, 2012). ...
... However, the original Nacional cocoa trees are currently in danger of extinction due to the introduction of an external unrelated germplasm (Solorzano et al., 2012). A large genetic admixture between native Nacional cocoa and foreign germplasm is currently found in modern Ecuador plantations (Solorzano et al., 2009), thus reducing the fine-flavoured cocoa aroma. Currently, pure Nacional cocoa varieties are rare and there is an increasing demand for fine flavour cocoa although Ecuador still represents 6.8% of the supply of 'arriba' flavoured cocoa in the world market (ICCO, 2012). ...
... However, the original Nacional cocoa trees are currently in danger of extinction due to the introduction of an external unrelated germplasm (Solorzano et al., 2012). A large genetic admixture between native Nacional cocoa and foreign germplasm is currently found in modern Ecuador plantations (Solorzano et al., 2009), thus reducing the fine-flavoured cocoa aroma. Currently, pure Nacional cocoa varieties are rare and there is an increasing demand for fine flavour cocoa although Ecuador still represents 6.8% of the supply of 'arriba' flavoured cocoa in the world market (ICCO, 2012). ...
... Cacao collections along the Ecuadorian territory continued during the 1930s and 1940s and have been maintained in the two largest germplasm banks of the country, the "Estación Experimental Tropical Pichilingue" in Quevedo and "Centro de Cacao Aroma Tenguel" (Loor et al. 2009). Moreover, the work of the breeder Homero Castro Zurita would have a significant impact on cacao production in Ecuador in the next decades. ...
Article
Cacao is a commodity crop from the tropics cultivated by about six million smallholder farmers. The tree, Theobroma cacao, originated in the Upper Amazon where it was domesticated ca. 5450–5300 B.P. From this center of origin, cacao was dispersed and cultivated in Mesoamerica as early as 3800–3000 B.P. After the European conquest of the Americas (the 1500s), cacao cultivation intensified in several loci, primarily Mesoamerica, Trinidad, Venezuela and Ecuador. It was during the colonial period that cacao diseases began emerging as threats to production. One early example is the collapse of the cacao industry in Trinidad in the 1720s, attributed to an unknown disease referred to as the “blast”. Trinidad would resurface as a production center due to the discovery of the Trinitario genetic group, which is still widely used in breeding programs around the world. However, a resurgence of diseases like frosty pod rot during the republican period (the late 1800s and early 1900s) had profound impacts on other centers of Latin American production, especially in Venezuela and Ecuador, shifting the focus of cacao production southward, to Brazil. Production in Brazil was, in turn, dramatically curtailed by the introduction of witches’ broom disease in the late 1980s. Today, most of the world’s cacao production occurs in West Africa and parts of Asia, where the primary Latin American diseases have not yet spread. In this review, we discuss the history of cacao cultivation in the Americas, and how that history has been shaped by the emergence of diseases.
... cacao genotypes by cacao producers. Some studies present the genotypes of cocoa Nacional and CCN-51 as the most appreciated variety in the international market Loor et al., 2009), which corroborates that these genotypes are the most used in the studies of this review systematic. The Nacional genotype produces special cacao of fine flavor, while CCN 51 provides cacao of inferior aromatic quality (Vargas Jentzsch et al., 2016; Beg et al., 2017). ...
Article
Cadmium (Cd) is a non-essential trace metal, highly toxic to plants, animals and humans. Its mobility in the soil is high and it is transferred with relative ease to crops. European Food Safety Agency (EFSA) has identified the consumption of chocolate as a source of Cd contamination, and established maximum Cd limits allowed in cacao-based products. Therefore, research related to tolerance and reduction of Cd toxicity in a cacao becomes important. The main objective of the present study was to systematize the main factors that interfere in the uptake of soil Cd by the cacao tree and its strategies for tolerance to toxicity. A systematic review of the literature was conducted using six databases for academic research (Google Academic, PubMed, Springer, CAPES Periodical, Scielo and Science Direct). To avoid publication bias, a previously established protocol and inclusion and exclusion criteria were used. The main factors related to the uptake of soil Cd by the cacao tree were soil pH, soil Cd availability, genotype, the geographical location, agronomic factors such as phosphate fertilizersand Cd interaction with other minerals/metal nutrients such as Zn and Mn present in the soil. To reduce the toxicity of this metal, cocoa promotes some tolerance strategies such as uptake and transfer of Cd from the root to the shoot, molecular and biochemical changes, Cd partition between plant organs and Cd sequestration at the cellular level. So, this systematic review contributed to the acquisition of knowledge for the genetic improvement of cacao tree, concerning toxicity tolerance strategies and reduction of soil Cd uptake.
... This variety, which was produced from a natural hybrid of Criollo and Lower Amazon Forastero family [20], inherited the traits of both family groups. Thus, clones from Trinitario variety were heterogeneous and displayed extreme diversity in the field [21][22][23], such as MCBC1 clone which developed significantly different measurements of stem height and diameter when compared to other clones. For the fruit and seed traits, an interaction between propagation type and cocoa clones was significant. ...
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This study was conducted to compare the agronomic performance of four elite cocoa clones (MCBC1, KKM22, KKM4 and PBC230) regenerated from staminode and immature zygotic embryo culture with conventional grafted cocoa clones. From the results, it was found that the KKM4 clone propagated from immature zygotic embryo culture exhibited variations in the fresh pod weight (339.6 g), fresh individual seed weight (4.13 g) and number of flat beans per pod (4 beans) compared with the rest of the regenerated clones. The genetic stability of the somatic embryogenesis cultured clones and the donor clones was then tested using fragment analysis with five SSR primers, i.e. mTcCIR7, mTcCIR18, mTcCIR22, mTcCIR33 and mTcCIR40. Four of these primers identified variations in the allele size and allele addition in KKM4 clone from immature zygotic embryo. Molecular analysis validated that the difference in agronomic performance of the KKM4 clone from immature zygotic embryo culture was due to genetic mutation created during the immature zygotic embryo culture process.
... Ecuador is the top delicate flavor cacao producer worldwide 2 with extensive production areas for the 'Nacional' and 'CCN51' types of cacaos. The Nacional cacao is preferred by consumers 3 but is more susceptible to the frosty pod rot disease (FPD) than CCN51 4 . The FPD has caused significant losses in the cacao production of Latin American countries 1 , and the production of Nacional cacao is partially being replaced by CCN51 in Ecuador 4 mostly because of FPD. ...
Article
Moniliopthora roreri is the frosty pod rot disease (FPD) and one of the most devastating cacao pathogens worldwide. However, M. roreri pathogenicity on harvested cacao pods and sensitivity to compost tea have not been fully described. Monosporic cultures of M. roreri from different morphology groups were obtained. The isolates’ pathogenicity was tested by inoculation onto harvested cacao pods, and symptoms were evaluated at 3-day intervals during 16 days before estimating the area under the disease progress curve (AUDPC). The sensitivity of M. roreri to compost tea was evaluated on potato dextrose agar (PDA) amended with 1 to 5 % compost tea. All morphology groups could infect harvested cacao pods during the 16 days with a disease severity index abode 75 %. Compost tea completely inhibited the growth of M. roreri when used at 4.5 % or higher. Results suggest a shortened biotrophic phase during the infection in harvested pods and a medium to high sensitivity of M. roreri to compost tea.
