Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate ... View Full Text


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Article Info

DATE

2011-07-27

AUTHORS

Frank A Feltus, Christopher A Saski, Keithanne Mockaitis, Niina Haiminen, Laxmi Parida, Zachary Smith, James Ford, Margaret E Staton, Stephen P Ficklin, Barbara P Blackmon, Chun-Huai Cheng, Raymond J Schnell, David N Kuhn, Juan-Carlos Motamayor

ABSTRACT

BackgroundBAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specific BAC clones representing the prioritized genomic interval are selected, pooled, and used to prepare a sequencing library.ResultsThis pooled BAC approach was taken to sequence and assemble a QTL-rich region, of ~3 Mbp and represented by twenty-seven BACs, on linkage group 5 of the Theobroma cacao cv. Matina 1-6 genome. Using various mixtures of read coverages from paired-end and linear 454 libraries, multiple assemblies of varied quality were generated. Quality was assessed by comparing the assembly of 454 reads with a subset of ten BACs individually sequenced and assembled using Sanger reads. A mixture of reads optimal for assembly was identified. We found, furthermore, that a quality assembly suitable for serving as a reference genome template could be obtained even with a reduced depth of sequencing coverage. Annotation of the resulting assembly revealed several genes potentially responsible for three T. cacao traits: black pod disease resistance, bean shape index, and pod weight.ConclusionsOur results, as with other pooled BAC sequencing reports, suggest that pooling portions of a minimum tiling path derived from a BAC-based physical map is an effective method to target sub-genomic regions for sequencing. While we focused on a single QTL region, other QTL regions of importance could be similarly sequenced allowing for biological discovery to take place before a high quality whole-genome assembly is completed. More... »

PAGES

379

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/1471-2164-12-379

    DOI

    http://dx.doi.org/10.1186/1471-2164-12-379

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1013322895

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/21794110


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