PAG-IX: DEVELOPMENT OF RESOURCES FOR FUNCTIONAL GENOMICS IN THE PIG: PRODUCTION OF 14 CDNA LIBRARIES AND SEQUENCING OF OVER 7,000 CLONES FROM FEMALE REPRODUCTIVE TISSUES.

PAG-IX   Plant & Animal Genome IX Conference

Town & Country Hotel, San Diego, CA, January 13-17, 2001.

Poster: Sequencing & EST
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DEVELOPMENT OF RESOURCES FOR FUNCTIONAL GENOMICS IN THE PIG: PRODUCTION OF 14 CDNA LIBRARIES AND SEQUENCING OF OVER 7,000 CLONES FROM FEMALE REPRODUCTIVE TISSUES.

CHRISTOPHER K. TUGGLE1, Jon Green2, Carolyn J. Fitzsimmons1, Rami Woods2, Randall Prather2, Sergey Malchenko3, Bento Soares3, Chad Roberts4, Kevin Pedretti1, Tom Casavant4, Carol Harger5, Yuandan Zhang1, Max F. Rothschild1

1 Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, 50011, USA
2 Department of Animal Science, 162 ASRC University of Missouri-Columbia, Columbia, MO, 65211, USA
3 Department of Pediatrics, University of Iowa, 451 Eckstein Medical Research Building, Iowa City, IA, 52242, USA
4 Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA, 52242, USA
5 National Center for Genomic Resources, Santa Fe, NM

Sequencing of cDNAs expressed in reproductive biology will provide useful information in identifying specific genes involved in quantitative traits for pig reproduction. We have produced 14 libraries from the following tissues: whole embryo (day 12, 14, 20 and 45 of gestation); term placenta, anterior pituitary (day 0, 5 and 12 of estrus), hypothalamus (day 0, 5 and 12 of estrus) and ovary (day 0, 5 and 12 of estrus). To determine the quality of these libraries, we have sequenced randomly selected clones from each library. A total of 7,011 sequences has been produced and will be submitted to Genbank. The average sequence read length across this dataset is 424 base pairs, with less than 22% shorter than 300 base pairs. As assessed by cluster analysis, these sequences represent 4,786 different genes for a novelty rate of 68.3%. A Genbank nr/dbEST analysis using the publicly available ESTs (ca. 35,944 porcine genes and ESTs as of October 9, 2000) indicates that 3,003 (63%) of these clusters are unique relative to existing porcine Genbank entries (BLAST score <50), and that 1,659 (35%) have a significant match with human sequences (BLAST score >200). As well, we have developed software to predict the pig cytogenetic location based on human cytogenetic and RH mapping data. A WWW site has been established for public access to these sequences and the analysis data. In summary, this EST project has currently identified over 7,000 pig reproduction ESTs, representing over 3,000 new genes, toward a project goal of 20,000 submissions.

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