Plant & Animal Genomes XI Conference Plant & Animal Genomes XI ConferenceJanuary 11-15, 2003
Town & Country Convention Center
San Diego, CA
Workshop: Swine
The University of Nebraska Lincoln (UNL) has developed unique swine lines with superior reproductive qualities by selecting animals on an index of components of litter size. The Index line ovulates 7.4 more ova then the Control line. We used cDNA microarrays to identify genes that are differentially expressed in ovarian/follicular tissue of pigs from the UNL selection lines. Ovaries and ovarian follicles were collected from gilts on days 2-6 of the follicular phase of the estrous cycle. cDNA derived from ovary and follicle RNA pooled from animals within selection line, treatment day and follicle size was labeled with a fluorescent dye (Cy3 or Cy5) and co-hybridized on microarray slides containing 4,608 follicle-derived probes printed in duplicate. A total of 6 hybridizations were performed with each pair of samples in a “flip-fluor” design. Data extracted from fluorescence intensities obtained from the scanned hybridized slides were analyzed with a mixed-model approach. A total of 92 and 76 clones showed significant RNA expression differences between swine lines in the ovaries and follicle pools, respectively, collected on one or more treatment days. Tertiary analysis with “Self-Organizing Maps” (SOM) methodology was used to identify groups of genes that have similar patterns of expression over the experiment period. More complex analyses are being performed to provide the foundation for future hypothesis-based studies of mechanisms that control ovulation rate in swine and that regulate polygenic control of this complex trait. These results may lead to new approaches for improving the reproductive capability of pigs.