Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle.

This corrects the article DOI: 10.1038/hdy.2016.79.

Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle.

The domestication of taurine cattle initiated ~10 000 years ago in the Near East from a wild aurochs (Bos primigenius) population followed by their dispersal through migration of agriculturalists to Europe. Although gene flow from wild aurochs still present at the time of this early dispersion is still debated, some of the extant primitive cattle populations are believed to possess the aurochs-like primitive features. In this study, we use genome-wide single nucleotide polymorphisms to assess relationship, admixture patterns and demographic history of an ancient aurochs sample and European cattle populations, several of which have primitive features and are suitable for extensive management. The principal component analysis, the model-based clustering and a distance-based network analysis support previous works suggesting different histories for north-western and southern European cattle. Population admixture analysis indicates a zebu gene flow in the Balkan and Italian Podolic cattle populations. Our analysis supports the previous report of gene flow between British and Irish primitive cattle populations and local aurochs. In addition, we show evidence of aurochs gene flow in the Iberian cattle populations indicating wide geographical distribution of the aurochs. Runs of homozygosity (ROH) reveal that demographic processes like genetic isolation and breed formation have contributed to genomic variations of European cattle populations. The ROH also indicate recent inbreeding in southern European cattle populations. We conclude that in addition to factors such as ancient human migrations, isolation by distance and cross-breeding, gene flow between domestic and wild-cattle populations also has shaped genomic composition of European cattle populations.

Iodine supplementation of the pregnant dam alters intestinal gene expression and immunoglobulin uptake in the newborn lamb.

Excess iodine intake by the pregnant dam reduces lamb serum antibody concentration, specifically immunoglobulin G (IgG). An experiment was conducted to investigate the mechanisms under pinning the reduced serum IgG concentration at 24 h postpartum in the progeny of iodine supplemented dams. Forty-five mature twin bearing ewes (n=15/treatment) were allocated to one of three dietary treatments as follows: basal diet (Control); basal diet plus 26.6 mg of iodine per ewe per day as calcium iodate (CaIO3); or potassium iodide (KI). Ewes were individually housed and fed from d 119 of gestation until parturition. All lambs received colostrum at 1, 10 and 18 h postpartum via stomach tube. At 1 h postpartum lambs from the control and an iodine supplemented treatment (n=10 per treatment from control and CaIO3) were euthanised before colostrum consumption and ileal segments isolated to determine the gene expression profile of a panel of genes identified as having a role in antibody transfer. Preceding euthanasia, lambs were blood sampled for determination of serum IgG, total thyroxine and free tri-iodothyronine concentrations. Progeny of CaIO3 supplemented dams had lower tri-iodothyronine concentrations (P<0.01) at 1 h postpartum and lower serum IgG concentrations (P<0.001) at 24 h postpartum when compared with the progeny of control dams. Iodine (CaIO3) supplementation of the dam increased the relative expression (P<0.05) of the B2M, PIGR and MYC genes in the ileum of the lamb, before colostrum consumption; while the expression of THRB declined when compared with the progeny of C dams (P<0.01). In conclusion, the results of this study show that it is the actual inclusion of excess iodine in the diet of the ewe, regardless of the carrier element, that negatively affects passive transfer in the newborn lamb. This study presents novel data describing the relationship between maternal iodine nutrition and its effect on the thyroid hormone status and subsequent gene expression in the newborn lamb; which results in a failure of passive transfer and a decline in serum IgG concentration.

Imprinted loci in domestic livestock species as epigenomic targets for artificial selection of complex traits.

The phenomenon of genomic imprinting, whereby a subset of mammalian genes display parent-of-origin-specific monoallelic expression, is one of the most active areas of epigenetics research. Over the past two decades, more than 100 imprinted mammalian genes have been identified, while considerable advances have been made in elucidating the molecular mechanisms governing imprinting. These studies have helped to unravel the epigenome--a separate layer of regulatory information contained in eukaryotic chromosomes that influences gene expression and phenotypes without involving changes to the underlying DNA sequence. Although most studies of genomic imprinting in mammals have focussed on mouse models or human biomedical disorders, there is burgeoning interest in the phenotypic effects of imprinted genes in domestic livestock species. In particular, research has focused on imprinted genes influencing foetal growth and development, which are associated with economically important production traits in cattle, sheep and pigs. These findings, when coupled with the data emerging from the various different livestock genome projects, have major implications for the future of animal breeding, health and management. Here, we review current scientific knowledge regarding genomic imprinting in livestock species and evaluate how this information can be used in modern livestock improvement programmes.

