A bacterial artificial chromosome-based physical map of Manihot esculenta ssp. flabellifolia

Abstract

Cassava ( Manihot esculenta ) is known as the third most important food crop in the tropics and also used for industrial feedstock for biofuels. Two new bacterial artificial chromosome (BAC) libraries were constructed for W14 ( M. Esculenta ssp. flabellifolia ), a wild ancestor of domesticated cassava. The libraries were constructed with Eco RI and Hin dIII insertion vectors, respectively. The Eco RI library has 29952 clones with an average insert size of 115 kb, while the Hin dIII library consists of 29952 clones with an average insert of 129 kb. The combined libraries contain a total of 59904 clones with an average insert size of 125 kb, representing approximately 10 × haploid genome equivalents. A total of 29952 clones were fingerprinted and resulted in a cassava physical map composed of 2485 contigs with an average physical length of 336 kb and 2909 singletons, representing approximately 762 Mb of the cassava genome. 5000 clones located at the ends of BAC contigs were selected and sequenced. A total of 6077 SNPs and 231 indels were identified, that covered 459 gene sequences, of which 6 genes were associated with starch and sucrose metabolism. This BAC-based physical map provides valuable tools to understand the genetics and evolution of cassava.

Graphical abstract

Keywords

cassava / BAC library / physical map

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Acknowledgements

This project was funded by the National Basic Research and Development Program (2010CB126600), China Agriculture Research System (CARS-12), and National International Science and Technology Cooperation Plan (2011DFB31690). Authors are grateful to bioinformatics researchers from the Cassava Genome Consortium for their help in integration of the BAC-based physical map with the assembled genome.

Compliance with ethics guidelines

Yuhua Fu, Zhiqiang Xia, Shujuan Wang, Xin Chen, Cheng Lu, Mingcheng Luo, Hongbin Zhang, and Wenquan Wang declare that they have no conflict of interest or financial conflicts to disclose.

This article does not contain any studies with human or animal subjects performed by any of the authors.

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The Author(s) 2016. Published by Higher Education Press. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0)