Juan C Motamayor

Juan C Motamayor
Mars, Inc. · Department of Plant Science

PhD

About

156
Publications
30,995
Reads
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3,101
Citations
Citations since 2017
49 Research Items
1581 Citations
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2017201820192020202120222023050100150200250300
2017201820192020202120222023050100150200250300
Introduction
Agricultural engineer and plant biologist with expertise in breeding, agronomy, phytopathology, genetics and genomics. Highly experience in design, implementation and oversight of global crop research for application in agribusinesses. People leader with budget and strategy responsibility. Skilled in large cooperative research partnerships with academia, suppliers, growers, and government agencies.
Additional affiliations
October 2018 - present
The Coca-Cola Company
Position
  • Managing Director
August 2017 - September 2018
Mars, Inc.
Position
  • Managing Director
September 2016 - present
University of Florida
Position
  • Courtesy Professor
Education
March 1997 - March 2001
Université Paris-Sud 11
Field of study
  • Plant Molecular Biology
June 1995 - December 1996
Institut National Agronomique Paris-Grignon
Field of study
  • Cellular and Molecular Plant Physiology

Publications

Publications (156)
Article
Full-text available
Economically, cacao (Theobroma cacao L.) is a major tropical commodity for the Americas; however, severe losses due to Moniliophthora roreri (Cif. and Par.), which causes frosty pod rot (FPR), and Phytophthora spp., which causes black pod rot (BPR), have reduced cacao production in the Americas. The objectives of this study are to (i) reconfirm the...
Article
Full-text available
Predicting the potential fate of a species in the face of climate change requires knowing the distribution of molecular adaptations across the geographic range of the species. In this work, we analyzed 79 genomes of Theobroma cacao, an Amazonian tree known for the fruit from which chocolate is produced, to evaluate how local and regional molecular...
Article
Full-text available
Background: Recombination plays an important evolutionary role by breaking up haplotypes and shuffling genetic variation. This process impacts the ability of selection to eliminate deleterious mutations or increase the frequency of beneficial mutations in a population. To understand the role of recombination generating and maintaining haplotypic v...
Article
Artificial pollination management strategies are a potential solution to improving the livelihoods of smallholder cacao farmers by increasing crop productivity in situations when pollination services are limiting. However, field-based research trials evaluating the yield benefits of artificial pollination management strategies within intensified ca...
Article
Full-text available
The main ingredients of chocolate are usually cocoa powder, cocoa butter, and sugar. Both the powder and the butter are extracted from the beans of the cacao tree (Theobroma cacao L.). The cocoa butter represents the fat in the beans and possesses a unique fatty acid profile that results in chocolate’s characteristic texture and mouthfeel. Here, we...
Article
Full-text available
A sweet solution for studying cacao genetics Genomic insights from an efficient, low-cost DNA sequencing strategy could enable more sustainable cacao cultivation. Growing demand for chocolate is currently being satisfied by increasing land use. A richer understanding of this plant’s genome could enable development of more productive strains, and Ju...
Preprint
Full-text available
Our study investigates the possible drivers of recombination hotspots in Theobroma cacao using ten recently diverged populations. This constitutes the first time that recombination rates from more than two populations of the same species have been compared, providing a novel view of recombination at the population-divergence time-scale. For each po...
Article
Full-text available
Domestication has had a strong impact on the development of modern societies. We sequenced 200 genomes of the chocolate plant Theobroma cacao L. to show for the first time to our knowledge that a single population, the Criollo population, underwent strong domestication ~3600 years ago (95% CI: 2481–13,806 years ago). We also show that during the pr...
Chapter
Theobroma cacao L. is a tropical tree originating in the Amazon, where it grows naturally in the shade of tropical rainforests. Cacao sub-products, such as butter and powder, are produced as principal components of chocolate and contain important nutritional compounds such as polyphenols and flavonoids. However, bean production is decreasing becaus...
Data
Tree information and heterozygosity of L10 (parents of L7) based on 96 markers spread throughout the genome and percent ancestry for each of the 10 cacao structural groups.
Data
Bivariate genetic trait correlations for yield, vigor, and disease traits.
Data
Best linear unbiased predictions and rankings of L7 population according to ideotype.
Data
Parental Best linear unbiased predictions for traits in Table 1 and the coordinates of the first two PCs.
Data
Genetic gains based on the percent increase between the average phenotypic values for tree ages 4–7 in the L7 progeny trial, and phenotypic values of the L10 (parental clonal trial) for tree ages 4–9. The traits represented are traits that overlapped between the two trials: TP, HP, MO, PHY, %HP, %MO, and %PHY. The absolute value of genetic gains we...
Data
