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ARS Home » Plains Area » Manhattan, Kansas » Center for Grain and Animal Health Research » Hard Winter Wheat Genetics Research » Research » Publications at this Location » Publication #191215
Title: THE EFFICACY OF COT-BASED GENE ENRICHMENT IN WHEAT (TRITICUM AESTIVUM L.)

Author
item LAMOUREUX, D - INRA, FRANCE
item PATTERSON, D - MISSISSIPPI STATE UNIV
item LI, WANLONG - KANSAS STATE UNIV
item GILL, B - KANSAS STATE UNIV
item Fellers, John

Submitted to: Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/22/2005
Publication Date: 12/9/2005
Citation: Lamoureux, D., Patterson, D.G., Li, W., Gill, B.S., Fellers, J.P. 2005. The efficacy of cot-based gene enrichment in wheat (triticum aestivum l.). Genome. 48:1120-1126.

Interpretive Summary: The wheat genome contains 16 billion letters of DNA, of which only 10-20% actually code for genes used by the wheat plant. Like the human genome project it would be useful to sequence all of the DNA in wheat to find all of the genes. However, with the large number of letters, it is inefficient and not cost effective with today’s technology to sequence wheat. The work described in this manuscript details a method to filter out repetitive and non-useful DNA. We demonstrate that we can reduce the level of repetitive DNA by three fold and increase the level of DNA sequence containing genes by nearly 14 fold. This allows for increased efficiency for the isolation and sequencing of gene containing DNA.

Technical Abstract: We report the results of a study on the effectiveness of Cot filtration (CF) in the characterization of the gene space of bread wheat (Triticum aestivum L.), a large genome species (1C = 16 700 Mb) of tremendous agronomic importance. Using published Cot data as a guide, 2 genomic libraries for hexaploid wheat were constructed from the single-stranded DNA collected at Cot values > 1188 and 1639 M•s. Compared with sequences from a whole genome shotgun library from Aegilops tauschii (the D genome donor of bread wheat), the CF libraries exhibited 13.7-fold enrichment in genes, 5.8-fold enrichment in unknown low-copy sequences, and a 3-fold reduction in repetitive DNA. CF is twice as efficient as methylation filtration at enriching wheat genes. This research suggests that, with improvements, CF will be a highly useful tool in sequencing the gene space of wheat.