A genetically anchored physical framework for Theobroma cacao cv. Matina 1-6

Abstract

AbstractBackgroundThe fermented dried seeds ofTheobroma cacao(cacao tree) are the main ingredient in chocolate. World cocoa production was estimated to be 3 million tons in 2010 with an annual estimated average growth rate of 2.2%. The cacao bean production industry is currently under threat from a rise in fungal diseases including black pod, frosty pod, and witches' broom. In order to address these issues, genome-sequencing efforts have been initiated recently to facilitate identification of genetic markers and genes that could be utilized to accelerate the release of robustT. cacaocultivars. However, problems inherent with assembly and resolution of distal regions of complex eukaryotic genomes, such as gaps, chimeric joins, and unresolvable repeat-induced compressions, have been unavoidably encountered with the sequencing strategies selected.ResultsHere, we describe the construction of a BAC-based integrated genetic-physical map of theT. cacaocultivar Matina 1-6 which is designed to augment and enhance these sequencing efforts. Three BAC libraries, each comprised of 10× coverage, were constructed and fingerprinted. 230 genetic markers from a high-resolution genetic recombination map and 96 Arabidopsis-derived conserved ortholog set (COS) II markers were anchored using pooled overgo hybridization. A dense tile path consisting of 29,383 BACs was selected and end-sequenced. The physical map consists of 154 contigs and 4,268 singletons. Forty-nine contigs are genetically anchored and ordered to chromosomes for a total span of 307.2 Mbp. The unanchored contigs (105) span 67.4 Mbp and therefore the estimated genome size ofT. cacaois 374.6 Mbp. A comparative analysis withA. thaliana, V. vinifera, andP. trichocarpasuggests that comparisons of the genome assemblies of these distantly related species could provide insights into genome structure, evolutionary history, conservation of functional sites, and improvements in physical map assembly. A comparison between the twoT. cacaocultivars Matina 1-6 and Criollo indicates a high degree of collinearity in their genomes, yet rearrangements were also observed.ConclusionsThe results presented in this study are a stand-alone resource for functional exploitation and enhancement ofTheobroma cacaobut are also expected to complement and augment ongoing genome-sequencing efforts. This resource will serve as a template for refinement of theT. cacaogenome through gap-filling, targeted re-sequencing, and resolution of repetitive DNA arrays.