biostudies-literatureKulesza EMondelez International, IncNational Institute of Food and Agriculture601https://www.ebi.ac.uk/biostudies/studies/S-EPMC11201900biostudies-literatureUnknown24(1)<h4>Background</h4>Theobroma cacao, the cocoa tree, is a tropical crop grown for its highly valuable cocoa solids and fat which are the basis of a 200-billion-dollar annual chocolate industry. However, the long generation time and difficulties associated with breeding a tropical tree crop have limited the progress of breeders to develop high-yielding disease-resistant varieties. Development of marker-assisted breeding methods for cacao requires discovery of genomic regions and specific alleles of genes encoding important traits of interest. To accelerate gene discovery, we developed a gene atlas composed of a large dataset of replicated transcriptomes with the long-term goal of progressing breeding towards developing high-yielding elite varieties of cacao.<h4>Results</h4>We describe the crBMC plant biologyThe cacao gene atlas: a transcriptome developmental atlas reveals highly tissue-specific and dynamically-regulated gene networks in Theobroma cacao L.PMC11201900Project #PEN04707Maximova SNKulesza EShalit-Kaneh APasha AWafula EProvart NdePamphilis CEsteban EKnollenberg BPraul CPrewitt SFGuiltinan MJThomas PLandherr LWinters NfalseThe cacao gene atlas: a transcriptome developmental atlas reveals highly tissue-specific and dynamically-regulated gene networks in Theobroma cacao L.<h4>Background</h4>Theobroma cacao, the cocoa tree, is a tropical crop grown for its highly valuable cocoa solids and fat which are the basis of a 200-billion-dollar annual chocolate industry. However, the long generation time and difficulties associated with breeding a tropical tree crop have limited the progress of breeders to develop high-yielding disease-resistant varieties. Development of marker-assisted breeding methods for cacao requires discovery of genomic regions and specific alleles of genes encoding important traits of interest. To accelerate gene discovery, we developed a gene atlas composed of a large dataset of replicated transcriptomes with the long-term goal of progressing breeding towards developing high-yielding elite varieties of cacao.<h4>Results</h4>We describe the cr2024-01-01T00:00:00Z2024 Jun2026-06-01T11:31:04.622Z2026-04-08T11:50:45.424ZS-EPMC112019003892685210.1186/s12870-024-05171-9