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United States Department of Agriculture

Agricultural Research Service


Location: Forage and Range Research

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

item Huang, Sanwen
item Du, Yongchen
item Wang, Xiaowu
item Gu, Xingfang
item Xie, Bingyan
item Zonghua, Zhang
item Wang, Jun
item Li, Ruiqiang
item Li, Songgang
item Staub, Jack

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 10/15/2008
Publication Date: 12/15/2009
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.

Interpretive Summary:

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.

Last Modified: 09/24/2017
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