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

BMC Genomics

Research Article

Christopher A Saski¹  Margaret E Staton¹  Barbara P Blackmon¹  Stephen P Ficklin¹  Frank A Feltus²  Howard Shapiro³  Raymond J Schnell⁴  David N Kuhn⁴  Juan Carlos Motamayor⁵ 

[1] Clemson University Genomics Institute, Clemson University, 51 New Cherry Street, 29634, Clemson, SC, USA;Clemson University Genomics Institute, Clemson University, 51 New Cherry Street, 29634, Clemson, SC, USA;Department of Genetics and Biochemistry, Clemson University, 51 New Cherry Street, 29634, Clemson, SC, USA;Mars, Inc., 800 High St., 07840, Hackettstown, NJ, USA;Subtropical Horticulture Research Station, USDA-ARS, 13601 Old Culter Road, 33158, Miami, FL, USA;Subtropical Horticulture Research Station, USDA-ARS, 13601 Old Culter Road, 33158, Miami, FL, USA;Mars, Inc., 800 High St., 07840, Hackettstown, NJ, USA;

关键词: Synteny Block;    Syntenic Block;    Minimum Tile Path;    Overgo Probe;    High Information Content Fingerprinting;   

DOI  :  10.1186/1471-2164-12-413

 received in 2011-04-26, accepted in 2011-08-16,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundThe fermented dried seeds of Theobroma 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 robust T. cacao cultivars. 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 the T. cacao cultivar 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 of T. cacao is 374.6 Mbp. A comparative analysis with A. thaliana, V. vinifera, and P. trichocarpa suggests 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 two T. cacao cultivars 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 of Theobroma cacao but are also expected to complement and augment ongoing genome-sequencing efforts. This resource will serve as a template for refinement of the T. cacao genome through gap-filling, targeted re-sequencing, and resolution of repetitive DNA arrays.

【 授权许可】

Unknown   
© Saski et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.