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United States Department of Agriculture

Agricultural Research Service

Research Project: ALLIUM, CUCUMIS, AND DAUCUS GERMPLASM ENHANCEMENT, GENETICS, AND BIOCHEMISTRY

Location: Vegetable Crops Research Unit

Title: Translational Genomics of Onion: Challenges of an Enormous Nuclear Genome

Author
item HAVEY, MICHAEL

Submitted to: Abstract of International Horticultural Congress
Publication Type: Abstract Only
Publication Acceptance Date: July 2, 2010
Publication Date: August 23, 2010
Citation: Havey, M.J. 2010. Translational Genomics of Onion: Challenges of an Enormous Nuclear Genome [abstract]. Abstract of International Horticultural Congress. Paper No. S04.006.

Technical Abstract: The use of high throughput DNA sequencing to address important production constraints has been termed “translational genomics”. Classical breeding of onion (Allium cepa) is expensive and slow due to a long generation time and the high costs of crossing with insects. Translational genomics should revolutionize onion breeding by reducing the cost of selection. However sequencing of onion is challenging because it has one of the largest nuclear genomes among all diploid plants. We undertook sequencing of expressed and genomic regions of the onion genome to learn about the structure of this enormous genome. Extensive sequencing of onion cDNAs revealed codon biases and GC contents more similar to the eudicots than the grasses, as well as many single nucleotide polymorphisms (SNPs) within coding regions. Pilot sequencing of onion genomic BACs revealed very low gene densities, averaging of one gene per 168 kb. Sequencing of random onion genomic clones after methyl filtration substantially increased hits to genic regions. These results indicate that sequencing of onion DNA should concentrate on expressed regions and reduced representation libraries to assemble the unigene set for onion and reveal SNPs for molecular-aided selection.

Last Modified: 8/19/2014