Mapping the Genetic Evolution of Cacao & March ’24 News/AMA | #PodSaveChocolate

Mapping the Genetic Evolution of Cacao & March ’24 News/AMA | #PodSaveChocolate

Episode 26 of #PodSaveChocolate features “All the (Chocolate) News That’s Fit to Eat” and the monthly AMA – Ask Me Anything (about cocoa or chocolate).

When and Where to Watch

This episode airs live from 10:00 PDT / 10:00 MST / 11:00 MDT / 12:00 CDT / 13:00 EDT on Tuesday, March 12th, 2024. UPDATED to include other news links mentioned.
Mapping the Genetic Evolution of Cacao & News/AMA | #PodSaveChocolate
Episode 26 OverviewThis episode of #PodSaveChocolate will focus most of its attention on a single news about mapping the genetic evolution of cacao. If there…

Click to watch in a new tab or window. Please subscribe (free!) to the @PodSaveChocolate YouTube channel as well as like this video, comment, and share to help grow the #PSC community.

Link to watch and comment from my LinkedIn profile.
Link to watch and comment on TheChocolateLife page on Facebook.

Interested in joining a Discover Chocolate in Paris tour during the Salon du Chocolat later this year? Email Member Support to be added to the early bird reminder list.

Episode 26 Overview

This episode of #PodSaveChocolate will focus most of its attention on a single news story about mapping the genetic evolution of cacao.

If there is time we will get to other stories, and, as always I will be taking AMA questions from participants during the livestream.

While the location of the origin of theobroma cacao is no longer in dispute, how it spread throughout the Americas has been an open question.

The story originally came to my attention in Ground News (card 1️⃣) and I followed the link to the Ancient Origins website (card 2️⃣). Fortunately, the Ancient Origins website cited the source for the article (card 3️⃣).

Scientists Map the Genetic Evolution of Cacao to Chocolate
Researchers have mapped the ancient dispersal of the cacao or cocoa plant from South America to Central America. Not only did they discover the plant Read moreSection: NewsHistory & ArchaeologyHistoryAncient TraditionsRead Later

Card 1️⃣

Scientists Map the Genetic Evolution of Cacao to Chocolate
Researchers have mapped the ancient dispersal of the cacao or cocoa plant from South America to Central America. Not only did they discover the plant

(Card 2️⃣)

A revisited history of cacao domestication in pre-Columbian times revealed by archaeogenomic approaches - Scientific Reports
Scientific Reports - A revisited history of cacao domestication in pre-Columbian times revealed by archaeogenomic approaches

(Card 3️⃣)

Related Resources

Geographic and Genetic Population Differentiation of the Amazonian Chocolate Tree (Theobroma cacao L)
Numerous collecting expeditions of Theobroma cacao L. germplasm have been undertaken in Latin-America. However, most of this germplasm has not contributed to cacao improvement because its relationship to cultivated selections was poorly understood. Germplasm labeling errors have impeded breeding and confounded the interpretation of diversity analyses. To improve the understanding of the origin, classification, and population differentiation within the species, 1241 accessions covering a large geographic sampling were genotyped with 106 microsatellite markers. After discarding mislabeled samples, 10 genetic clusters, as opposed to the two genetic groups traditionally recognized within T. cacao, were found by applying Bayesian statistics. This leads us to propose a new classification of the cacao germplasm that will enhance its management. The results also provide new insights into the diversification of Amazon species in general, with the pattern of differentiation of the populations studied supporting the palaeoarches hypothesis of species diversification. The origin of the traditional cacao cultivars is also enlightened in this study.
The use and domestication of Theobroma cacao during the mid-Holocene in the upper Amazon - Nature Ecology & Evolution
Evidence from starch grains, theobromine residues and ancient DNA demonstrate cacao use in the upper Amazon circa 5,300 years ago. This is earlier than previous evidence for cacao domestication in Mesoamerica.

This study, published in 2008, completely changed our understanding of cacao genetics.

Criollo, Forastero, and Trinitario are linguistic labels, not genetic labels. The first two are relics of colonial oppression.

