ARS | Publication request: A LINEAR MIXED MODEL APPROACH TO IDENTIFYING EXPRESSED SINGLE FEATURE POLYMORPHISMS

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: August 5, 2006
Publication Date: November 12, 2006
Citation: Bischoff, S.R., Tsai, S., Freking, B.A., Nonneman, D.J., Rohrer, G.A., Piedrahita, J.A. 2006. A linear mixed model approach to identifying expressed single feature polymorphisms [abstract]. International Mammalian Genome Society (IMGS) Annual Meeting, Charleston, SC, November, 2006. Abstract #P12.

Technical Abstract: Using Affymetrix Porcine short oligonucleotide microarrays, we developed a novel approach to identifying expressed single feature polymorphisms (SFP) between two breeds of pigs, Meishan and white composite (1/4 each of Large White, Landrace, Chester White, and Yorkshire). Gene specific linear mixed models were fit to each of the log2 transformed probe intensities on these arrays, using fixed effects for breed, probe, and breed by probe interaction, and a random effect for array. After correcting for average breed effects, we identified 2,452 probes (approximately 1% of all probes represented on the array) with significant probe by breed interactions as putative SFPs at a significance threshold of q<0.05. We developed pyrosequencing assays to confirm the identity of a selection of high confidence SFPs. All working pyrosequencing assays corroborated the existence of polymorphisms within the probe sequence. By this method we detected both transition and transversion single nucleotide polymorphisms, as well as insertions/deletions. These results demonstrate that this approach can sensitively identify polymorphisms between two breeds and/or lines of any species for which a short oligonucleotide array is available, and can be used to rapidly develop markers for genetic mapping and association analysis in species where high density genotyping platforms are otherwise unavailable. This work was supported by a National Research Initiative Grant (2005-35604-15343) from the USDA Cooperative State Research, Education, and Extension Service to JP and BF and by a NSF Integrative Graduate Education and Research Traineeship (9987555) to ST.