... En la literatura, la mayoría de los estudios coinciden en este aspecto [38][39][40]. Las actividades agroturísticas vinculadas a las actividades al aire libre, las instalaciones de ocio y las atracciones para los visitantes realizados en tierras agrícolas deben estar estrechamente vinculadas a las características de la explotación y la agricultura actual sin cambiar su carácter ni requerir grandes inversiones [39,41]. ...
Article
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Resumen: El agroturismo auténtico representa un paradigma de felicidad e integración intersectorial y un ejemplo exitoso de desarrollo urbano-rural. Mejorar la combinación y la cooperación entre la agricultura y el turismo tiene un mayor potencial, lo que conduce a múltiples perspectivas que dan como resultado situaciones de beneficio mutuo que aumentan el valor agregado local y regional. El objetivo del estudio se centró en el análisis del agroturismo, sus tipos e intenta vincular la esencia de conceptos para marcar una diferencia entre un macro turismo rural y el agroturismo puro. Datos que sirven como punto de partida para nuevos proyectos en la región amazónica norte del Ecuador. Se logró recopilar diferencias significativas que permitirán crear, planificar y diseñar rutas agroturísticas robustas que aporten a la dinamización económica local, regional y nacional. Abstract: Authentic agrotourism represents a paradigm of happiness and intersectoral integration and a successful example of urban-rural development. Improving the combination and cooperation between agriculture and tourism has greater potential, leading to multiple perspectives that result in mutually beneficial situations that increase local and regional added value. The objective of the study focused on the analysis of agrotourism, its types and attempts to link the essence of concepts to make a difference between a rural macro tourism and pure agrotourism. These data serve as a starting point for new projects in Ecuador's northern Amazon region. It was possible to compile significant differences that will allow the creation, planning and design of robust agrotourism routes that will contribute to the local, regional and national economic dynamization.
... En la literatura, la mayoría de los estudios coinciden en este aspecto [38][39][40]. Las actividades agroturísticas vinculadas a las actividades al aire libre, las instalaciones de ocio y las atracciones para los visitantes realizados en tierras agrícolas deben estar estrechamente vinculadas a las características de la explotación y la agricultura actual sin cambiar su carácter ni requerir grandes inversiones [39,41]. ...
Article
Full-text available
Resumen: El agroturismo auténtico representa un paradigma de felicidad e integración intersectorial y un ejemplo exitoso de desarrollo urbano-rural. Mejorar la combinación y la cooperación entre la agricultura y el turismo tiene un mayor potencial, lo que conduce a múltiples perspectivas que dan como resultado situaciones de beneficio mutuo que aumentan el valor agregado local y regional. El objetivo del estudio se centró en el análisis del agroturismo, sus tipos e intenta vincular la esencia de conceptos para marcar una diferencia entre un macro turismo rural y el agroturismo puro. Datos que sirven como punto de partida para nuevos proyectos en la región amazónica norte del Ecuador. Se logró recopilar diferencias significativas que permitirán crear, planificar y diseñar rutas agroturísticas robustas que aporten a la dinamización económica local, regional y nacional. Abstract: Authentic agrotourism represents a paradigm of happiness and intersectoral integration and a successful example of urban-rural development. Improving the combination and cooperation between agriculture and tourism has greater potential, leading to multiple perspectives that result in mutually beneficial situations that increase local and regional added value. The objective of the study focused on the analysis of agrotourism, its types and attempts to link the essence of concepts to make a difference between a rural macro tourism and pure agrotourism. These data serve as a starting point for new projects in Ecuador's northern Amazon region. It was possible to compile significant differences that will allow the creation, planning and design of robust agrotourism routes that will contribute to the local, regional and national economic dynamization.
... This gap of knowledge has been identified, but it is being filled mostly by European researchers as evidenced by a recent review (De Vuyst and Weckx 2016;Romanens et al. 2018). Some efforts have been undertaken to survey the genetic diversity of 'Nacional' cultivars (Solorzano et al. 2012;Loor et al. 2009;Boza et al. 2014). Associating individual 'Nacional' cultivars to cocoa liquor quality is practically impossible because cacao is produced by a large number of small farms that ferment it under non-standardized and uncontrolled conditions. ...
Chapter
The quality of chocolate is affected by a multitude of factors including cacao cultivar, maturity, fermentation management, drying, roasting, grinding, conching and, the addition of ingredients. In the sequence of unit operations, perhaps the most complex is fermentation because it is affected by the variability of microbial populations, the variability in the amount of mucilage, and the variability in the concentration of fermentable sugars. Several fermentation studies have been published but very few detail the progress of the fermentation in multiple points in a 1-m3 fermentation box. Both yeast and bacterial fermentations of cacao produce heat. Therefore, we monitored temperature profiles as indirect indicators of microbial activity. Measurement of fermentation temperature at the centre of fermentation boxes and only five other locations in a box have been previously reported. In this research study, we continuously monitored temperature profiles in 27 locations in a symmetric cubic matrix in a 1-m3 box. Temperature right before the removal from one box to the next varied by 10–13 °C for a single batch and up to 16 °C for six batches. The maximal reported temperature was 54 °C. Highest temperatures occurred in the highest layer and lowest temperatures in the lowest layer. However, there was not a clear symmetry in the temperature profiles of the corners in each layer, suggesting non-uniform microbial growth or non-uniform heat losses. Alternation of top and bottom layers when changing from one box to the next reduced the heat non-uniformities. Cut tests at each stage of fermentation indicated the progress of the fermentation is very variable among batches and within a batch. Finally, analysis of headspace volatiles confirms the very large variability of fermentation conditions within and among batches.
... The PCoA plot grouped the 150 reference accessions into seven clusters representing known cacao germplasm groups of Amelonado, Criollo, IMC (Iquitos), Nacional, Nanay, Parinari (Marañon) and Scavina (Contamana). Origin and identity of these seven clusters (or populations) have been reported previously by Solorzano et al. (2009), Zhang et al. (2009, Motamayor et al. (2008) and Motilal et al. (2011). Most of the Yunnan samples were dispersed among the Amelonado group and the other reference groups, indicating admixed ancestral background primarily based on Amelonado ancestry ( Fig. 1A and B). ...
Article
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Cacao is an economically important crop, since it provides the raw material for the multibillion dollar global chocolate industry. Yunnan Province is in the far southwestern region of China where tropical agriculture makes up a significant part of the provincial GDP. There is great potential for cacao production in Yunnan, given the rapid increase of chocolate consumption in China. Understanding the genetic background of available germplasm is essential for effective genebank management and crop genetic improvement. The objectives of this investigation were to assess the genetic identity of the cacao germplasm maintained in Yunnan, China; and to quantify the level of genetic diversity in comparison with available diversity in international collections. Using Single Nucleotide Polymorphism (SNP) markers, we genotyped the cacao collection maintained in the Xishuangbanna Tropical Botanical Garden in Yunnan. Multivariate analysis and Bayesian assignment test, using 150 reference cacao accessions, showed that these introduced cacao germplasm accessions have a narrow genetic background and were mostly comprised of Amelonado hybrids. Of the 88 Yunnan accessions, 59% of the parentage is contributed by Amelonado and 17% by two Upper Amazon Forastero populations. The study demonstrated that these introduced cacao germplasm accessions have a narrow genetic background thus lacking multiple sources of resistance to major cacao diseases. The present results therefore suggest that new introductions are needed to enrich genetic diversity in this collection. An improved germplasm collection would serve as a foundation for broader on-farm diversity for cacao cultivation in Yunnan, as well as in other tropical regions of China.
