Genomic insights into the domestication of the chocolate tree,<i>Theobroma cacao</i>L

Oe, Cornejo; Domínguez,; Andrews, Mary E.; Sockell, Alexandra; Strandberg, Erika; Livingstone, Donald; Stack, Conrad; Romero, Alfonso; Umaharan, Pathmanathan; Royaert, Stefan; Nr, Tawari; Pauline, N'Douba Amako; Schnell, Ray; Phillips, Wilbert; Mockaitis, Keithanne; Bustamante, Carlos D.; Jc, Motamayor

doi:10.1101/223438

Cited by 4 publications

(3 citation statements)

References 39 publications

(49 reference statements)

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“…The genetic group Criollo is the only one that is separated by the PCA analysis. This result is consistent with the study reported by Cornejo et al (2017) in which they conclude that this differentiation could be to the early diversification or recent domestication of the Criollo population from the rest of the genetic clusters. The other cacao samples do not form distinguishable groups consistent with the study of McElroy et al (2018) but the distribution probably corresponds to a geographical gradient as explained by Cornejo et al (2018).…”

Section: Genotypic Analysissupporting

confidence: 93%

Genome-Wide Association Study Reveals Novel Candidate Genes Associated with Productivity and Disease Resistance to Moniliophthora spp. in Cacao (Theobroma cacao L.)

Osorio-Guarín

Berdugo-Cely

Coronado-Silva

et al. 2020

G3 Genes|Genomes|Genetics

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Cacao (Theobroma cacao L.), the source of chocolate, is one of the most important commodity products worldwide that helps improve the economic livelihood of farmers. Diseases like frosty pod rot caused by Moniliophthora roreri and witches’ broom caused by Moniliophthora perniciosa limit the cacao productivity, this can be solved by using resistant varieties. In the current study, we sequenced 229 cacao accessions using genotyping-by-sequencing to examine the genetic diversity and population structure employing 9,003 and 8,131 single nucleotide polymorphisms recovered by mapping against two cacao genomes (Criollo B97-61/B2 v2 and Matina 1-6 v1.1). In the phenotypic evaluation, three promising accessions for productivity and 10 with good tolerance to the frosty pod rot and witches’ broom diseases were found. A genome-wide association study was performed on 102 accessions, discovering two genes associated with productivity and seven to disease resistance. The results enriched the knowledge of the genetic regions associated with important cacao traits that can have significant implications for conservation and breeding strategies like marker-assisted selection.

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Section: Genotypic Analysissupporting

confidence: 93%

Genome-Wide Association Study Reveals Novel Candidate Genes Associated with Productivity and Disease Resistance to Moniliophthora spp. in Cacao (Theobroma cacao L.)

Osorio-Guarín

Berdugo-Cely

Coronado-Silva

et al. 2020

G3 Genes|Genomes|Genetics

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“…differentiation model derived from the sequencing of 200 individuals representing highly diverse cocoa trees (Cornejo et al, 2017). This latter analysis revealed the Curaray group as the most closely related to the Criollo group, suggesting that the origin of Criollo domestication came from a subset of ancient Curaray individuals.…”

Section: Discussionmentioning

confidence: 97%

“…Accessions are shown as horizontal bar colored in proportion to their ancestry within each group. Colors on the bar plot of the collected accessions refer to the control populations differentiation model derived from the sequencing of 200 individuals representing highly diverse cocoa trees(Cornejo et al, 2017). This latter analysis revealed the Curaray group as the most closely related to the Criollo group, suggesting that the origin of Criollo domestication came from a subset of ancient Curaray individuals.…”

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confidence: 99%

Collection of native Theobroma cacao L. accessions from the Ecuadorian Amazon highlights a hotspot of cocoa diversity

Fouet

Solorzano

Rhoné

et al. 2022

Plants People Planet

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Societal Impact Statement “Fine flavor” cocoa, known for its superior flavor and aroma, commands a higher price for farmers than “bulk” cocoa produced for market. These fine flavor cocoa varieties make an important contribution to the agricultural sector in Ecuador. However, cocoa diversity is threatened by deforestation. The effective preservation, characterization, and use of cocoa tree diversity are therefore essential to the future development of this market. We carried out participatory collection surveys with local communities in the Ecuadorian Amazon Forest, to evaluate the genetic diversity of native cocoa trees and protect trees as a resource for local communities. Accessing this wealth of diversity will aid farmers to safeguard cocoa against climate change and develop new varieties for market. Summary The aromatic Nacional variety of Theobroma cacao, emblematic of Ecuador, is highly sought after by the chocolate industry. The modern Nacional is a hybrid population resulting from genetic admixture that has lost the specificity of the ancestral variety. In the context of progressive forest disappearance, the objective of our study was to collect, safeguard, and evaluate native aromatic cocoa trees from Ecuadorian Amazon areas previously identified as areas of origin of the Nacional variety, as well as those that extend toward the northern Amazon. Four collection expeditions were organized in the Ecuadorian Amazon provinces of Zamora‐Chinchipe, Morona‐Santiago, and Pastaza in close collaboration with local communities. A total of 283 native accessions were collected and safeguarded at experimental stations and in local communities. The genetic diversity of the cocoa trees was analyzed by comparison to known genetic groups with a set of 48 simple sequence repeat (SSR) markers. This new collection clearly enriches the currently known diversity and improves knowledge of the global genetic structure of cocoa trees. Our results clarify the geographic origin of the Nacional variety in the vicinity of an archeological site that housed a Maya Chinchipe population that consumed cacao 5,000 years ago. In addition, our analyses revealed clues to the origin of Criollo, another ancient variety with a fine flavor. These new genetic resources will be used in breeding programs for the varietal improvement of new aromatic cocoa varieties and more globally for the selection of new varieties adapted to environmental changes.

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Low-cost assembly of a cacao crop genome is able to resolve complex heterozygous bubbles

et al. 2019

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Cacao ( Theobroma cacao ) is a tropical tree that produces the essential raw material for chocolate. Because yields have been stagnant, land use has expanded to provide for increasing chocolate demand. Assembled genomes of key parents could modernize breeding programs in the remote and under-resourced locations where cacao is grown. The MinION, a long read sequencer that runs off of a laptop computer, has the potential to facilitate the assembly of the complex genomes of high-yielding F 1 hybrids. Here, we validate the MinION’s application to heterozygous crops by creating a de novo genome assembly of a key parent in breeding programs, the clone Pound 7. Our MinION-only assembly was 20% larger than the latest released cacao genome, with 10-fold greater contiguity, and the resolution of complex heterozygosity and repetitive elements. Polishing with Illumina short reads brought the predicted completeness of our assembly to similar levels to the previously released cacao genome assemblies. In contrast to previous cacao genome projects, our assembly required only a small scientific team and limited reagents. Our sequencing and assembly methods could easily be adopted by under-resourced breeding programs, speeding crop improvement in the developing world.

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Genomic insights into the domestication of the chocolate tree,Theobroma cacaoL

Cited by 4 publications

References 39 publications

Genome-Wide Association Study Reveals Novel Candidate Genes Associated with Productivity and Disease Resistance to Moniliophthora spp. in Cacao (Theobroma cacao L.)

Genome-Wide Association Study Reveals Novel Candidate Genes Associated with Productivity and Disease Resistance to Moniliophthora spp. in Cacao (Theobroma cacao L.)

Collection of native Theobroma cacao L. accessions from the Ecuadorian Amazon highlights a hotspot of cocoa diversity

Low-cost assembly of a cacao crop genome is able to resolve complex heterozygous bubbles

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