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Weisz F.,Academy of Sciences of the Czech Republic | Weisz F.,Mendel University in Brno | Bartenschlager H.,University of Hohenheim | Knoll A.,Academy of Sciences of the Czech Republic | And 5 more authors.
Animal Genetics | Year: 2012

The serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 (SERPINE1) gene encodes plasminogen activator inhibitor type 1 (PAI), which is the major physiological inhibitor of tissue-type and urokinase-type plasminogen activators and plays a role in obesity and insulin resistance in women but not in men. We detected SNP FN396538:g.566G>A in intron 3 and a non-synonymous substitution NM-213910:c.612A>G in exon 3 (p.Ile159Val) and mapped the gene to position 8.4 cM on the linkage map of chromosome 3. Association analyses were conducted on the 12th-15th generation of the Meishan × Large White (MLW) cross (n = 565), with records for weight at the end of test, lifetime daily gain, test time daily gain, loin depth and backfat depth, as well as on a European wild boar × Meishan (W × M) F2 population (n = 333) with 47 traits recorded for carcass composition and meat quality. Analyses performed across the entire MLW population or in the male animals did not show any trait significantly associated with the loci studied. In female animals, both SNPs were associated with loin depth at nominal P < 0.05 with adjusted P values equal to 0.051 (g.566) and 0.057 (c.612). Differences between homozygotes were up to 0.65 SD. In the entire W × M population and female animals, SERPINE1 was significantly associated at adjusted P < 0.05 in descending order with muscling, growth and fat accretion and in male animals with meat quality (R-value). In the studied populations, allele effects were in opposite directions, which implies that the SNPs are markers that are in linkage disequilibrium with a causative mutation. © 2011 The Authors, Animal Genetics © 2011 Stichting International Foundation for Animal Genetics. Source


Scheffler T.L.,Virginia Polytechnic Institute and State University | Scheffler J.M.,Virginia Polytechnic Institute and State University | Kasten S.C.,Virginia Polytechnic Institute and State University | Sosnicki A.A.,Genus PIC | Gerrard D.E.,Virginia Polytechnic Institute and State University
Meat Science | Year: 2013

Extent of postmortem pH decline influences meat quality development. To better understand physiological determination of ultimate pH (pHu), we utilized female and castrated male pigs from a line whose selection index includes differentiated pHu. All genotypes of AMP-activated protein kinase γ3 subunit (AMPKγ3) V199I site were present. The mutant 199II genotype increased pHu, but only in castrated males. Genotype affected glycolytic potential (GP), but GP was weakly associated with pHu. A subset of animals was selected based on low (-Gly) and high (+Gly) residual glycogen content, and compared with AMPKγ3 200Q, which is associated with low pHu. Both +Gly and 200Q muscle contained glycolytic substrate at 24h; however, 200Q muscle generated low pHu and greater lactate compared to +Gly. Additionally,-Gly and +Gly groups exhibited similar pHu despite a large difference in GP. In conclusion, high GP does not appear to directly impact the extent of postmortem pH decline. © 2013 The Authors. Source


Masopust M.,Academy of Sciences of the Czech Republic | Vykoukalova Z.,Mendel University in Brno | Knoll A.,Mendel University in Brno | Bartenschlager H.,University of Hohenheim | And 4 more authors.
Molecular Biology Reports | Year: 2011

Using PCR and inverse PCR techniques we obtained a 4,498 bp nucleotide sequence FN424076 encompassing the complete coding sequence of the porcine insulin receptor substrate 4 (IRS4) gene and its proximal promoter. The 1,269 amino acid porcine protein deduced from the nucleotide sequence shares 92% identity with the human IRS4 and possesses the same domains and the same number of tyrosine phosphorylation motifs as the human protein. We detected substitution FN424076:g.96C\G in the promoter region that segregates in Meishan and a synonymous substitution FN424076:g.1829T\C in the coding sequence with allele C present only in Meishan. Linkage mapping placed the IRS4 gene at position 82 cM on the current USDA-USMARC linkage map of porcine chromosome X. Association analyses were performed on 555 animals of 12th-15th generation of the Meishan 9 Large White cross and showed that both SNPs were highly significantly associated with backfat depth (P = 0.0005) and that the SNP FN424076:g1829T\C was also associated with loin depth (P = 0.017). The Meishan alleles increased back fat depth and decreased loin depth. IRS4 can be considered a positional candidate gene for at least some of the QTL located at the centromeric region of porcine chromosome X. © Springer Science+Business Media B.V. 2010. Source


Lourenco D.A.L.,University of Georgia | Misztal I.,University of Georgia | Tsuruta S.,University of Georgia | Aguilar I.,Instituto Nacional Of Investigacion Agropecuaria | And 3 more authors.
Journal of Dairy Science | Year: 2014

Data sets of US Holsteins, Israeli Holsteins, and pigs from PIC (a Genus company, Hendersonville, TN) were used to evaluate the effect of different numbers of generations on ability to predict genomic breeding values of young genotyped animals. The influence of including only 2 generations of ancestors (A2) or all ancestors (Af) was also investigated. A total of 34,506 US Holsteins, 1,305 Israeli Holsteins, and 5,236 pigs were genotyped. The evaluations were computed by traditional BLUP and single-step genomic BLUP, and computing performance was assessed for the latter method. For the 2 Holstein data sets, coefficients of determination (R2) and regression (δ) of deregressed evaluations from a full data set with records up to 2011 on estimated breeding values and genomic estimated breeding values from the truncated data sets were computed. The thresholds for data deletion were set by intervals of 5 yr, based on the average generation interval in dairy cattle. For the PIC data set, correlations between corrected phenotypes and estimated or genomic estimated breeding values were used to evaluate predictive ability on young animals born in 2010 and 2011. The reduced data set contained data up to 2009, and the thresholds were set based on an average generation interval of 3 yr. The number of generations that could be deleted without a reduction in accuracy depended on data structure and trait. For US Holsteins, removing 3 and 4 generations of data did not reduce accuracy of evaluations for final score in Af and A2 scenarios, respectively. For Israeli Holsteins, the accuracies for milk, fat, and protein yields were the highest when only phenotypes recorded in 2000 and later were included and full pedigrees were applied. Of the 135 Israeli bulls with genotypes (validation set) and daughter records only in the complete data set, 38 and 97 were sons of Israeli and foreign bulls, respectively. Although more phenotypic data increased the prediction accuracy for sons of Israeli bulls, the reverse was true for sons of foreign bulls. Also, more phenotypic data caused large inflation of genomic estimated breeding values for sons of foreign bulls, whereas the opposite was true with the deletion of all but the most recent phenotypic data. Results for protein and fat percentage were different from those for milk, fat, and protein yields; however, relatively, the changes in coefficients of determination and regression were smaller for percentage traits. For PIC data set, removing data from up to 5 generations did not erode predictive ability for genotyped animals for the 2 reproductive traits used in validation. Given the data used in this study, truncating old data reduces computation requirements but does not decrease the accuracy. For small populations that include local and imported animals, truncation may be beneficial for one group of animals and detrimental to another group. © 2014 American Dairy Science Association. Source

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