... La variété CCN-51 en Equateur est connue pour être un hybride entre le Nacional et le Trinitario (Beckett, 2009;Loor et al., 2009). L'appellation « Arriba » fait référence à deux définitions : la première fait référence à la région d'origine de la production, tandis que la seconde renvoie aux particularités aromatiques et aux saveurs qu'elle génère (Loor Solórzano, 2007). ...
Thesis
Le cacao est la 3ème denrée la plus commercialisée dans le monde et 23 pays sont classés selon l’ICCO comme producteurs de cacao fin, dont Madagascar. Le cacao de Madagascar est classé cacao fin à 100 % selon l’ICCO depuis 2016. Il est un des plus réputés au monde, même s'il ne représente que 0,2 % de la production mondiale. Peu d’études existent concernant la caractérisation du cacao malgache et sa fermentation. La fermentation est une étape post-récolte pour l’obtention des caractéristiques aromatiques et sensorielles d’un cacao de qualité. Ce travail a permis de déterminer les critères de qualité et de suivre les évolutions des critères organoleptiques, de la composition volatile et les micro-organismes au cours de la fermentation. Le cacao produit à Madagascar appartient principalement aux variétés Criollo et Trinitario. Le suivi de la fermentation montre qu’au niveau sensoriel, les descripteurs « végétal, terreux, astringent, amer » des fèves de cacao non ou peu fermentées (24-48 h) s’estompent pour laisser place aux descripteurs cacao, chocolat, fruité, acide pour des fèves de cacao en fin de fermentation (96 h-144 h). De même, les teneurs en composés volatils liés aux descripteurs sensoriels recherchés tels que l’acétate de 3-méthylbutyle, l’acétate d'éthyle, le benzaldéhyde, la tétraméthylpyrazine, l’acide acétique augmentent au cours de la fermentation. L’étude de la flore microbienne a permis d’identifier l’origine de la production de certains composés volatils. Notamment, la levure Hanseniaspora opuntiae présente un intérêt particulier car elle est associée à la production de 2-phényléthanol. L’étude des communautés levuriennes par voie moléculaire a confirmé la présence des levures isolées et a mis en évidence d’autres souches notamment du genre Pichia qui sont aussi productrices de molécules volatiles telles que l’acétate de 2-phényléthyle et l’acétate d'éthyle.
... This gap of knowledge has been identified, but it is being filled mostly by European researchers as evidenced by a recent review (De Vuyst and Weckx 2016;Romanens et al. 2018). Some efforts have been undertaken to survey the genetic diversity of 'Nacional' cultivars (Solorzano et al. 2012;Loor et al. 2009;Boza et al. 2014). Associating individual 'Nacional' cultivars to cocoa liquor quality is practically impossible because cacao is produced by a large number of small farms that ferment it under non-standardized and uncontrolled conditions. ...
Chapter
The debate on the adoption and development of GMOs continues today. The polarizations on their use have been established and do not seem to change. This polarization has also been established in Latin America, although two countries permit the cultivation of GMOs (Brazil and Argentina). After 30 years of the first GMO plant, what happened in Latin America? What position have your countries taken on the adoption, adaptation, and development of GM crops? It seems that the struggle for the development of these crops originated on other continents, but their consequences had an impact in Latin America. This debate has meant rising revenues in some countries and the delay of others in the use of this powerful technology. Is it ethical? This debate has left some countries in Latin America and the Caribbean in a technological unit, and others have been able to close the gap between the developer countries and them. GMO technology continues to be surrounded by controversial debates involving different actors. This chapter draws attention to the conflicts generated in polarized contexts and shows how, in situations of a wanted polarization, strategies are used only to defend themselves and maintain control of the situation in both positions. The point of view is from the scientific and technological development.
... Varias investigaciones (Zarrillo et al. 2018;Loor et al. 2009 y 2012) dan cuenta de la antigüedad del uso cultural del cacao (o Theobroma cacao L.) y reconocen que los antiguos pobladores de lo que hoy se conoce como la cultura Mayo Chinchipe, en el actual Ecuador, fueron los primeros en el mundo en utilizar la planta de cacao con fines alimenticios, hace aproximadamente 5.300 años. La revista Nature Ecology & Evolution, en octubre de 2018, publicó "The Use and Domestication of Theobroma Cacao During the mid-Holocene in the Upper Amazon", cuya autoría pertenece a 19 investigadores, entre ellos el arqueólogo ecuatoriano Francisco Valdez, investigador del Institut de Recherche pour le Développement (IRD). ...
Article
Full-text available
Esta investigación tiene por objetivos describir los principales elementos culturales y económicos de la historia del cacao en la Costa ecuatoriana, y coadyuvar en la comprensión de la articulación de estas dimensiones. Se basa en el método descriptivo, con técnicas de análisis documental y bibliográfico en perspectiva histórica, para evidenciar la trascendencia acerca del sentido cultural del cacao vinculado con su aspecto económico. Según la metáfora aquí planteada, la urdimbre del tejido del cacao se relaciona con los factores menos evidentes, los aspectos histórico y cultural del producto; la trama, que es lo más visible, corresponde al contexto económico y comercial del cacao.
... An important advantage of Ecuador is its ideal agroecological conditions for cacao production as well as great diversity and varietal richness. This is associated with Ecuador's genetic resources; the country is considered to be the center of origin of the Nacional variety (Loor et al., 2009). ...
Article
Purpose Motivated by transformations in global food systems and increasing demand for multidimensional credence attributes, the authors analyze cacao value chains in Ecuador – the main producer of fine and flavor cacao worldwide. The authors identify opportunities and discuss how private and public sector initiatives can help meet emerging challenges. Design/methodology/approach Primary information was collected through interviews of actors in the Ecuadorian industry during spring/summer 2020, including cacao producer associations, exporter associations, chocolate processing firms, public institutions and local universities. Two focus groups were also conducted with producers from associations in the Ecuadorian Amazon. Findings Findings suggest new opportunities for cacao producers and chocolate processors have emerged from the global market transformation. To exploit these, firms need to personalize and differentiate their products, for example, by using quality certifications such as organic and fair trade. Market developments, such as European cadmium regulations and the necessity of worldwide traceability systems, are driving exporters to enhance Ecuador’s cacao value chains. The sector still requires coordination to reap the benefits associated with demands for credence attributes. Originality/value Findings are supported by two case studies. The first focuses on how associativity can help those producing high-quality beans to differentiate themselves in modern agri-food markets. The second describes the success of a local chocolate firm and its links with local farmers.
