A bacterial artificial chromosome-based physical map of <i>Manihot esculenta </i> ssp. <i>flabellifolia </i>

doi:10.15302/J-FASE-2016124

Front. Agr. Sci. Eng.

2016, Vol. 3

Issue (4) : 321-329 https://doi.org/10.15302/J-FASE-2016124

RESEARCH ARTICLE

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

Yuhua FU^1,², Zhiqiang XIA¹, Shujuan WANG¹, Xin CHEN¹, Cheng LU¹, Mingcheng LUO³, Hongbin ZHANG⁴, Wenquan WANG¹(

)

¹. Institute of tropical Biosciences & Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
². Guizhou Institute of Subtropical Crops, Guizhou Academy of Agricultural Sciences, Xinyi 562400, China
³. Department of Plant Sciences, UC Davis, Davis, CA 95616, USA
⁴. Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA

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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.

Keywords cassava BAC library physical map

Corresponding Author(s): Wenquan WANG

Just Accepted Date: 23 December 2016 Online First Date: 10 January 2017 Issue Date: 22 January 2017

Cite this article:

Yuhua FU,Zhiqiang XIA,Shujuan WANG, et al. A bacterial artificial chromosome-based physical map of Manihot esculenta ssp. flabellifolia [J]. Front. Agr. Sci. Eng. , 2016, 3(4): 321-329.

URL:

https://academic.hep.com.cn/fase/EN/10.15302/J-FASE-2016124
https://academic.hep.com.cn/fase/EN/Y2016/V3/I4/321

Fig.1 A random sample of bacterial artificial chromosomes (BAC) selected from the Eco RІ library and analyzed on a pulsed-field gel. BAC DNA was digested with Not І to release the entire insert from the BAC vector. M indicates lambda ladder pulsed-field gel electrophoresis marker.

Fig.2 Insert size distribution of the bacterial artificial chromosome libraries with 80 clones from the Eco RI library and 85 clones from Hin dIII library

Tab.1 Statistics of the bacterial artificial chromosome (BAC)-based physical map of the wild cassava genome

Tab.2 The index statistics of bacterial artificial chromosome-end sequence and assembly

Tab.3 Integrated draft genome of W14 based on the physic map and 5000 bacterial artificial chromosome-end sequences

Fig.3 Statistics of single-nucleotide polymorphisms and indels developed from bacterial artificial chromosome-end sequences

Fig.4 Gene ontology analysis of 459 genes involving single-nucleotide polymorphisms and indels

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