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Title: Cucumber applied genomics: where we are five years after release of cucumber draft genome

item Weng, Yiqun

Submitted to: International Symposium on Cucurbits Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 4/5/2015
Publication Date: 6/23/2015
Citation: Weng, Y. 2015. Cucumber applied genomics: where we are five years after release of cucumber draft genome [abstract]. International Symposium on Cucurbits Proceedings. Paper No. S3.

Interpretive Summary:

Technical Abstract: The first cucumber draft genome (North China fresh market type inbred line 9930) was released in 2009 (Version 1.0). Since then, due to the use of next generation sequencing technologies, seven high-density SSR- or SNP-based cucumber genetic maps have been constructed with mapped loci ranging from 700 to more than 12,000, which have helped improve the Gy14 (North American pickling cucumber) and 9930 draft genome assemblies. The current Gy14 assembly (V1.5) contains 198.2 Mbp covering ~54% of the 367 Mbp cucumber genome. The genome sequences and molecular markers have greatly facilitated molecular mapping and gene cloning in cucumber. Approximately 50 simply inherited genes have been molecularly tagged and several have been cloned. Many QTLs for horticulturally or evolutionarily important traits have also been identified. Molecular marker-based phylogenetic studies have provided new insights into the genetic diversity and population structural of worldwide cucumber collections. Comparative analysis has established syntenic relationships at both chromosomal and DNA sequence levels among cucumber and its relatives, which has increased our understanding of chromosome evolution in the genus Cucumis. This knowledge will help more efficient introgression of alien chromatins from cucumber relatives into cucumber. While these rapidly accumulating genetic and genomics resources provide powerful tools for accelerating classical cucumber breeding, to maximize of power of applied genomics in cucumber improvement, we need to develop a better draft genome assembly and improve the genome annotation. We need more mutants through mutagenesis to understand gene functions, and develop efficient functional genomics tools (for example, genetic transformation, virus-induced gene silencing etc.) for function validation of candidate genes.