... In Ecuador, cacao (Theobroma cacao L.) is one of the primary sources of economic income for the agricultural and agribusiness sectors. The national variety (Forastero) is the most commonly cultivated in Ecuador and has high prestige in international markets due to its organoleptic benefits (Loor et al., 2009;Solorzano et al., 2012). Fine aroma cocoa accounts for only 6% of the world production. ...
... In Ecuador, cacao (Theobroma cacao L.) is one of the primary sources of economic income for the agricultural and agribusiness sectors. The national variety (Forastero) is the most commonly cultivated in Ecuador and has high prestige in international markets due to its organoleptic benefits (Loor et al., 2009;Solorzano et al., 2012). Fine aroma cocoa accounts for only 6% of the world production. ...
Article
Cocoa is a primary source of economic income in the agricultural and agroindustrial sectors of Ecuador. However, cocoa crops are vulnerable to meteorological conditions that affect reproduction processes, including pollen production, which has encouraged the study of factors related to low crop yields and practical implications in breeding programs. The objective of this study was to assess the pollen production per flower in 11 genotypes of Theobroma cacao national type and CCN-51 clone. The number of pollen grains per flower was estimated by collecting 10 flower buds from each genotype for 12 consecutive months and directly counting pollen grains using an optical microscope and a Neubauer chamber. An average of 32,611 pollen grains per flower was estimated, with the largest amount of pollen (44,000) produced by the CCN-51 genotype. There was a moderate positive correlation between the environmental variables and pollen production (temperature, r = 0.33; p = 0.028; precipitation, r = 0.43; p = 0.0025). Since pollen production is an important indicator used for the selection of promising genotypes, the genotypes identified with the highest pollen production should be used in breeding programs.
... With a total cacao bean production of 121,825 tons in 2017, Peru exported more than $235 million of cacao and derivatives, 50% of it directed to the European market [79]. The majority of cacao varieties (i.e., forastero) grown in the world (95%) are native to the Amazon Basin [80,81], and that produced in Peru and other South America countries has been considered suitable for fine chocolate manufacture [82]. Although we did not measure Cd contents in the cacao beans or plants at our study sites, multiple studies have directly associated Cd contents in soils with those found in the cacao beans. ...
Article
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Soil contamination by potentially toxic trace elements (PTEs) such as Cadmium (Cd), is a major environmental concern because of its potential implications to human health. Cacao-based products have been identified as food sources with relatively high Cd contents. Here, we assessed Cd concentrations of cacao-growing soils in four major agricultural regions with contrasting climates in Peru, one of the main exporters of cacao products worldwide. At each study site (n = 40) a broad range of potential factors affecting Cd concentration in soils, i.e., site, soil and management, were evaluated. Concentrations of Cd ranged between 1.1-3.2 mg kg −1. Mean values per region were below 2.7 mg kg −1 , usually established as upper-limit for non-polluted soils. Cadmium concentrations were significantly (p < 0.001) higher in sites at higher elevations and in a temperate, drier climate. Cadmium correlated positively with pH (r = 0.57; p < 0.05) and was higher (p < 0.001) in alluvial sediments and Leptosols. Management factors (cacao variety, cultivation year, management practices) and agroecology did not affect Cd concentrations directly. Overall, this study highlights the importance of considering a broad range of both natural and anthropogenic factors to evaluate Cd concentrations in cacao-growing soils and contribute to effective and sustainable cacao production by improving land management and planning.
... Molecular tools have been widely used to fingerprint the genetic diversity of cacao in most cocoa-producing countries: in Brazil (Carvalho et al. 2003;Marita et al. 2001;Santos et al. 2005;Sereno et al. 2006); Ecuador (Loor et al. 2009;Loor-Solorzano et al. 2013); Honduras and Nicaragua (Ji et al. 2013;Trognitz et al 2013); Bolivia ; French Guiana (Lachenaud and Zhang 2008); Peru (Zhang et al. 2006); Mexico (Whitkus et al. 1998); the Caribbean (Boza et al. 2013;Irish et al. 2010;Johnson et al. 2009;Martinez et al. 2014;Motilal et al. 2010); West Africa (Aikpokpodion 2012;Efombagn et al. 2006Efombagn et al. , 2008Opoku et al. 2007;, 2000Pokou et al. 2014, and South East Asia (Indonesia) (Dinarti et al. 2015;Susilo et al. 2011). The research findings of Motamayor et al. (2008) were among the most significant since they revealed 10 genetic groups among 1241 wild type cacao accessions from a broad geographic area. ...
Chapter
The suboptimal productivity in cocoa farmers’ fields, particularly those of small-holders who produce over 80% of the global supply, and the demand for cocoa that meets stringent quality and flavor criteria necessitate enhanced breeding methods and outcomes. Progress in cacao breeding has been hindered by a long-generation cycle, limitations in land availability for large-scale breeding trials, and challenging abiotic and biotic stress factors, including several major diseases. Cacao tends to be outbreeding and cocoa production is often reduced by the incompatibility status of planting material and pollination inefficiency. The complex breeding mechanisms in cacao and difficulty in predicting the performance of promising selections as parents also pose challenges to breeders. Reciprocal recurrent selection schemes have been most successful to date. The advent of breeding with genomics and the unravelling of the cacao genome portend unprecedented advancements in cocoa breeding. This chapter explores the past, present and future prospects of cacao breeding, and describes how the use of traditional breeding allied with molecular and genomic approaches can empower cocoa breeders to meet the need for improved planting material with high productivity and yield efficiency, disease resistance, climate change adaptations, nutraceutical value and superior flavor and quality attributes.
... Molecular tools have been widely used to fingerprint the genetic diversity of cacao in most cocoa-producing countries: in Brazil (Carvalho et al. 2003;Marita et al. 2001;Santos et al. 2005;Sereno et al. 2006); Ecuador (Loor et al. 2009;Loor-Solorzano et al. 2013); Honduras and Nicaragua (Ji et al. 2013;Trognitz et al 2013); Bolivia ; French Guiana (Lachenaud and Zhang 2008); Peru (Zhang et al. 2006); Mexico (Whitkus et al. 1998); the Caribbean (Boza et al. 2013;Irish et al. 2010;Johnson et al. 2009;Martinez et al. 2014;Motilal et al. 2010); West Africa (Aikpokpodion 2012;Efombagn et al. 2006Efombagn et al. , 2008Opoku et al. 2007;, 2000Pokou et al. 2014, and South East Asia (Indonesia) (Dinarti et al. 2015;Susilo et al. 2011). The research findings of Motamayor et al. (2008) were among the most significant since they revealed 10 genetic groups among 1241 wild type cacao accessions from a broad geographic area. ...
Preprint
The sub-optimal productivity in cocoa farmers' fields, particularly those of smallholders who produce over 80% of the global supply, and the demand for cocoa that meets stringent quality and flavour criteria necessitate enhanced breeding methods and outcomes. Progress in cacao breeding has been hindered by a long generation cycle, limitations in land availability for large-scale breeding trials, and challenging abiotic and biotic stress factors, including several major diseases. Cacao tends to be outbreeding and cocoa production is often reduced by the incompatibility status of planting material and pollination inefficiency. The complex breeding mechanisms in cacao and difficulty in predicting the performance of promising selections as parents also pose challenges to breeders. Reciprocal recurrent selection schemes have been most successful to date. The advent of breeding with genomics and the unravelling of the cacao genome portend unprecedented advancements in cocoa breeding. This chapter explores the past, present and future prospects of cacao breeding, and describes how the use of traditional breeding allied with molecular and genomic approaches can empower cocoa breeders to meet the need for improved planting material with high productivity and yield efficiency, disease resistance, climate change adaptations, nutraceutical value and superior flavour and quality attributes.
