ANNUAL PROGRESS REPORT
NATIONAL RESEARCH SUPPORT PROJECT - NRSP-8
Year Ending 2002
Preliminary Information-Not for Publication
Purdue University
West Lafayette, IN
I. PROJECT TITLE:
National Animal Genome Research Program (NAGRP)
II. COOPERATING AGENCIES AND PRINCIPAL LEADERS:
Purdue University, Department of Animal Science
Diane Moody (leader)
Christopher Bidwell
III. NATURE OF WORK AND PRINCIPAL RESULTS OF YEAR:
Objective: 1. Develop high-resolution comparative genome maps aligned across species that link agricultural animal maps to those of the human and mouse genomes.
No projects.
Objective: 2. Increase marker density of existing linkage maps used in QTL mapping and integrate them with physical maps of animal chromosomes.
No projects.
Objective: 3. Expand and enhance internationally shared species genome databases and provide other common resources that facilitate genome mapping.
Project 1: Genomics Database Development. A collaborative effort is underway at Purdue University to develop a relational database for the maintenance and query of multiple types of genomics data, including gene expression and sequence data from the pig. Particular emphasis has been placed on the ability to integrate different types of data, such as phenotypic, gene expression, and SAGE data, with other efforts focused on mapping and annotation of pig gene sequences. A microarray database schema has been developed and implemented. Currently, the database is being populated and tested using data generated from multiple types of microarray experiments. Preliminary resources that allow datasets to be defined and created from the database have been developed.
Project 2: Serial Analysis of Gene Expression (SAGE). Libraries for the serial analysis of gene expression (SAGE) have been generated from pig skeletal muscle, heart, and adipose tissues. A total of 56,678 SAGE tags have been sequenced, including 34,566 from skeletal muscle, 20,380 from heart, and 1,732 from adipose tissue. These SAGE tags represent a total of 4,999 unique transcripts. Comparison of all unique tags with the TIGR Porcine Gene Index Database revealed hits for 2,673 (53%) of the SAGE tags. However, this hit rate is likely overestimated because the relative position of the SAGE tag within the gene sequence was not evaluated. SAGE tags common to all libraries, as well as unique to each individual library, were identified.
IV. APPLICATION OF FINDINGS:
Project 1: Genomics Database Development. Our long-term goal is to make the Purdue database available as a centralized resource for the maintenance and query of multiple types of genomic data for the pig genome community. Such a resource will facilitate the integration of functional genomics data (ie., gene expression data) with sequence, annotation, and mapping resources.
Project 2: Serial Analysis of Gene Expression (SAGE). The establishment of pig SAGE libraries and tags is a first step toward defining the complete transcriptome of the targeted tissues. The SAGE tags provide a resource that will aid in the identification of novel genes for genetic mapping or marker development.
V. WORK PLANNED FOR NEXT YEAR:
Project 1: Genomics Database Development. The existing database will be further developed and improved to strengthen the integration of gene expression data with existing sequencing and mapping resources. The ability of the database to accept and manage multiple types of gene expression data will be improved. The database will be made available to all Purdue researchers and their collaborators.
Project 2: Serial Analysis of Gene Expression (SAGE). Additional sequencing of the adipose SAGE library will be completed. A web site making the complete pig SAGE tag database available to the community will be developed.
VI. PUBLICATIONS:
Moody, D., W. Aref, R. Doerge, L. McIntyre, M. Mokbel, A. Valova, and C. Bidwell. 2002. Development of a database for the functional and expression annotation of sequence tags (FEAST) in the pig. Plant and Animal Genome Conference X, San Diego, CA. http://www.intl-pag.org/pag/10/abstracts/PAGX_P810.html