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Single nucleotide polymorphisms (SNPs) represent the most common form of DNA sequence variation in mammalian livestock genomes. While the past decade has witnessed major advances in SNP genotyping technologies, genotyping errors caused, in part, by the biochemistry underlying the genotyping platform used, can occur. These errors can distort project results and conclusions and can result in incorrect decisions in animal management and breeding programs; hence, SNP genotype calls must be accurate and reliable. In this study, 263 Bos spp. samples were genotyped commercially for a total of 16 SNPs. Of the total possible 4,208 SNP genotypes, 4,179 SNP genotypes were generated, yielding a genotype call rate of 99.31% (standard deviation ± 0.93%). Between 110 and 263 samples were subsequently re-genotyped by us for all 16 markers using a custom-designed SNP genotyping platform, and of the possible 3,819 genotypes a total of 3,768 genotypes were generated (98.70% genotype call rate, SD ± 1.89%). A total of 3,744 duplicate genotypes were generated for both genotyping platforms, and comparison of the genotype calls for both methods revealed 3,741 concordant SNP genotype call rates (99.92% SNP genotype concordance rate). These data indicate that both genotyping methods used can provide livestock geneticists with reliable, reproducible SNP genotypic data for in-depth statistical analysis.

peer-reviewed Genetic (or ‘genomic’) imprinting, a feature of approximately 100 mammalian genes, results in monoallelic expression from one of the two parentally inherited chromosomes. To date, most studies have been directed on imprinted genes in murine or human models; however, there is burgeoning interest in the effects of imprinted genes in domestic livestock species. In particular, attention has focused on imprinted genes that influence foetal growth and development and that are associated with several economically important production traits in cattle, sheep and pigs. We have re-sequenced regions in 20 candidate bovine imprinted genes in order to validate single nucleotide polymorphisms (SNPs) that may influence important production traits in cattle. Putative SNPs detected via re-sequencing were subsequently re-formatted for high-throughput SNP genotyping in 185 cattle samples comprising 138 performance-tested European Bos taurus (all Limousin bulls), 29 African B. taurus and 18 Indian B. indicus samples. Analysis of the resulting genotypic data identified 117 validated SNPs. Preliminary genotype–phenotype association analyses using 83 SNPs that were polymorphic in the Limousin samples with minor allele frequencies >0.05 revealed significant associations between two candidate bovine imprinted genes and a range of important beef production traits: average daily gain, average feed intake, live weight, feed conversion ratio, residual feed intake and residual gain. These genes were the Ras proteinspecific guanine nucleotide releasing factor gene ( RASGRF1) and the zinc finger, imprinted 2 gene ( ZIM2). Despite the relatively small sample size used in these analyses, the observed associations with production traits are supported by the purported biological function of the RASGRF1 and ZIM2 gene products. These results support the hypothesis that imprinted genes contribute significantly to important complex production traits in cattle. Furthermore, these SNPs may be usefully incorporated into future marker-assisted and genomic selection breeding schemes. Department of Agriculture, Fisheries and Food, Ireland - Research Stimulus Fund (Grant RSF 06 406); Science Foundation Ireland Investigator Programme Grant (SFI/01/F.1/B028).

Basal hormone/metabolite concentrations and responses to intravenous challenges of glucose, insulin and epinephrine were examined in Friesian cows from selection lines of low or high genetic merit treated with recombinantly-derived bovine somatotropin (bST) or control formulation in a 2 x 2 factorial design. Cows from the low genetic merit (low breeding index, LBI) line had previously been shown to be more responsive to the galactopoietic effects of bST (50 mg/day) than those from the high breeding index (HBI) line. Despite this, comparisons of metabolic differences were not confounded by differences in energy balance because bST treatment had also caused an increase in voluntary intake of cut pasture. Circulating levels of somatotropin, insulin-like growth factor-I (IGF-I) and insulin were greater in bST-treated than control cows but neither bST treatment nor selection line influenced basal concentrations of glucose, non-esterified fatty acids (NEFA), beta-hydroxybutyrate, urea or creatinine. Treatment with bST produced a small increase in sensitivity of cows to the lipolytic effects of epinephrine and this effect was similar in both selection lines. HBI cows had greater circulating insulin levels following the glucose challenge than LBI cows but bST treatment did not affect the insulin response to exogenous glucose. Whereas bST treatment retarded the glycogenolytic response to epinephrine and the clearance of blood glucose in response to insulin in LBI cows, it had no effect on epinephrine-stimulated glycogenolysis, and caused enhanced glucose clearance in response to insulin, in HBI cows. Results are consistent with bST altering the homeorhetic control of metabolism but do not adequately explain the greater responsiveness of LBI cows to the galactopoietic effects of bST.

peer-reviewed Background: Bovine tuberculosis is a significant veterinary and financial problem in many parts of the world. Although many factors influence infection and progression of the disease, there is a host genetic component and dissection of this may enlighten on the wider biology of host response to tuberculosis. However, a binary phenotype of presence/absence of infection presents a noisy signal for genomewide association study. Methodology/Principal Findings: We calculated a composite phenotype of genetic merit for TB susceptibility based on disease incidence in daughters of elite sires used for artificial insemination in the Irish dairy herd. This robust measure was compared with 44,426 SNP genotypes in the most informative 307 subjects in a genome wide association analysis. Three SNPs in a 65 kb genomic region on BTA 22 were associated (i.e. p,1025, peaking at position 59588069, p = 4.0261026) with tuberculosis susceptibility. Conclusions/Significance: A genomic region on BTA 22 was suggestively associated with tuberculosis susceptibility; it contains the taurine transporter gene SLC6A6, or TauT, which is known to function in the immune system but has not previously been investigated for its role in tuberculosis infection.