... It is now the most commonly grown cacao in the world (Wood 1985). However, Forasteros are less valuable because their fermented beans are not generally considered to produce a high quality flavor (Wood 1985 ), although there are exceptions such as the " Nacional " variety of Forastero from Ecuador (Loor et al. 2009). ...
Article
Full-text available
Trinidad and Tobago has a long history of producing high-quality cacao (Theobroma cacao L.). Cacao genotypes in Trinidad and Tobago are of a highly distinctive kind, the so-called “Trinitario” cultivar group, widely considered to be of elite quality. The origin of Trinitario cacao is unclear, although it is generally considered to be of hybrid origin. We used massive parallel sequencing to identify polymorphic plastidic single nucleotide polymorphisms (cpSNPs) and polymorphic plastidic simple sequence repeats (cpSSRs) in order to determine the origin of the Trinitario cultivar group by comparing patterns of polymorphism to a reference set of ten completely sequenced chloroplast genomes (nine T. cacao and one outgroup, T. grandiflorum (Willd. ex Spreng.) Schum). Only three cpSNP haplotypes were present in the Trinitario cultivars sampled, each highly distinctive and corresponding to reference genotypes for the Criollo (CRI), Upper Amazon Forastero (UAF) and Lower Amazon Forastero (LAF) varietal groups. These three cpSNP haplotypes likely represent the founding lineages of cacao to Trinidad and Tobago. The cpSSRs were more variable with eight haplotypes, but these clustered into three groups corresponding to the three cpSNP haplotypes. The most common haplotype found in farms of Trinidad and Tobago was LAF, followed by UAF and then CRI. We conclude that the Trinitario cultivar group is of complex hybrid origin and has derived from at least three original introduction events.
Article
The worldwide demand for cocoa is rising but, in the supply chain, several cases of adulteration, usually of fine cocoa with bulk cocoa, are reported while industry requires cocoa stocks with constant aromas and quality. In cocoa chain, adulteration and lots misidentification can happen along the entire chain from the bean to the production of liquor. The availability of a DNA traceability system able to recognize the different cocoa varieties is something expected to have a big impact on cocoa sector. Several studies carried out at the laboratory level support the use of DNA in traceability but, clearly, the situation can change completely when moving from the lab to real cases. In the present paper, samples were recovered from big lots of beans and liquors provided by an Italian big brand. Two different cocoa types labelled as “Nacional” and “CCN51” from Ecuador have been examined; DNA was extracted from both beans and cocoa liquor and successfully amplified and examined by using cocoa reference SSR markers. Allele profiles revealed that “Nacional” is an admixture of several genotypes as confirmed also by single beans and leaves profiling. Contrary to Nacional, analyses suggest that CCN51 from Ecuador is characterised by a single diploid genotype. The comparison of CCN51 alleles with data present in databases revealed that misidentification is present also for this modern vegetatively propagated variety and that in different countries are present different CCN51. The production of artificial mixtures demonstrates that DNA markers are able to identify even small traces of unwanted genotypes. Finally, the results suggest that, while for Nacional DNA traceability is not feasible, because of the multigenotype nature of the variety, for CCN51 traceability is possible. However, before doing this, it is necessary to precisely define the genetic identity of CCN51 by comparing accessions coming from the different countries where it is present and cultivated.
Article
Moniliophthora roreri—the causal agent of the frosty pod rot (FP) disease—is one of the most devastating cacao pathogens in Ecuador and worldwide. The center of diversity of this pathogen is believed to be in areas near Ecuador or Colombia but molecular, morphological, and growth studies of this pathogen in Ecuador are scarce. Monosporic cultures of M. roreri from the six cacao-producing regions of Ecuador, including Esmeraldas, El Oro, Los Rios, Guayas, Manabi, and Amazon were obtained. Morphological characteristics, such as mycelial growth, colony shape, color and texture, as well as type and size of meiospores, were recorded for each isolate. Molecular variation was assessed by direct sequencing the ITS1, 5.8s, and ITS2 rDNA regions as well as by RFLP analyses on the same regions. Results showed little variation of morphological traits across isolates. Mycelial growth rate fitted to a Gompertz model with parameters estimates that were significantly affected by mycelial color. Molecular analysis data showed an average polymorphism of 48.98% and Shannon’s diversity index of 0.21. Multiple discriminant analyses carried out on the RFLP patterns showed a 100% accurate grouping by both sampling province and mycelial color.
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The cacao has become an essential part of the fight against the effects of illegal crops and rural poverty in Colombia. Because of their bromatological characteristics, cocoa beans are preferred in markets. However, there are few studies on the variability of the regional genotypes. The goal of this study was to characterize the cacao trees in Tumaco, Nariño (Colombia) and establish their morpho-agronomic variability. Plant collections were conducted in five production zones of the municipality between 0 to 270 m. On each farm, the productivity and plant health variables were recorded for the outstanding plants. The characterization was carried out using a Principal Component Analysis (PCA), Multiple Correspondence Analysis (MCA) and Cluster analysis. In the PCA, the first five components explained 70.2% of the variation. The first three components were characterized by productivity, while the last two components showed a low pod and grain index. In the MCA, the first three factors expressed 39.5% of the variation. The first three corresponded to the cundeamor cacao, acute pod apex, absence of anthocyanin in ripe fruits, without notable pulvinus, staminodes without anthocyanins, and moderately susceptible to Moniliophthora perniciosa . The last two components reported tolerance to M. roreri and Crinnipellis perniciosa, intense anthocyanin pigmentation on the floral buttons and Angoleta-shaped fruit. The selected genotypes showed important characteristics that must be analyzed with molecular and sensorial analyses.
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Cocoa Theobroma cacao L. native populations are valued in international markets because their organoleptic characteristics typical of the high quality cocoas. Never the less, this quality is threatened by more productive hybrids, coming from foreign genetic material which has been replacing gradually the native populations. The genetic diversity and structure of 165 cocoa lines from Tumaco region and the germplasm banks of the Corpoica and Fedecacao institutions, was assessed through twelve loci analysis located by microsatellites markers. Resulting data were processed by the Arlequin ver. 3.5 and TFPGA ver. 1.3 software. Markers were highly discriminating, informative and representative for the species. The average of expected (He) and observed (Ho) heterozygosity were 0,73 and 0,72 respectively, indicating high genetic variability and high rate of heterocygotes in the analyzed populations. The fixation index value FST= 0,0355 indicates minimum levels of genetic differentiation among the populations, and the average Nm= 6,80 indicates a highly exchange of genes existence. The hierarchical cluster analysis using UPGMA grouping allowed confirming the existing genetic similarity among populations.
