ARS | Publication request: The Cucumber Genome Initiative-An International Effort to Unlock the Genetic Potential of an Orphan Crop Using Novel Genomic Technology

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: October 15, 2008
Publication Date: December 15, 2009
Citation: Huang, S., Du, Y., Wang, X., Gu, X., Xie, B., Zonghua, Wang, J., Li, R., Li, S., Staub, J.E. 2009. The Cucumber Genome Initiative-An International Effort to Unlock the Genetic Potential of an Orphan Crop Using Novel Genomic Technology. Plant and Animal Genome Conference.

Technical Abstract: Cucumber is an important vegetable in the world. However, its narrow genetic basis makes it a less desirable species for genetic study and molecular breeding. The Cucumber Genome Initiative (CuGI) was established with aims: 1) to obtain a complete sequence of the genome; 2) to get an in-depth understanding of the genetic and molecular bases of major agronomical traits; 3) to generate a comprehensive toolbox for molecular breeding; 4) to create a model of biology and genetics for the botanical family Cucurbitaceae. We apply a hybrid strategy for whole genome sequencing that takes advantage of read length and paired-end of the conventional Sanger sequencing and of the extra-high throughput of the next generation Solexa sequencing. We have finished 4x Sanger sequencing of the genome and preliminary assembly showing 90% the genome was covered. Using the 454 method, 410K EST was generated with average length 205bp. We constructed a genetic map that consists of 700 Diversity Array Technology markers and 1000 microsatellite markers, distributed on seven linkage group. A 20X coverage fosmid library has been end-sequenced. With the genetic map and super-scaffold from shotgun assembly, we are generating a whole-genome physical map and current version which covers 1/4 of the genome. Fosmids on the physical map is being sequenced using the Solexa technology. In addition, a 10x coverage BAC library is ready for end-sequencing. Fosmids mapped to the SSR map is being FISHed to align chromosomes and linkage group. The complete genome sequence will be released in 2008.