Pig Traits and Genotypic Analysis

Data from 144 pigs (25% Iberian × 75% Landrace), representing 26 full-sib families, from backcrossing five F1 males with 26 Landrace sows was utilized. Details about the management conditions and the phenotype information have been previously reported [65 (link)-67 (link)]. For this study and based on an previous principal components analysis [66 (link)] we selected 15 of the total 48 traits representing the most informative phenotypes within the dataset. Nine of the 15 traits were related to IMF fatty acid (FA) composition in LD muscle, seven correspond to indices of FA metabolism and the last one is the IMF percentage (Additional file 11: Table S8). The Porcine SNP60K BeadChip (Illumina) [68 (link)] was used to genotype a total 197 pigs, including the 144 phenotyped animals and the founder population. Quality control excluded SNPs with minor allele frequency < 5% and with call rate < 95%. A subset of 48,119 SNPs were retained for subsequent analysis, in addition, previously detected polymorphisms in the MTTP, FABP4, FABP5, and ELOVL6 genes were also tested [67 (link),69 (link),70 (link)]. The genomic coordinates of the SNP correspond to the Sus scrofa genome sequence assembly (Sscrofa10.2, August 2011) [71 (link)] and were annotated using as reference the pig assembly 10.2 [ftp://ftp.ncbi.nlm.nih.gov/genomes/Sus_scrofa/GFF/].

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Ramayo-Caldas Y., Ballester M., Fortes M.R., Esteve-Codina A., Castelló A., Noguera J.L., Fernández A.I., Pérez-Enciso M., Reverter A, & Folch J.M. (2014). From SNP co-association to RNA co-expression: Novel insights into gene networks for intramuscular fatty acid composition in porcine. BMC Genomics, 15, 232.

Publication 2014

Porcine SNP60K BeadChip

Animals Conditions management Fabp4 Fatty acid Genes Genomes Genotype Males Metabolism Mttp Muscle Pigs Polymorphisms Sus scrofa

Corresponding Organization :

Other organizations : Consejo Superior de Investigaciones Científicas, Universitat Autònoma de Barcelona, University of Queensland, Institució Catalana de Recerca i Estudis Avançats, Commonwealth Scientific and Industrial Research Organisation

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Variable analysis

independent variables

Genotypes of 48,119 SNPs
Genotypes of previously detected polymorphisms in the MTTP, FABP4, FABP5, and ELOVL6 genes

dependent variables

15 phenotypes representing IMF fatty acid (FA) composition in LD muscle, indices of FA metabolism, and IMF percentage

control variables

Management conditions and phenotype information as previously reported [65-67]

notes

No explicit mention of positive or negative controls.

Annotations

Based on most similar protocols

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