Predicted family values (including missing cross, GU-154 x IMC-60) for yield and vigor traits. The families are ranked by highest yielding (Ym). Definition of traits are presented in Table 1.
Data
Phenotypic averages for the L10 (parental clonal trial) for ages 4–9.
Data
Genetic gains based on breeding values of selected progenies, overall progenies and parents in the L7 trial. Progenies from the L7 population were ranked from most favorable to least favorable and the average values (i.e., genetic gains) from the top 1% (n = 27) and 5% (n = 136) performing hybrids trees were calculated. Genetic gains were expressed...
Data
Bivariate genetic trait correlations for yield traits.
Data
Genetic gains based on breeding values of selected progenies in the L7 trial. Progenies from the L7 population were ranked from most favorable to least favorable and the average values (i.e., genetic gains) from the top 1% (n = 27) and 5% (n = 136) performing hybrids trees were calculated. Genetic gains were expressed as the percent increase of the...
Article
Full-text available
A comprehensive understanding of the genetic basis of target traits in any crop is critical to design breeding strategies for the development and release of new improved varieties. In this study, 34 cacao families were evaluated for vigor and yield related traits over the course of 6 years in Costa Rica. Linear mixed models provided the variance co...
Article
Full-text available
Nigeria is the sixth largest cacao producer in the world. Field performance and quality of cacao hybrid families is largely dependent on the genetic integrity of parental clones obtained in field genebank collections. However, information on the impact of mislabeling on seed garden output in Nigeria is lacking. Using 63 single nucleotide polymorphi...
Article
Full-text available
Cacao (Theobroma cacao) is a globally important crop, and its yield is severely restricted by disease. Two of the most damaging diseases, witches’ broom disease (WBD) and frosty pod rot disease (FPRD), are caused by a pair of related fungi: Moniliophthora perniciosa and Moniliophthora roreri, respectively. Resistant cultivars are the most effective...
Data
Dialell crosses per genetic types: (a) Wild Types, (b) Known Clones, and (c) Nacional. Number refers to the total crosses performed per combination.
Data
Genomic position, P-value and variance explained (r2) of SNPs significantly associated with five phenotypes among three populations of cacao.
Data
Adjusted means of seven phenotypic traits (count of vegetative brooms, count of cherimoya pods, count of cushion brooms, count of total pods, percent of healthy pods, total pod fresh weight) by accessions of three populations of cacao.
Article
Full-text available
Cacao is an important crop, its beans are key raw materials for the chocolate and cosmetic industries. Ceratocystis wilt of cacao (CWC) caused by Ceratocystis cacaofunesta is a lethal disease for the crop. Therefore, the selection of resistant cacao varieties is one of the viable ways to minimize losses in cacao production. In this paper, we descri...
Article
Full-text available
Cacao (Theobroma cacao L.) is an important cash crop in tropical regions around the world and has a rich agronomic history in South America. As a key component in the cosmetic and confectionary industries, millions of people worldwide use products made from cacao, ranging from shampoo to chocolate. An Illumina Infinity II array was created using 13...
Data
Correlation plots of the phenotypic traits for Stalin A. Stalin A correlations between the yield –related and disease resistance traits. The upper diagonal entries show the Pearson correlation coefficient (ρ). The lower diagonal entries show pairwise plots for each trait combination and their corresponding fitted line (in red) of the linear regress...
Data
Correlation plots of the phenotypic traits for Stalin B. Stalin B correlations between the yield –related and disease resistance traits. The upper diagonal entries show the Pearson correlation coefficient (ρ). The lower diagonal entries show pairwise plots for each trait combination and their corresponding fitted line (in red) of the linear regress...
Data
List of SNPs included on the 15kcacao array and their sequences and genomic positions.
Data
Linkage map table for the Stalin A population.
Data
R-script for inferring the paternal genotype from Stalin B.
Data
Plots of the Matina 1-6 genome assembly position against the linkage map position of the two Stalin populations. The SNP marker position (bp) from the Matina 1-6 genome assembly (y-axis) is plotted against the genetic linkage map position (cM, x-axis) from the Stalin A (left) and Stalin B (right) linkage maps.
Data
Linkage map table for the Stalin B population.
Article
Full-text available
In commercial terms, Criollo cacao trees (Theobroma cacao L.) are reputed to be the source of the commercial product (fermented and dried cocoa beans), which sells for the best price on the market. Nevertheless, the term “Criollo” has numerous meanings and interpretations depending on if it is used by commercial users or botanists, growers or breed...
Article
Full-text available
Breeding programs of cacao (Theobroma cacao L.) trees share the many challenges of breeding long-living perennial crops, and genetic progress is further constrained by both the limited understanding of the inheritance of complex traits and the prevalence of technical issues, such as mislabeled individuals (off-types). To better understand the genet...
Data
