ARS | Publication request: Evidence of Allelic Suppression for Transcripts Expressed in Day 30 Pig Embryos by SNP Genotyping

Submitted to: Midwestern Section of the American Society of Animal Science
Publication Type: Abstract
Publication Acceptance Date: November 16, 2007
Publication Date: September 22, 2008
Publisher's URL: http://asas.org
Reprint URL: http://asas.org/abstracts/2008sectional/Supplement_3-38.pdf
Citation: Freking, B.A., Nonneman, D.J., Rohrer, G.A., Bischoff, S.R., Tsai, S., Piedrahita, J.A. 2008. Evidence of allelic suppression for transcripts expressed in day 30 pig embryos by SNP genotyping [abstract]. Journal of Animal Science. 86(E-Suppl. 3):51. Abstract #44.

Technical Abstract: Genomic imprinting results in alleles being differentially expressed in a parent-of-origin specific manner. Parthenogenetic and biparental pig embryo gene expression profiles were compared using three cDNA microarray platforms. Comparison of the profiles of the two tissue types indicated differential expression for maternally and paternally imprinted genes previously established in the human or mouse as well as novel loci without prior imprinting evidence. Genomic DNA from parents, two Meishan and four occidental white composite, and two crossbred embryos were sequenced for discovery of single nucleotide polymorphisms (SNP) within transcribed regions of targets. Successful amplicons (n=178) were sequenced both directions and SNP (n=303) were identified. Four litters (n=44 embryos) of crossbred d30 embryos were used to test differential allele expression using 138 SNP assays from 49 unique loci. Amplification products from templates representing genomic, as well as cDNA from fetal liver were generated in multiplex Sequenom MassArray assays. Peak areas for cDNA templates were adjusted to correct for ratio of alleles in genomic DNA within each embryo. Frequency of the cDNA allele was expressed as an absolute value deviation from 0.50. A mean value for this deviation was calculated for each assay and a one tailed t-test was used to detect significant deviations of allele frequency from 0.5. Thirty-six loci were detected with significant allelic suppression (P < 0.05). Seventeen of these loci were previously known imprinted genes and nineteen loci were novel. These data allow a more complete estimate of the conservation of imprinted loci across mammals as well as provide data for novel imprinted genes in the pig.