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

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 EcoR I and Hind III insertion vectors, respectively.The EcoR I library has 29952 clones with an average insert size of 115 kb, while the Hind III 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 approximately762 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 covered459 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.