Present Spatial Diversity Patterns of Theobroma cacao L. in the Neotropics Reflect Genetic Differentiation in Pleistocene Refugia Followed by Human-Influenced Dispersal
Cacao (Theobroma cacao L.) is indigenous to the Amazon basin, but is generally believed to have been domesticated in Mesoamerica for the production of chocolate beverage. However, cacao’s distribution of genetic diversity in South America is also likely to reflect pre-Columbian human influences that were superimposed on natural processes of genetic differentiation. Here we present the results of a spatial analysis of the intra-specific diversity of cacao in Latin America, drawing on a dataset of 939 cacao trees genotypically characterized by means of 96 SSR markers. To assess continental diversity patterns we performed grid-based calculations of allelic richness, Shannon diversity and Nei gene diversity, and distinguished different spatially coherent genetic groups by means of cluster analysis. The highest levels of genetic diversity were observed in the Upper Amazon areas from southern Peru to the Ecuadorian Amazon and the border areas between Colombia, Peru and Brazil. On the assumption that the last glaciation (22,000–13,000 BP) had the greatest pre-human impact on the current distribution and diversity of cacao, we modeled the species’ Pleistocene niche suitability and overlaid this with present-day diversity maps. The results suggest that cacao was already widely distributed in the Western Amazon before the onset of glaciation. During glaciations, cacao populations were likely to have been restricted to several refugia where they probably underwent genetic differentiation, resulting in a number of genetic clusters which are representative for, or closest related to, the original wild cacao populations. The analyses also suggested that genetic differentiation and geographical distribution of a number of other clusters seem to have been significantly affected by processes of human management and accompanying genetic bottlenecks. We discuss the implications of these results for future germplasm collection and in situ, on farm and ex situ conservation of cacao.
The Genetic Diversity of Cacao and Its Utilization
The cacao (Theobroma cacao) plant is an important Neo-Tropical species whose natural habitat is the Amazon basin. Over the last 30 years there has been a considerable geographical expansion in the availability of cacao genetic resources. As a result the plant has a rich genetic diversity that exists at two levels: that of the primitive populations in the area of original distribution of the species, and that of the derived cultivated populations. This book provides a comprehensive review of our current knowledge of the diversity of the species. It starts by examining the diversity and inheritance of the characteristics of primitive populations in the Amazonian and Caribbean regions. It then looks at the evolution of diversity within cultivated populations first in South America and around the Caribbean, and then beyond the Americas. The book describes the inter-relationships between populations based on morphological and molecular markers. It also examines the conservation of genetic resources and how these genetic resources can be utilized to produce new cultivars.