Pedigree of trees including off-types in PT08.
Data
96 SNP off-typing markers for cacao.
Preprint
Full-text available
Domestication has had a strong impact on the development of modern societies. We sequenced 200 genomes of the chocolate plant Theobroma cacao L. to show for the first time that a single population underwent strong domestication approximately 3,600 years (95% CI: 2481 – 10,903 years ago) ago, the Criollo population. We also show that during the proc...
Article
Full-text available
Chocolate is a highly valued and palatable confectionery product. Chocolate is primarily made from the processed seeds of the tree species Theobroma cacao. Cacao cultivation is highly relevant for small-holder farmers throughout the tropics, yet its productivity remains limited by low yields and widespread pathogens. A panel of 148 improved cacao c...
Conference Paper
Full-text available
Background Witches’ broom disease (WBD) caused by the fungus Moniliophthora perniciosa is responsible for considerable economic losses for cacao producers. One of the ways to combat WBD is to plant resistant cultivars. Resistance may be governed by a few genetic factors, mainly found in wild germplasm. ResultsWe developed a dense genetic linkage ma...
Article
Full-text available
Theobroma cacao is a species of great economic importance with its beans used for chocolate production. The tree has been a target of various molecular studies. It contains many polyphenols, which complicate the extraction of nucleic acids with the extraction protocols requiring a large amount of plant material. These issues, therefore, necessitate...
Article
Full-text available
Background: Witches’ broom disease (WBD) caused by the fungus Moniliophthora perniciosa is responsible for considerable economic losses for cacao producers. One of the ways to combat WBD is to plant resistant cultivars. Resistance may be governed by a few genetic factors, mainly found in wild germplasm. Results: We developed a dense genetic linkage...
Article
Full-text available
Theobroma cacao, the key ingredient in chocolate production, is one of the world's most important tree fruit crops, with ∼4,000,000 metric tons produced across 50 countries. To move towards gene discovery and marker-assisted breeding in cacao, a single-nucleotide polymorphism (SNP) identification project was undertaken using RNAseq data from 16 div...
Article
Full-text available
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...
Conference Paper
Theobroma cacao L. (cacao) is a perennial tree native to the Amazon and is widely known for its use in the production of chocolate and cocoa butter. Theobroma grandiflorum Schum (cupuaçu), closely related to T. cacao and also native to the Amazon, is commercially grown in Brazil for its flavorful pulp and for its butter used in the cosmetic industr...
Article
This study evaluates resistance to witches’ broom disease in flower cushions of Theobroma cacao under field conditions. Our aim was to determine optimal inoculation methods to evaluate the disease incidence using flower cushions in the field. We analyzed a segregating mapping population of 580 trees (‘TSH 1188′ x ‘CCN 51’) under two field condition...
Article
Full-text available
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...
Conference Paper
Ceratocystis wilt in Theobroma cacao is caused by the ascomycete Ceratocystis cacaofunesta. Infection occurs primarily through wounds caused by common agricultural practices or through insect lesions. The fungus multiplies quickly in the secondary xylem, causing wilting and eventually leads to sudden plant death. Disease control includes removal of...
Article
Full-text available
Background: We address the task of extracting accurate haplotypes from genotype data of individuals of large F1 populations for mapping studies. While methods for inferring parental haplotype assignments on large F1 populations exist in theory, these approaches do not work in practice at high levels of accuracy. Results: We have designed iXora (...
Article
Full-text available
Background Theobroma cacao L. cultivar Matina 1-6 belongs to the most cultivated cacao type. The availability of its genome sequence and methods for identifying genes responsible for important cacao traits will aid cacao researchers and breeders. Results We describe the sequencing and assembly of the genome of Theobroma cacao L. cultivar Matina 1-...
Article
Full-text available
The majority of the world's cacao for chocolate manufacture is produced in West Africa. Cocoa breeding programs in West Africa need genetic markers to reduce the time needed for improving cocoa by screening seedlings for the presence of the markers rather than mature plants for the phenotypic traits (i.e., marker-assisted selection [MAS]). For MAS...
Article
Full-text available
Background Ancestral recombinations graph (ARG) is a topological structure that captures the relationship between the extant genomic sequences in terms of genetic events including recombinations. IRiS is a system that estimates the ARG on sequences of individuals, at genomic scales, capturing the relationship between these individuals of the specie...
Data
Full-text available
Supplementary Material. The complete set of results for the: (a) the classical clustering algorithms in conjunction with the Euclidean distance; (b) the hiarchical clustering algorithms in conjunction with the distance matrix obtained from the Ensemble method; (c) all the results not included in the main manuscript for the Solo and Ensemble Methods...