Expression of key genes of the somatotropic axis in longissimus dorsi muscle of beef heifers phenotypically divergent for residual feed intake.

This study evaluated the effect of residual feed intake (RFI) on the expression of constituent genes of the somatotropic axis in skeletal muscle across 2 diverse dietary regimes. Beef heifers (n=86; initial BW=191.8 kg; SD=37) fed a low-forage (LF) total mixed ration comprising 70:30 concentrate:corn silage (11.0 MJ ME/kg DM) were ranked on RFI. The 10 greatest- (high-RFI) and 10 lowest- (low-RFI) ranking animals were selected for the current study. Biopsies of the LM were harvested at the end of LF dietary period and again after a 6-wk period during which heifers were offered a high-forage grass-silage-only diet (9.7 MJ ME/kg DM). Real-time PCR was used to quantify mRNA transcripts of 11 genes including IGF-1, IGF-2, their receptors (IGF-1R and IGF-2R), 6 IGFBP, and GH receptor (GHR). There was no evidence of a RFI phenotype×diet interaction (P>0.10) for any of the genes examined. An effect (P=0.02) of RFI phenotype was evident for the abundance of GHR mRNA, with twofold greater expression detected in the low-RFI compared with the high-RFI phenotype. Additionally, mRNA expression of IGF-1R was upregulated (1.7-fold; P=0.04) for the low-RFI compared with high-RFI heifers. Residual feed intake was negatively associated with IGF-1R (r=-0.41; P<0.05) and GHR (r=-0.50; P<0.05) mRNA. Moderate negative correlation coefficients were also observed between feed conversion ratio (F:G) and gene expression levels for IGF-1R (r=-0.61; P<0.01) as well as for GHR (r=-0.49; P<0.05). Moreover, associations were detected between DMI with IGF-1R (r=-0.42; P=0.07) and IGF-2R (r=0.40; P=0.07). The IGF-1R mRNA was positively correlated with IGF-1 (r=0.34; P<0.05) and IGF-2 (r=0.71; P<0.001) mRNA. Associations between IGF-1R and IGF-2R with IGFBP5 and GHR were positive (ranging from, r=0.32 to 0.49). These data suggest that components of the somatotropic axis expressed within muscle tissue may be involved in the regulation of feed efficiency in beef cattle. This effect is apparently consistent across contrasting dietary regimens.

PHLDA2 is an imprinted gene in cattle.

Genomic imprinting is an epigenetic non-Mendelian phenomenon found predominantly in placental mammals. Imprinted genes display differential expression in the offspring depending on whether the gene is maternally or paternally inherited. Currently, some 100 imprinted genes have been reported in mammals, and while some of these genes are imprinted across most mammalian species, others have been shown to be imprinted in only a few species. The PHLDA2 gene that codes for a pleckstrin homology-like domain, family A (member 2), protein has to date been shown to be a maternally expressed imprinted gene in humans, mice and pigs. Genes subject to imprinting can have major effects on mammalian growth, development and disease. For instance, disruption of imprinted genes can lead to aberrant growth syndromes in cloned domestic mammals, and it has been demonstrated that PHLDA2 mRNA expression levels are aberrant in the placenta of somatic clones of cattle. In this study, we demonstrate that PHLDA2 is expressed across a range of cattle foetal tissues and stages and provide the first evidence that PHLDA2 is a monoallelically expressed imprinted gene in cattle foetal tissues, and also in the bovine placenta.

Single nucleotide polymorphisms in the imprinted bovine insulin-like growth factor 2 receptor gene (IGF2R) are associated with body size traits in Irish Holstein-Friesian cattle.

