ArticleGenome biology2013
The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color.
Article in Genome biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 131 papers, 1 of them a synthesis that pooled it.
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Who cites it
131 citing papers in PubMed, 1 synthesis or guideline pooled it, 306 citations in OpenAlex.
- State of the Art of the Molecular Biology of the Interaction between Cocoa and Witches' Broom Disease: A Systematic Review.International journal of molecular sciences · 2023Pooled it
- Adaptive Responses of Tropical Crops: A Multi-Scale Omics Integrated Perspective.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Chromosomal-scale and haplotype-resolved genome assembly of the first Trinitario hybrid cacao ICS 1.Scientific data · 2026Article
- Stable Inheritance of Transgene and Yellow Fluorescent Protein Gene Expression in Progeny of Transgenic Cacao (Plants (Basel, Switzerland) · 2026Article
- Review
- Transcriptional regulation of root development in cacao: a genome-wide comparative analysis between zygotic and somatic embryo-derived seedlings.Frontiers in plant science · 2026Article
- Single nucleotide polymorphism information estimates breed and variety composition ratio in food.Current research in food science · 2026Article
- All roads lead to Rome: integrated physiological and transcriptomic analysis of cacao drought response reveals different ways to achieve tolerance in two hybrid clones.Frontiers in plant science · 2026Article
- Near T2T haplotype-resolved genomes of cacao (Theobroma cacao) variety CCN51.Scientific data · 2025Article
- Evolutionary dynamics of the proanthocyanidin biosynthesis gene LAR.BMC genomics · 2025Article
- From genome to gene expression: the genomic landscape of a hybrid species of Eucalyptus urophylla × Eucalyptus grandis and its divergence from parental species hybrid.BMC plant biology · 2025Article
- Genome-Wide Identification ofPlants (Basel, Switzerland) · 2025Article
- Local gene duplications drive extensive NLR copy number variation across multiple genotypes of Theobroma cacao.G3 (Bethesda, Md.) · 2025Article
- Machine learning-driven GWAS uncovers novel candidate genes for resistance to frosty pod rot and witches' broom disease in cacao.The plant genome · 2025Article
- Reticulate allopolyploidy and subsequent dysploidy drive evolution and diversification in the cotton family.Nature communications · 2025Article
- Pangenome analysis reveals yield- and fiber-related diversity and interspecific gene flow in Gossypium barbadense L.Nature communications · 2025Article
- Polyploidy-mediated variations in glutamate receptor proteins linked to Fusarium wilt resistance in upland cotton.The Plant journal : for cell and molecular biology · 2025Article
- Population structure and genetic diversity of a coffee germplasm collection in China revealed by RAD-seq.Frontiers in plant science · 2025Article
- Scaffolded and annotated nuclear and organelle genomes of the North American brown algaFrontiers in genetics · 2025Article
- Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback.The plant genome · 2024Article
71 more citing papers are in PubMed but not listed here.
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Authors and funding
30 authors at 11 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTheobroma 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.
resultsWe describe the sequencing and assembly of the genome of Theobroma cacao L. cultivar Matina 1-6. The genome of the Matina 1-6 cultivar is 445 Mbp, which is significantly larger than a sequenced Criollo cultivar, and more typical of other cultivars. The chromosome-scale assembly, version 1.1, contains 711 scaffolds covering 346.0 Mbp, with a contig N50 of 84.4 kbp, a scaffold N50 of 34.4 Mbp, and an evidence-based gene set of 29,408 loci. Version 1.1 has 10x the scaffold N50 and 4x the contig N50 as Criollo, and includes 111 Mb more anchored sequence. The version 1.1 assembly has 4.4% gap sequence, while Criollo has 10.9%. Through a combination of haplotype, association mapping and gene expression analyses, we leverage this robust reference genome to identify a promising candidate gene responsible for pod color variation. We demonstrate that green/red pod color in cacao is likely regulated by the R2R3 MYB transcription factor TcMYB113, homologs of which determine pigmentation in Rosaceae, Solanaceae, and Brassicaceae. One SNP within the target site for a highly conserved trans-acting siRNA in dicots, found within TcMYB113, seems to affect transcript levels of this gene and therefore pod color variation.
conclusionsWe report a high-quality sequence and annotation of Theobroma cacao L. and demonstrate its utility in identifying candidate genes regulating traits.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.