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 Matina1-6. 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.
Highlights
Theobroma cacao L. cultivar Matina 1-6 belongs to the most cultivated cacao type
Genome size The flow cytometry (FCM) estimate of the Matina 1-6 genome size is 445 Mbp; this value approximates the mean determined for 28 different T. cacao genotypes, including representatives of all 10 structural diversity groups defined by Motamayor et al [2]
We developed a six-component fluorescence in situ hybridization (FISH) ‘cocktail’ that simultaneously identified every chromosome in a single mitotic chromosome spread (Figure 1)
Summary
Theobroma cacao L. cultivar Matina 1-6 belongs to the most cultivated cacao type. The cacao tree (Theobroma cacao L.) is a neotropical species native to Amazonian lowland rainforests [1,2] and is grown in more than 50 countries throughout the humid tropics. Compared with traditional cacao classification schemes, this new system more accurately reflects the genetic diversity available to breeders. The Matina 1-6 clone is a traditional cultivar that exhibits the Amelonado phenotype and belongs to the Amelonado genetic group. This group shows little genetic diversity compared with the other nine groups [2,8] and, critically, it is the most common cultivated type of cacao worldwide [8,9,10]
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