The regulation of the bioavailability of insulin-like growth factors (IGFs) is critical for normal mammalian growth and development. The imprinted insulin-like growth factor 2 receptor gene (IGF2R) encodes a transmembrane protein receptor that acts to sequester and degrade excess circulating insulin-like growth factor 2 (IGF-II) - a potent foetal mitogen - and is considered an important inhibitor of growth. Consequently, IGF2R may serve as a candidate gene underlying important growth- and body-related quantitative traits in domestic mammalian livestock. In this study, we have quantified genotype-phenotype associations between three previously validated intronic bovine IGF2R single nucleotide polymorphisms (SNPs) (IGF2R:g.64614T>C, IGF2R:g.65037T>C and IGF2R:g.86262C>T) and a range of performance traits in 848 progeny-tested Irish Holstein-Friesian artificial insemination sires. Notably, all three polymorphisms analysed were associated (P ≤ 0.05) with at least one of a number of performance traits related to animal body size: angularity, body depth, chest width, rump width, and animal stature. In addition, the C-to-T transition at the IGF2R:g.65037T>C polymorphism was positively associated with cow carcass weight and angularity. Correction for multiple testing resulted in the retention of two genotype-phenotype associations (animal stature and rump width). None of the SNPs analysed were associated with any of the milk traits examined. Analysis of pairwise r(2) measures of linkage disequilibrium between all three assayed SNPs ranged between 0.41 and 0.79, suggesting that some of the observed SNP associations with performance may be independent. To our knowledge, this is one of the first studies demonstrating associations between IGF2R polymorphisms and growth- and body-related traits in cattle. These results also support the increasing body of evidence that imprinted genes harbour polymorphisms that contribute to heritable variation in phenotypic traits in domestic livestock species.

Associations between newly discovered polymorphisms in the Bos taurus growth hormone receptor gene and performance traits in Holstein-Friesian dairy cattle.

Variations in the growth hormone receptor (GHR) gene sequence are associated with performance traits in cattle. For example, the single nucleotide polymorphism (SNP) F279Y in transmembrane exon 8 has a strong association with milk yield. In this study, 32 previously unreported, putative novel SNPs (31 in the 5' non-coding region) were identified by resequencing ∼19 kb of the GHR gene in genomic DNA from 22 cattle of multiple breeds. A population of 848 Holstein-Friesian AI sires was subsequently genotyped for the 32 putative novel SNPs and seven published SNPs (including F279Y, one in exon 1A promoter and five in exon 10). Associations between each segregating SNP and genetic merit for performance were quantified in the 848 Holstein-Friesians using weighted animal linear mixed models. Six of the published SNPs and seven of the novel SNPs were associated with at least one of the traits--milk yield, fat yield, protein yield, fat percentage, protein percentage, somatic cell score, calving interval, survival and growth and size traits. Even when the allelic substitution effect (P < 0.001) of F279Y was accounted for, the allelic substitution effect of one of the novel SNPs (GHR4.2) in the 5' non-coding region of GHR was associated with a lactation milk yield of 37.46 kg (P < 0.001). GHR4.2 and F279Y were not in linkage disequilibrium (r(2) = 0.00, D' = 0.04) in the 848 Holstein-Friesians, indicating that their association with milk yield was independent.

Associations between novel single nucleotide polymorphisms in the Bos taurus growth hormone gene and performance traits in Holstein-Friesian dairy cattle.

Growth hormone, produced in the anterior pituitary gland, stimulates the release of insulin-like growth factor-I from the liver and is of critical importance in the control of nutrient utilization and partitioning for lactogenesis, fertility, growth, and development in cattle. The aim of this study was to discover novel polymorphisms in the bovine growth hormone gene (GH1) and to quantify their association with performance using estimates of genetic merit on 848 Holstein-Friesian AI (artificial insemination) dairy sires. Associations with previously reported polymorphisms in the bovine GH1 gene were also undertaken. A total of 38 novel single nucleotide polymorphisms (SNP) were identified across a panel of 22 beef and dairy cattle by sequence analysis of the 5' promoter, intronic, exonic, and 3' regulatory regions, encompassing approximately 7 kb of the GH1 gene. Following multiple regression analysis on all SNP, associations were identified between 11 SNP (2 novel and 9 previously identified) and milk fat and protein yield, milk composition, somatic cell score, survival, body condition score, and body size. The G allele of a previously identified SNP in exon 5 at position 2141 of the GH1 sequence, resulting in a nonsynonymous substitution, was associated with decreased milk protein yield. The C allele of a novel SNP, GH32, was associated with inferior carcass conformation. In addition, the T allele of a previously characterized SNP, GH35, was associated with decreased survival. Both GH24 (novel) and GH35 were independently associated with somatic cell count, and 3 SNP, GH21, 2291, and GH35, were independently associated with body depth. Furthermore, 2 SNP, GH24 and GH63, were independently associated with carcass fat. Results of this study further demonstrate the multifaceted influences of GH1 on milk production, fertility, and growth-related traits in cattle.

