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New predictors for pork quality derived from gene expression profiles of skeletal muscle during prenatal development

Exploitable results

The various techniques of expression profiling that were applied (including subtractive hybridisation, microarray analyses and differential display) revealed in total of 584 genes that were either temporal regulated during myogenesis or differentially expressed between the two breeds. Selection of loci for further analysis was based on: - The consistency of the expression pattern and its reproducibility; - Knowledge on the function of the particular gene (categorized as structural gene, metabolic, translational, transcriptional, receptor/endocrine factors, differentiation, proliferation and "unknown"); - The map position allowing giving preference to those genes located in QTL regions for meat quality traits. Other criteria to establish a short list of candidate genes were possible repeated detection by more than one method; preference for breed-specific expressed genes with a higher likelihood to represent genetic variation useful in breeding than temporal regulated genes and the desired for an equal proportion of Pietrain- and Duroc-preferentially expressed genes. The short list of functional candidate genes covers 52 loci. For these loci the mRNA expression pattern was analysed also by qRT-PCR in the seven stages of embryonic development for both breeds. The results indicate that there are differences in the expression level of the majority of the analysed genes between breeds or between stages or between breeds within stages. Screening for polymorphism was done by comparative sequencing of a set of DNAs of animals of the breeds Duroc, Pietrain, and German Landrace shared by all partners. In summary in 36 out of 49 genes screened for polymorphism either SNPs or InDels were detected that are suitable for genotyping. PCR-RFLPs, PCR-SSCPs, single base extension assays, TaqMan assays, as well as melting curve analysis protocols were established for high throughput genotyping of the polymorphisms.
A short list of functional candidate genes covering 52 loci was established. Screening for polymorphism was done by comparative sequencing of a set of DNAs of animals of the breeds Duroc, Pietrain, and German Landrace shared by all partners. In summary in 36 out of 49 genes screened for polymorphism either SNPs or InDels were detected that are suitable for genotyping. PCR-RFLPs, PCR-SSCPs, single base extension assays, TaqMan assays, as well as melting curve analysis protocols were established for high throughput genotyping of the polymorphisms. First selective genotyping was performed for 22 loci. Chi-square analyses as well as analyses of variance indicated possible association with drip loss of a number of candidate genes. The most promising twelve loci were finally selected to perform the association analysis using the whole set of sample and data. Pordictor has reported evidence for 10 genetic markers in linkage equilibrium (LE-marker) that are significantly associated with several pork quality traits within population. A short summary of perspectives for each gene: - ANK1: there are some significant genetic effects for driploss and associated traits in Duroc crossbreds, but gene effects are neither clearly additive nor dominant. - CA3: there are some major gene effects across populations, especially for conductivity, cookloss and intramuscular fat. This seems an interesting gene for further research. - EPOR: there are some significant genetic effects for several traits across populations, especially for driploss and associated traits (including pH) but gene effects are not consistent for traits across populations and most of them are neither clearly additive nor dominant. Further research for this gene is relevant for driploss related traits. - MYOP: there are some major gene effects across populations for pH and loin depth/weight. This seems an interesting gene for further research and perhaps implementation in breeding programs for both traits. - bR10D1: there are some significant genetic effects for several traits, but gene effects are not clearly additive nor dominant, partly due to the distribution of the alleles. - PDGFRA: the gene with least interesting results. - HGMA2: this gene has only significant effects in 1 population. - ELKS: there are some major gene effects across populations for colour and lean weight. This seems an interesting gene for further research and perhaps implementation in breeding programs for both traits. - NME1: there are some significant genetic effects for several traits, but gene effects are neither clearly additive nor dominant, partly due to the distribution of the alleles. - TTN: there are some significant genetic effects for several traits, but gene effects are neither clearly additive nor dominant.
The various techniques of expression profiling that were applied (including subtractive hybridisation, microarray analyses and differential display) revealed in total of 584 genes that were either temporal regulated during myogenesis or differentially expressed between the two breeds.

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