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United States Department of Agriculture

Agricultural Research Service

Title: Sequence Evaluation of Four Pooled-Tissue Normalized Bovine Cdna Libraries and Construction of a Gene Index for Cattle

Authors
item Smith, Timothy
item Grosse, William - U.S. MARC (FORMERLY)
item Freking, Bradley
item Roberts, Andrew
item Stone, Roger
item Casas, Eduardo
item Wray Jr, James
item White, Joseph - INST. GENOMIC RESEARCH
item Cho, Jennifer - INST GENOMIC RESEARCH
item Fahrenkrug, Scott

Submitted to: Genome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 12, 2001
Publication Date: N/A

Interpretive Summary: This manuscript reports completion of a pilot project to obtain DNA sequence from thousands of genes from cattle. More than 80,000 DNA gene segments, called expressed sequence tags, from cattle have been sequenced in this project. The EST sequence information is accessible through the national sequence database at the National Center for Biotechnology Information, from where researchers worldwide can access the data for research in medicine as well as animal science. Additional analysis of the sequence information has been developed by The Institute for Genomic Research, who used information from the human genome project to predict the function of many of the livestock genes. Studies based on the sequence data are expected to one day provide a means to increase production values in livestock herds by increasing the accuracy and speed of selection for specific characteristics. They may also lead to the development of new management strategies to increase efficiency of production. The project involved producing libraries of expressed genes from a variety of tissues important to livestock growth, composition, reproduction, animal health, and food safety. The clones from this library and the sequence information derived from them will be used to support efforts worldwide to construct DNA chips, or microarrays, that can be used to monitor activity of thousands of genes in a single experiment. Microarrays from other organisms such as yeast, fruit flies, mice, and humans, have revolutionized research in basic science and biomedicine, and it is anticipated they will have an equally large impact on research in livestock

Technical Abstract: An essential component of functional genomics studies is the sequence of DNA expressed in tissues of interest. In order to provide a resource of bovine-specific expressed sequence data to facilitate this powerful approach in cattle research, four normalized cDNA libraries were produced and arrayed for high- throughput sequencing. The libraries were made with RNA pooled from multiple tissues, to increase efficiency of normalization and maximize the number of independent genes for which sequence data was obtained. Target tissues included those with highest likelihood to have impact on production parameters of animal health, growth, reproductive efficiency, and carcass merit. Success of normalization and inter- and intra-library redundancy were assessed by collecting 6,000-23,000 sequences from each of the libraries (68,520 total sequences deposited in GenBank). Sequence comparison and assembly of these sequences was performed, in combination with 56,500 other bovine EST sequences present in the Genbank dbEST database, to construct a cattle Gene Index. The 124,381 bovine ESTs present in GenBank at the time of the analysis form 16,740 assemblies that are listed and annotated on the web site. Analysis of individual library sequence data indicates that the pooled- tissue approach was highly effective in preparing libraries for efficient deep sequencing.

Last Modified: 10/21/2014
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