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The Maya archaeological site at Colha in northern Belize, Central America, has yielded several spouted ceramic vessels that contain residues from the preparation of food and beverages. Here we analyse dry residue samples by using high-performance liquid chromatography coupled to atmospheric-pressure chemical-ionization mass spectrometry, and show that chocolate (Theobroma cacao) was consumed by the Preclassic Maya as early as 600 BC, pushing back the earliest chemical evidence of cacao use by some 1,000 years. Our application of this new and highly sensitive analytical technique could be extended to the identification of other ancient foods and beverages.
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Cyclic, pseudocyclic, and noncyclic photosynthetic phosphorylation are mutually interdependent. Evidence for this is reviewed, in particular where it has to do with regulation of net ATP synthesis during the onset and maintenance of photosynthesis in vivo. It is concluded that both cyclic and noncyclic phosphorylation contribute to photosynthesis and that their relative rates may be controlled by redox poising of their respective electron carriers. The effect of phosphorylation of light‐harvesting‐chlorophyll‐protein on electron transport is to maintain the redox poise of ¡ntersystem electron carriers, notably plastoquinone; it will thereby regulate both cyclic and noncyclic electron transport. The cyclic pathway of ATP synthesis is energetically advantageous only where there exists a mechanism for redistribution of excitation between the photosystems. Protein phosphorylation is therefore implicated in regulation of coupling and stoicheiometry of ATP production and in the maintenance of efficient energy conversion in photosynthesis.
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 Random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphism (RFLP) markers were used to evaluate genetic relationships within the Theobroma cacao species and to assess the organization of its genetic diversity. Genetic variability was estimated with 18 primers and 43 RFLP probes on 155 cocoa trees belonging to different morphological groups and coming from various geographic origins. The majority of the RFLP probes issued from low-copy DNA sequences. On the basis of on the genetic distance matrices, the two molecular methods gave related estimates of the genetic relationship between genotypes. Although an influence of cocoa morphological groups and geographical origins of trees was observed, a lack of gene differentiation characterized the T. cacao accessions studied. The continuous RFLP variability observed within the species may reflect the hybridization and introgressions between trees of different origins. Nevertheless, the Nacional type was detected to be genetically specific and different from well-known types such as Forastero, Criollo and Trinitario. Some of those genotypes were characterized by a low heterozygosity rate and may constitute the original Nacional pool. These results also provide information for the constitution of a cocoa tree core collection.
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Disease resistance and defence gene analog (RGA/DGA) sequences were isolated in cocoa using a PCR approach with degenerate primers designed from conserved domains of plant resistance and defence genes: the NBS (nucleotide binding site) motif present in a number of resistance genes such as the tobacco N, sub-domains of plant serine/threonine kinases such as the Pto tomato gene, and conserved domains of two defence gene families: pathogenesis-related proteins (PR) of classes 2 and 5. Nucleotide identity between thirty six sequences isolated from cocoa and known resistance or defence genes varied from 58 to 80%. Amino acid sequences translated from corresponding coding sequences produced sequences without stop codons, except for one NBS –like sequence. Most of the RGAs could be mapped on the cocoa genome and three clusters of genes could be observed : NBS-like sequences clustered in two regions located on chromosomes 7 and 10, Pto-like sequences mapped in five genome regions of which one, located on chromosome 4, corresponded to a cluster of five different sequences. PR2-like sequences mapped in two regions located on chromosome 5 and 9 respectively. An enrichment of the genetic map with microsatellite markers allowed us to identify several co-localisations of RGAs, DGAs and QTL for resistance to Phytophthora detected in several progenies, particularly on chromosome 4 where a cluster of Pto-like sequences and 4 QTL for resistance to Phytophthora were observed. Many other serious diseases affect cocoa and the candidate genes, isolated in this study, could be of broader interest in cocoa disease management.
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The quality of Ecuadorian cacao is presently threatened by the introduction of hybrid material. An estimation of genetic diversity in Ecuador is required in order to avoid the loss of fine flavored cocoa. Genetic variability amongst 60 Ecuadorian genotypes of Theobroma cacao has been evaluated using molecular and phenotypic markers. The two distance matrices derived from the molecular and phenotypic data were found to be correlated (R2 = 0.5). Dynamic clustering analyses classified the genotypes in two or three groups depending on the markers used. The genotypes coming from Sebasti{àn Arteaga (SA) and Balao Chico (BCH) plantations appeared related to each other suggesting a common genetic origin. They also may be considered as a distinct group with high RFLP homozygosity. The EETP (Estací}on Experimental Tropical Pichilingue of Ecuador) collection was comprised of more variable genotypes possessing variable heterozygosity levels. The low heterozygous genotypes may be genetically related to SA and BCH trees, whereas the higher heterozygous genotypes may have resulted from hybridizations between original Nacional material of Ecuador and genotypes imported from Trinidad at the beginning of the century. Thus genetic introgression may have occurred giving rise to a range of variation between Nacional and hybrid forms.
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Formulae are given for estimators for the parameters F, θ, f (FIT, FST, FIS) of population structure. As with all such estimators, ratios are used so that their properties are not known exactly, but they have been found to perform satisfactorily in simulations. Unlike the estimators in general use, the formulae do not make assumptions concerning numbers of populations, sample sizes, or heterozygote frequencies. As such, they are suited to small data sets and will aid the comparisons of results of different investigators. A simple weighting procedure is suggested for combining information over alleles and loci, and sample variances may be estimated by a jackknife procedure.
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The Maya archaeological site at Colha in northern Belize, Central America, has yielded several spouted ceramic vessels that contain residues from the preparation of food and beverages. Here we analyse dry residue samples by using high-performance liquid chromatography coupled to atmospheric-pressure chemical-ionization mass spectrometry, and show that chocolate (Theobroma cacao) was consumed by the Preclassic Maya as early as 600 bc, pushing back the earliest chemical evidence of cacao use by some 1,000 years. Our application of this new and highly sensitive analytical technique could be extended to the identification of other ancient foods and beverages.
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Criollo cacao (Theobroma cacao ssp. cacao) was cultivated by the Mayas over 1500 years ago. It has been suggested that Criollo cacao originated in Central America and that it evolved independently from the cacao populations in the Amazon basin. Cacao populations from the Amazon basin are included in the second morphogeographic group: Forastero, and assigned to T. cacao ssp. sphaerocarpum. To gain further insight into the origin and genetic basis of Criollo cacao from Central America, RFLP and microsatellite analyses were performed on a sample that avoided mixing pure Criollo individuals with individuals classified as Criollo but which might have been introgressed with Forastero genes. We distinguished these two types of individuals as Ancient and Modern Criollo. In contrast to previous studies, Ancient Criollo individuals formerly classified as 'wild', were found to form a closely related group together with Ancient Criollo individuals from South America. The Ancient Criollo trees were also closer to Colombian-Ecuadorian Forastero individuals than these Colombian-Ecuadorian trees were to other South American Forastero individuals. RFLP and microsatellite analyses revealed a high level of homozygosity and significantly low genetic diversity within the Ancient Criollo group. The results suggest that the Ancient Criollo individuals represent the original Criollo group. The results also implies that this group does not represent a separate subspecies and that it probably originated from a few individuals in South America that may have been spread by man within Central America.
