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The aim of this study was to validate previously reported associations between microarray gene expression levels and pork quality traits using real-time PCR. Meat samples and meat quality data from 100 pigs were collected from a different pig breed to the one tested by microarray (Large White versus Pietrain) and a different country of origin (Denmark versus Germany). Ten genes (CARP, MB, CSRP3, TNNC1, VAPB, TNNI1, HSPB1, TNNT1, TIMP-1, RAD-like) were chosen from the original microarray study on the basis of the association between gene expression levels and the meat quality traits meat %, back fat, pH24, drip loss %, colour a*, colour b*, colour L*, WB-SF, SFA, MUFA, PUFA. Real-time PCR detection methods were developed for validation of all ten genes, confirming association with drip loss (two of two genes), ultimate pH (three of four genes), a* (redness) (two of six genes) and L*(lightness) (two of four genes). Furthermore, several new correlations for MUFA and PUFA were established due to additional meat quality trait information on fatty acid composition not available for the microarray study. Regression studies showed that the maximum explanation of the phenotypic variance of the meat quality traits was 50% for the ultimate pH trait using these ten genes only. Additional studies showed that the gene expression of several of the genes was correlated with each other. We conclude that the genes initially selected from the microarray study were robust, explaining variances of the genes for the meat quality traits., (© 2014 Blackwell Verlag GmbH.)

Pathway information provides insight into the biological processes underlying microarray data. Pathway information is widely available for humans and laboratory animals in databases through the internet, but less for other species, for example, livestock. Many software packages use species-specific gene IDs that cannot handle genomics data from other species. We developed a species-independent method to search pathways databases to analyse microarray data. Three PERL scripts were developed that use the names of the genes on the microarray. (1) Add synonyms of gene names by searching the Gene Ontology (GO) database. (2) Search the Kyoto Encyclopaedia of Genes and Genomes (KEGG) database for pathway information using this GO-enriched gene list. (3) Combine the pathway data with the microarray data and visualize the results using color codes indicating regulation. To demonstrate the power of the method, we used a previously reported chicken microarray experiment investigating line-specific reactions to Salmonella infection as an example. [ABSTRACT FROM AUTHOR]

The full-length cDNA of porcine genes (PSME1andPSME2) encoding proteasome activators PA28α- andβ-subunits were obtained by the rapid amplification of cDNA ends (RACE). The nucleotide sequences and the predicted protein sequences share high sequence identity with their mammalian counterparts. The reverse transcriptase-polymerase chain reaction (RT-PCR) revealed that porcinePSME1andPSME2genes are expressed in all eight tissues studied (liver, spleen, bladder, small intestine, kidney, heart, skeletal muscle and lung). The full-length genomic DNA of the porcinePSME1andPSME2genes were amplified by PCR. These two genes shared the same structure and were similar in size. A C/T single nucleotide polymorphism inPSME1intron 8 detected as anSphI PCR-restriction fragment length polymorphism (PCR–RFLP) shows allele frequency differences between Meishan, Tibetan, Large White, Qingping, and Duroc pigs. The association analysis using two experimental GY selection lines selected for growth rate or leanness suggested that thePSME1genotype was associated with weaning weight. Analyses of somatic cell hybrid (SCHP) and radiation hybrid (IMpRH) panels revealed that both genes map to SSC7q15.3-q21 and closely linked to the T-cell receptorα (TCRA) gene. [ABSTRACT FROM AUTHOR]

The leptin receptor ( LEPR) gene consists of 20 exons divided over 1.75 Mb. Parts of bovine LEPR exon 4 (79 bp), exon 11 (95 bp) and exon 20 (513 bp) of 20 cows (Holstein-Friesian) were sequenced ( ; ; ) in an attempt to find polymorphisms. In exons 4 and 11 no SNPs were found. In exon 20, a T to C missense mutation was found at nucleotide 115, which causes an amino acid substitution at residue 945 (T945M). Frequencies for alleles C and T were 0.93 and 0.07 respectively, in a population of 323 Holstein-Friesian cows and TT animals were not detected. Using genotypes of these cows an association study was performed for leptin concentrations during late pregnancy and lactation. Leptin concentrations were determined by radioimmunoassay (RIA). The T945M mutation showed an association with circulating leptin concentrations only during late pregnancy ( P < 0.05) but not during lactation ( P > 0.05). The CC genotype had higher concentrations than the CT genotype during this period. A combined effect with previously described leptin polymorphisms on prepartum leptin concentrations was observed, with one genotype combination having significantly lower levels of leptin up to 50 days, but interaction effects were not significant. The T945M polymorphism may have induced a structural change in the intracellular domain of the LEPR, which may have influenced the signal transduction pathway. However, the effect was found only for the heterozygous genotype because the TT genotype was not detected in this population of 323 Holstein-Friesian cows. [ABSTRACT FROM AUTHOR]