High concordance of bovine single nucleotide polymorphism genotypes generated using two independent genotyping strategies.

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.

Technical note: High fidelity of whole-genome amplified sheep (Ovis aries) deoxyribonucleic acid using a high-density single nucleotide polymorphism array-based genotyping platform.

Advances in high-throughput genotyping technologies have afforded researchers the opportunity to study ever-increasing numbers of SNP in animal genomes. However, many studies encounter difficulties in obtaining sufficient quantities of high-quality DNA for such analyses, particularly when the source biological material is limited or degraded. The recent development of in vitro whole-genome amplification approaches has permitted researchers to circumvent these challenges by increasing the amount of usable DNA in normally small-quantity samples. Here, we assess the performance of whole-genome amplification products generated from ovine genomic DNA using a high-throughput SNP genotyping platform, the newly developed Illumina ovineSNP50 BeadChip. Our results demonstrate a high genotype call rate for conventional genomic DNA and whole-genome amplified genomic DNA. The data also reveal an exceptionally high concordance rate ( > or = 99%) between the genotypes generated from whole-genome amplified products and their conventional genomic DNA counterparts. This study supports the use of whole-genome amplification as a viable solution for the analysis of high-density SNP genotypic data using compromised or limited starting material.

A catalogue of validated single nucleotide polymorphisms in bovine orthologs of mammalian imprinted genes and associations with beef production traits.

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 protein-specific 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.

A partial african ancestry for the creole cattle populations of the Caribbean.

Seventy-eight cattle samples from three Creole Caribbean islands and one Brazilian breed were analyzed for sequence variation in the hypervariable segment of the mitochondrial DNA control region. Seventy-three samples displayed Bos taurus haplotypes, and five samples exhibited haplotypes that were of Bos indicus ancestry. Phylogenetic analysis revealed that all sampled B. taurus sequences fell into two distinct clusters with separate African and European origins. European sequences were encountered in each population; however, the distribution of African haplotypes was uneven, with the highest proportion of African influence found in the Guadeloupe Creole. The reduced levels of African haplotypic variation within the Caribbean and Brazilian are consistent with prior founder effects. Additionally, genetic variation at three microsatellite loci illustrated African influence uniquely in the Guadeloupe Creole. Collectively, the data suggest that this African influence is, at least in part, attributable to the historical importation of African cattle to the Americas. Furthermore, alleles of B. indicus ancestry were detected at appreciable frequencies in all Caribbean Creole populations and may reflect zebu introgressions from either West Africa or the Indian subcontinent.

Genetic evidence for Near-Eastern origins of European cattle.

The limited ranges of the wild progenitors of many of the primary European domestic species point to their origins further east in Anatolia or the fertile crescent. The wild ox (Bos primigenius), however, ranged widely and it is unknown whether it was domesticated within Europe as one feature of a local contribution to the farming economy. Here we examine mitochondrial DNA control-region sequence variation from 392 extant animals sampled from Europe, Africa and the Near East, and compare this with data from four extinct British wild oxen. The ancient sequences cluster tightly in a phylogenetic analysis and are clearly distinct from modern cattle. Network analysis of modern Bos taurus identifies four star-like clusters of haplotypes, with intra-cluster diversities that approximate to that expected from the time depth of domestic history. Notably, one of these clusters predominates in Europe and is one of three encountered at substantial frequency in the Near East. In contrast, African diversity is almost exclusively composed of a separate haplogroup, which is encountered only rarely elsewhere. These data provide strong support for a derived Near-Eastern origin for European cattle.

Stem cell transplantation for metastatic breast cancer: analysis of tumor contamination.