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Cacao (Theobroma cacao L.) has been cultivated in Central America since pre-Columbian times. The type of cacao cultivated in this region was called Criollo; cacao populations from the Amazon basin were called Forastero. The type of Forastero most commonly cultivated until 1950 was named Amelonado. Historical data show Trinitario cacao to have originated in Trinidad, resulting from natural hybridisation between Criollo and Amelonado Forastero. Doubts persist on the source of the Amelonado Forastero involved in the origin of Trinitario; the Amelonado parent may have come from the Lower Amazon, the Orinoco or the Guyanas. Most of the cacao cultivated worldwide until 1950 consisted of Criollo, Trinitario and Amelonado. From the early 1950s, Forastero material collected in the Upper Amazon region during the 1930s and 1940s began to be employed in breeding programmes. To gain a better understanding of the origin and the genetic basis of the cacao cultivars exploited before the utilisation of germplasm collected in the Upper Amazon, a study was carried out using restriction fragment length polymorphism and microsatellite markers. Trinitario samples from 17 countries were analysed. With molecular markers, it was possible to clearly identify three main genotypes (represented by clones SP1, MAT1-6 and SIAL70) implicated in the origin of most Trinitario clones.
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A linkage map of cacao based on codominant markers has been constructed by integrating 201 new simple sequence repeats (SSR) developed in this study with a number of isoenzymes, restriction fragment length polymorphisms (RFLP), microsatellite markers and resistance and defence gene analogs (Rgenes-RFLP) previously mapped in cacao. A genomic library enriched for (GA)(n) and (CA)(n) was constructed, and 201 new microsatellite loci were mapped on 135 individuals from the same mapping population used to establish the first reference maps. This progeny resulted from a cross between two heterozygous cacao clones: an Upper-Amazon Forastero (UPA 402) and a Trinitario (UF 676). The new map contains 465 markers (268 SSRs, 176 RFLPs, five isoenzymes and 16 Rgenes-RFLP) arranged in ten linkage groups corresponding to the haploid chromosome number of cacao. Its length is 782.8 cM, with an average interval distance between markers of 1.7 cM. The new microsatellite markers were distributed throughout all linkage groups of the map, but their distribution was not random. The length of the map established with only SSRs was 769.6 cM, representing 94.8% of the total map. The current level of genome coverage is approximately one microsatellite every 3 cM. This new reference map provides a set of useful markers that is transferable across different mapping populations and will allow the identification and comparison of the most important regions involved in the variation of the traits of interest and the development of marker-assisted selection strategies.
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The magnitudes of the systematic biases involved in sample heterozygosity and sample genetic distances are evaluated, and formulae for obtaining unbiased estimates of average heterozygosity and genetic distance are developed. It is also shown that the number of individuals to be used for estimating average heterozygosity can be very small if a large number of loci are studied and the average heterozygosity is low. The number of individuals to be used for estimating genetic distance can also be very small if the genetic distance is large and the average heterozygosity of the two species compared is low.
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The variability of the cocoa (Theobroma cacao) nuclear genome was investigated. A total of 203 cocoa clones was surveyed for restriction fragment length polymorphisms (RFLPs) using four restriction endonuclease and 31 seed cDNA probes. A high level of polymorphism has been found. This study points to a structuring of the species that fits with the distinction between the Criollo and Forastero populations. These results combined with previously obtained nuclear rDNA and mtDNA data allow us to propose new hypotheses on the origin and evolution of the different cocoa populations.
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‘Nacional’ cocoa from Ecuador is a genetic group acknowledged for its ‘Arriba’ floral flavour, which has partly been lost due to the introduction of other more productive varieties. Between 1996 and 2000, 115 Nacional cocoa trees were identified by high yield, resistance to diseases and intense floral flavour, and reproduced by grafting. Some of the progeny are now fruiting and show resistance to Crinipellis perniciosa with an intense floral flavour. Copyright © 2004 Whurr Publishers Ltd
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The genetic structure of 175 genotypes of Theobroma cacao L. was investigated using 27 RFLP/cDNA loci. The number of alleles per locus was never higher than four and a high genetic diversity was found. Criollo genotypes appeared differentiated from Forastero genotypes. A deficiency of heterozygotes was found in all populations and some alleles were fixed in some populations. Within population gene diversity was high. When four morphological groups were considered, Upper Amazon Forastero was the most polymorphic and diverse population. Almost all the alleles of the whole species could be found within this group. Observed heterozygosity was the highest within Criollo and Trinitario populations but a certain proportion of homozygous genotypes was present in all groups.
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The first linkage map established by Lanaud et al. (1995) was used as a starting point to produce a high-density molecular linkage map. A mapping population of 181 progenies resulting from a cross between two heterozygous genotypes, a Forastero and a Trinitario (hybrid between Forastero and Criollo), was used for the linkage analysis. A new DNA isolation protocol was established, which allows enough good quality DNA to construct a genetic map with PCR-based markers. The map comprises 424 markers with an average spacing between markers of 2.1 cM. The marker types used were five isozymes, six loci from known function genes, 65 genomic RFLPs, 104 cDNA RFLPs, three telomeric probes, 30 RAPDs, 191 AFLPs and 20 microsatellites. The use of new marker types, AFLP and microsatellites, did not disturb the original order of the RFLP loci used on the previous map. The genetic markers were distributed over ten linkage groups and cover 885.4 cM. The maximum distance observed between adjacent markers was 16.2 cM, and 9.4% of all loci showed skewed segregation.
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A measure of genetic distance (D) based on the identity of genes between populations is formulated. It is defined as D = -logeI, where I is the normalized identity of genes between two populations. This genetic distance measures the accumulated allele differences per locus. If the rate of gene substitution per year is constant, it is linearly related to the divergence time between populations under sexual isolation. It is also linearly related to geographical distance or area in some migration models. Since D is a measure of the accumulated number of codon differences per locus, it can also be estimated from data on amino acid sequences in proteins even for a distantly related species. Thus, if enough data are available, genetic distance between any pair of organisms can be measured in terms of D. This measure is applicable to any kind of organism without regard to ploidy or mating scheme.
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The genetic diversity of 106 genotypes of Theobroma cacao L. was assessed using RFLP and RAPD methods. Thirty-one cDNA probes and 19 primers generated, respectively, 87 and 49 polymorphic bands that were submitted to factorial and cluster analyses. Both RFLP and RAPD bands separated the individuals into three distinctive groups. Some genotypes did not correspond to the currently accepted classification and are considered to have been originally misclassified. The nature of RAPD bands was investigated by Southern analysis. There were as many highly repeated sequences as single copy sequences but the two types of sequences did not structure the variability in the same way. Similar results were obtained with RFLPs and RAPDs with regard to the genetic structure of Theobroma cacao L. Therefore, RAPDs appear to be as efficient as RFLPs for classifying cocoa genotypes.