Preview – published 2005

Insight into the Wild Origin, Migration and Domestication History of the Fine Flavour Nacional Theobroma cacao L. Variety from Ecuador
Ecuador’s economic history has been closely linked to Theobroma cacao L cultivation, and specifically to the native fine flavour Nacional cocoa variety. The original Nacional cocoa trees are presently in danger of extinction due to foreign germplasm introductions. In a previous work, a few non-introgressed Nacional types were identified as potential founders of the modern Ecuadorian cocoa population, but so far their origin could not be formally identified. In order to determine the putative centre of origin of Nacional and trace its domestication history, we used 80 simple sequence repeat (SSR) markers to analyse the relationships between these potential Nacional founders and 169 wild and cultivated cocoa accessions from South and Central America. The highest genetic similarity was observed between the Nacional pool and some wild genotypes from the southern Amazonian region of Ecuador, sampled along the Yacuambi, Nangaritza and Zamora rivers in Zamora Chinchipe province. This result was confirmed by a parentage analysis. Based on our results and on data about pre-Columbian civilization and Spanish colonization history of Ecuador, we determined, for the first time, the possible centre of origin and migration events of the Nacional variety from the Amazonian area until its arrival in the coastal provinces. As large unexplored forest areas still exist in the southern part of the Ecuadorian Amazonian region, our findings could provide clues as to where precious new genetic resources could be collected, and subsequently used to improve the flavour and disease resistance of modern Ecuadorian cocoa varieties.
Genetic Population Structure of Cacao Plantings within a Young Production Area in Nicaragua
Significant cocoa production in the municipality of Waslala, Nicaragua, began in 1961. Since the 1980s, its economic importance to rural smallholders increased, and the region now contributes more than 50% of national cocoa bean production. This research aimed to assist local farmers to develop production of high-value cocoa based on optimal use of cacao biodiversity. Using microsatellite markers, the allelic composition and genetic structure of cacao was assessed from 44 representative plantings and two unmanaged trees. The population at Waslala consists of only three putative founder genotype spectra (lineages). Two (B and R) were introduced during the past 50 years and occur in >95% of all trees sampled, indicating high rates of outcrossing. Based on intermediate allelic diversity, there was large farm-to-farm multilocus genotypic variation. GIS analysis revealed unequal distribution of the genotype spectra, with R being frequent within a 2 km corridor along roads, and B at more remote sites with lower precipitation. The third lineage, Y, was detected in the two forest trees. For explaining the spatial stratification of the genotype spectra, both human intervention and a combination of management and selection driven by environmental conditions, appear responsible. Genotypes of individual trees were highly diverse across plantings, thus enabling selection for farm-specific qualities. On-farm populations can currently be most clearly recognized by the degree of the contribution of the three genotype spectra. Of two possible strategies for future development of cacao in Waslala, i.e. introducing more unrelated germplasm, or working with existing on-site diversity, the latter seems most appropriate. Superior genotypes could be selected by their specific composite genotype spectra as soon as associations with desired quality traits are established, and clonally multiplied. The two Y trees from the forest share a single multilocus genotype, possibly representing the Mayan, ‘ancient Criollo’ cacao.
Genetic Structure and Molecular Diversity of Cacao Plants Established as Local Varieties for More than Two Centuries: The Genetic History of Cacao Plantations in Bahia, Brazil
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.
Different shades of early shamanism in the Upper Amazon
The identification of a previously unknown early archaeological culture in the Upper Amazon frontier zone between southeastern Ecuador and northeastern Peru has shown evidence of early complexity that suggests that the tropical forest groups were actively participating in the initial process that characterized the Formative period in the Americas (Olivera Nunez 2014; Valdez 2008, 2013; Valdez et al. 2005). The material remains of this new culture have been identified throughout the Mayo Chinchipe hydraulic drainage basin, which flows down the eastern flanks of the Andes to its confluence with an important tributary of the Amazon, the Maranon River. Thus the newly discovered culture has been given the same name as the basin : Mayo Chinchipe- Maranon.

Other News Mentioned

AVPA Paris Contest: Chocolates processed at the origin
Concours International de Chocolats élaborés à l’origine

As Hershey battles cocoa costs, chocolate lovers may help cool inflation. And found in my feed for the same day:

Sales of Chocolate and Candy Reach All-Time High of $48 Billion in 2023
Confectionery sales hit $48 billion in 2023, a number largely driven by inflation, according to the 2024 State of Treating report published today by the National Confectioners Association. The report projects that U.S. confectionery sales will reach $61 billion by 2028.

Episode Hashtags and Related Accounts to Follow

#News #AMA #AskMeAnything
#cocoa #cacao #cacau
#chocolate #chocolat
#PodSaveChocolate #PodSaveChoc #PSC
#LaVidaCocoa #TheChocolateLife

Next Episode

The Friday, March 15th episode of PodSaveChocolate will feature an interview and live tasting with Chef Andrea Young of Sweet Vegan Chocolates (NYC).

#PodSaveChocolate and #TheChocolateLifeLIVE Archives

To read an archived post and find the links to watch archived episodes, click on one of the bookmark cards, below.

Pod Save Chocolate Calendar and Archive
News, views, and conversations on topics in cocoa and chocolate streamed live to YouTube, LinkedIn, and Facebook. #PodSaveChocolate!
#TheChocolateLifeLIVE Archive
News, views, and conversations on topics in cocoa and chocolate streamed live to YouTube, LinkedIn, and Facebook.

You've successfully subscribed to The Chocolate Life
Great! Next, complete checkout for full access to The Chocolate Life
Welcome back! You've successfully signed in.
Success! Your account is fully activated, you now have access to all content.
Success! Your billing info is updated.
Billing info update failed.