The purpose of this study was to determine the efficacy, engraftment kinetics, effect of bone marrow tumor contamination, and safety of high-dose therapy and granulocyte-colony stimulating factor (G-CSF) mobilized peripheral blood progenitor cell (PBPC) support for patients with responding metastatic breast cancer. Forty two patients underwent G-CSF (10 microg/kg) stimulated PBPC harvest. PBPC and bone marrow aspirates were analyzed by histologic and immunocytochemical methods for tumor contamination. Thirty-seven patients received high-dose therapy consisting of cyclophosphamide 6 g/m2, thiotepa 500 mg/m2, and carboplatin 800 mg/m2 (CTCb) given as an infusion over 4 d followed by PBPC reinfusion and G-CSF (5 microg/kg) support. No transplant related deaths or grade 4 toxicity was recorded. CD34+ cells/kg infused was predictive of neutrophil and platelet recovery. With a median follow-up of 38 months, three year survival was 44% with relapse-free survival of 19%. Histological bone marrow involvement, found in 10 patients, was a negative prognostic factor and was associated with a median relapse-free survival of 3.5 months. Tumor contamination of PBPC by immunohistochemical staining was present in 22.5% of patients and found not to be correlated with decreased survival. G-CSF stimulated PBPC collection followed by a single course of high dose chemotherapy and stem cell infusion with G-CSF stimulated marrow recovery leads to rapid, reliable engraftment with low toxicity and promising outcome in women with responding metastatic breast cancer.

An autologous fibrinogen-based adhesive for use in otologic surgery.

Successful middle ear surgery requires the availability of a safe, effective bonding material. Side effects caused by synthetic materials have led to the use of biologic adhesives; however, they carry the risk of transmission of infectious disease if they are prepared from pooled human blood. A procedure for the production of an autologous fibrinogen-based adhesive using polyethylene glycol to precipitate the fibrinogen-factor XIII component from plasma is described. This procedure requires 40 ml of whole blood and approximately 3 hours' preparation time, and it can be performed in any blood bank with the facilities for sterile techniques. This adhesive has been used successfully for otologic surgery in 12 patients, and further study of the use of this biologic adhesive for other microsurgical techniques should be undertaken.

Effect of stretch exercises on suxamethonium induced fasciculations and myalgia.

Muscle fasciculations and pain following the administration of suxamethonium were assessed in a group of patients who performed a series of stretch exercises approximately 1 h before operation. Comparison was made with a group who received suxamethonium but no pretreatment. Fasciculations were significantly reduced in the exercised group, and the incidence of muscle pain decreased from 52% in the untreated group to 12% in the exercised group. A significant relationship was shown between the severity of visible fasciculations and muscle pain.

"Self-taming" of suxamethonium and serum potassium concentration.

Fifty patients undergoing routine surgery were randomly divided into two groups. Group 1 were pretreated with a small (10-mg) dose of suxamethonium ("self-taming") before administration of suxamethonium 1 mg kg-1, while group 2 received no pretreatment. Potassium concentrations were measured immediately before induction of anaesthesia and, subsequently, for 7 min. A small increase in mean plasma potassium concentration was seen in the group who were not pretreated, while the patients who received a "self-taming" dose of suxamethonium showed a sustained decrease below pre-induction values. Mean plasma potassium concentrations were significantly less in the "self-taming" group than in the group not pretreated.

Bicornuate uterus and aortocaval compression.

A severe case of supine hypotensive syndrome associated with a bicornuate uterus is presented. It is suggested that failure of left lateral tilt to prevent the syndrome was associated with anatomical displacement of the uterus to the right. The importance of trying right lateral tilt, if response to left tilt is poor, is noted.

Epidural anaesthesia with mixtures of bupivicaine and lidocaine.

In a randomized double-blind trial in 30 patients receiving lumbar epidural anaesthesia, the onset and duration of sensory blockade with 0.375 per cent bupivicaine was compared with a mixture of 0.375 per cent bupivicaine and one per cent lidocaine hydrochloride and a mixture of 0.375 per cent bupivicaine and one per cent carbonated lidocaine. Onset (9.3 +/- 1.16 minutes) and complete spread (23.3 +/- 4.8 minutes) for bupivicaine was significantly slower than in the mixtures containing carbonated lidocaine (onset 4.7 +/- 0.48 minutes, complete spread 14.8 +/- 2.49 minutes) and lidocaine hydrochloride (onset 5.0 +/- 0.67 minutes, complete spread 16.3 +/- 3.2 minutes). There was no significant difference in times of onset and complete spread between the two mixtures. The duration of sensory blockade for bupivicaine alone (165 +/- 20 minutes) was not significantly different from the duration in either the mixture containing carbonated lidocaine (161 +/- 51.24 minutes) or lidocaine hydrochloride (143 +/- 33.7 minutes). The results indicate a clinical advantage in speed of onset without significant shortening of duration of action for mixtures of carbonated lidocaine or lidocaine hydrochloride with bupivicaine as compared to bupivicaine alone.