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Paternity inference using highly polymorphic codominant markers is becoming common in the study of natural populations. However, multiple males are often found to be genetically compatible with each offspring tested, even when the probability of excluding an unrelated male is high. While various methods exist for evaluating the likelihood of paternity of each nonexcluded male, interpreting these likelihoods has hitherto been difficult, and no method takes account of the incomplete sampling and error-prone genetic data typical of large-scale studies of natural systems. We derive likelihood ratios for paternity inference with codominant markers taking account of typing error, and define a statistic delta for resolving paternity. Using allele frequencies from the study population in question, a simulation program generates criteria for delta that permit assignment of paternity to the most likely male with a known level of statistical confidence. The simulation takes account of the number of candidate males, the proportion of males that are sampled and gaps and errors in genetic data. We explore the potentially confounding effect of relatives and show that the method is robust to their presence under commonly encountered conditions. The method is demonstrated using genetic data from the intensively studied red deer (Cervus elaphus) population on the island of Rum, Scotland. The Windows-based computer program, CERVUS, described in this study is available from the authors. CERVUS can be used to calculate allele frequencies, run simulations and perform parentage analysis using data from all types of codominant markers.
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PowerMarker delivers a data-driven, integrated analysis environment (IAE) for genetic data. The IAE integrates data management, analysis and visualization in a user-friendly graphical user interface. It accelerates the analysis lifecycle and enables users to maintain data integrity throughout the process. An ever-growing list of more than 50 different statistical analyses for genetic markers has been implemented in PowerMarker. Availability:www.powermarker.net Contact:powermarker@hotmail.com
Data analysis methods Genetic diversity of cultivated tropical plants
  • X Perrier
  • A Flori
  • Bonnot
  • P Hamon
  • M Seguin
  • X Perrier
  • Glaszmann
Cacao and witches’ broom disease (Marasmius perniciosus) of South America, with notes on other species of Theobroma. Yuille’s Printerie, Port of Spain, Trinidad and Tobago
  • Pound
Estimating F-statistics for the analysis of population structure
  • Weir Bs
  • Cockerhan
  • Cc
Weir BS, Cockerhan CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370 Tree Genetics & Genomes (2009) 5:421–433
Antecedentes históricos Botánica del cacao
  • Hall
  • Cj
Hall CJ (1932) Cocoa, 2nd edn. MacMillan, London, pp 304–320 Vera BJ (1987) Antecedentes históricos. Manual del cultivo de cacao. INIAP, EET-Pichilingue, Quevedo, Ecuador, pp 6–9 Vera BJ (1993) Botánica del cacao. Manual del cultivo de cacao 2da edición. INIAP, EET-Pichilingue, Quevedo, Ecuador, pp 10–15
L'analyse des données Tome 2: L'analyse des correspondances Notes on the nomenclature, classification and possible relationships of cacao populations
  • Cnrs Umr
CNRS UMR 5000. Université Montpellier II, France Benzecri JP (1973) L'analyse des données. Tome 2: L'analyse des correspondances. Dunod, Paris, France Cheesman EE (1944) Notes on the nomenclature, classification and possible relationships of cacao populations. Trop Agric 21:144– 159
Comparative genetic diversity of Theobroma cacao L. using RFLP and RAPD markers The genetic structure of cocoa populations (Theobroma cacao L.) revealed by RFLP analysis Data analysis methods
  • N Goran
  • Laurent V Jak
  • Am
  • C Lanaud
  • Laurent V Jak
  • Am
  • Lanaud
M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583– 590 N'Goran JAK, Laurent V, Risterucci AM, Lanaud C (1994) Comparative genetic diversity of Theobroma cacao L. using RFLP and RAPD markers. Heredity 73:589–597 N'Goran JAK, Laurent V, Risterucci AM, Lanaud C (2000) The genetic structure of cocoa populations (Theobroma cacao L.) revealed by RFLP analysis. Euphytica 115:83–90 Pastorelly RD (1992) Evaluación de algunas características del cacao tipo Nacional, en la zona de Tenguel. Tesis Ingeniero Agrónomo. Universidad Agraria del Ecuador. Guayaquil, Ecuador Perrier X, Flori A, Bonnot F (2003) Data analysis methods. In: Hamon P, Seguin M, Perrier X, Glaszmann JC (eds) Genetic diversity of cultivated tropical plants. Enfield, Science Publishers, Montpel-lier, France, pp 43–76
4 = Forastero from Upper Amazon (SCA-6)
  • Ref
Ref. 4 = Forastero from Upper Amazon (SCA-6)
The cacao industry of Ecuador Principles of population genetics Archaeology: cacao usage by the earliest Maya civilization
  • Rl Lopez
RL, Lopez GH (1949) The cacao industry of Ecuador. Foreign Agriculture Report No. 34, US Department of Agriculture, Washington, USA Hartl DL, Clark AG (1997) Principles of population genetics, 3rd edn. Sinauer, Sunderland, Massachusetts, USA Hurst WJ, Tarka SM, Powis TG, Valdez F, Hester RT (2002) Archaeology: cacao usage by the earliest Maya civilization. Nature 418:289–290
Power marker: integrated analysis environ-ment for genetic marker data Obtención de híbridos de cacao tipo Nacional provenientes de materiales de alta productividad y resistentes a enfermedades
  • K Muse
K, Muse VS (2005) Power marker: integrated analysis environ-ment for genetic marker data. Bioinformatics 21:2128–2129 Loor RG (1998) Obtención de híbridos de cacao tipo Nacional provenientes de materiales de alta productividad y resistentes a enfermedades. Tesis de Ingeniero Agrónomo. Universidad Técnica de Manabí, Portoviejo, Ecuador Loor RG, Saunders JA, Amores F (2002) Characterization of Ecuadorian cacao (Theobroma cacao L.) Mid Atlantic Plant Molecular Biology Society Proceedings. Beltsville, Maryland, USA 19:18
GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations, Laboratoire Génome, Populations, Interactions; CNRS UMR 5000
  • K Belkhir
  • P Borsa
  • L Chikhi
  • N Raufaste
  • F Bonhomme
Characteristics of cacao “Nacional” of Ecuador. International Workshop on Conservation, Characterisation and Utilisation of Cocoa Genetic Resources in the 21st century
  • G A Enriquez
The cacao industry of Ecuador
  • R L Fowler
  • G H Lopez
London cocoa trade Amazon project. Final report phase 1
  • B J Allen
  • A R Lass
  • BJ Allen
Progresos alcanzados en el Ecuador en el estudio de selección para resistencia de la Escoba de Bruja
  • E Ampuero
Analyses des Correspondances. Comment interpréter les résultats? Collection STAT-ITCF
  • C Dervin
Obtención de híbridos de cacao tipo Nacional provenientes de materiales de alta productividad y resistentes a enfermedades. Tesis de Ingeniero Agrónomo
  • R G Loor
Data analysis methods Genetic diversity of cultivated tropical plants. Enfield
  • X Perrier
  • Flori A Bonnot
Correspondence analysis. Social research update
  • D Phillips
Estudio de la compatibilidad en algunos cultivares de cacao
  • J Quiroz
Characterization of Ecuadorian cacao (Theobroma cacao L.) Mid Atlantic Plant Molecular Biology Society Proceedings
  • R G Loor
  • J A Saunders
  • F Amores
Evaluación de algunas características del cacao tipo Nacional, en la zona de Tenguel. Tesis Ingeniero Agrónomo
  • R D Pastorelly
Cacao and witches’ broom disease (Marasmius perniciosus) of South America, with notes on other species of Theobroma. Yuille’s Printerie, Port of Spain
  • F J Pound
  • FJ Pound