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Using internet-based software known as 1000Minds, choice-experiment surveys were administered to experts and farmers from the Irish sheep industry to capture their preferences with respect to the relative importance – represented by part-worth utilities – of target traits in the definition of a breeding objective for sheep in Ireland. Sheep production in Ireland can be broadly separated into lowland and hill farming systems; therefore, each expert was asked to answer the survey first as if he or she were a lowland farmer and second as a hill farmer. In addition to the experts, a group of lowland and a group of hill farmers were surveyed to assess whether, and to what extent, the groups’ preferences differ from the experts’ preferences. The part-worth utilities obtained from the surveys were converted into relative economic value terms per unit change in each trait. These measures – referred to as ‘preference economic values’ (pEVs) – were compared with economic values for the traits obtained from bio-economic models. The traits ‘value per lamb at the meat processor’ and ‘lamb survival to slaughter’ were revealed as being the two most important traits for the surveyed experts responding as lowland and hill farmers, respectively. In contrast, ‘number of foot baths per year for ewes’ and ‘number of anthelmintic treatments per year for ewes’ were the two least important traits. With the exception of ‘carcase fat class’ (P < 0.05), there were no statistically significant differences in the mean pEVs obtained from the surveyed experts under both the lowland and hill farming scenarios. Compared with the economic values obtained from bio-economic models, the pEVs for ‘lambing difficulty’ when the experts responded as lowland farmers were higher (P < 0.001); and they were lower (P < 0.001) for ‘carcase conformation class’, ‘carcase fat class’ (less negative) and ‘ewe mature weight’ (less negative) under both scenarios. Compared with surveyed experts, pEVs from lowland farmers differed significantly for ‘lambing difficulty’, ‘lamb survival to slaughter’, ‘average days to slaughter of lambs’, ‘number of foot baths per year for ewes’, ‘number of anthelmintic treatments per year for ewes’ and ‘ewe mature weight’. Compared with surveyed experts, pEVs from hill farmers differed significantly for ‘lambing difficulty’, ‘average days to slaughter of lambs’ and ‘number of foot baths per year for ewes’. This study indicates that preference-based tools have the potential to contribute to the definition of breeding objectives where production and price data are not available.

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.

Breeding objectives for meat sheep in Ireland have been defined and used in the development of selection sub-indices to provide commercial producers with an economic comparison of animals for specific performance trait groups. Using trait-by-trait bio-economic models and a range of methodologies, economic weights (in € per lamb born per genetic standard deviation in the trait) have been calculated for maternal and terminal sire performance traits as follows: production traits; −€1.41 for days to slaughter, €0.35 for carcase conformation class, −€0.52 for carcase fat class, lambing traits; −€0.69 for lambing difficulty for single-bearing ewes, −€0.37 for lambing difficulty for multiple-bearing ewes, €1.15 for lamb survival, maternal traits; €0.83 for number of lambs born, −€1.49 for ewe mature weight, health traits; −€0.09 for lamb foot rot, and −€0.82 for ewe foot rot. Results indicate the significant value of improving the ability of lambs to survive to weaning, without increasing number of lambs born. The highly negative economic weight for both days to slaughter and mature size represents a powerful unfavourable relationship between the two traits. Economic values for lambing difficulty and foot rot represent the significant costs these traits have in the Irish sheep production system. In the early stages of the development of the genetic improvement program for sheep in Ireland the breeding objective defined in this paper provides directed emphasis for trait recording, selection strategies, and mating systems. In addition the economic weights provide indications as to how much genetic improvement in a specific trait would be worth paying for. The proposed formulation of the total economic index as sub-indices provides the ability for commercial farmers to adjust breeding emphasis towards specific market outcomes or address key production aspects in their particular farming system.

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).

Breeding objectives for beef cattle in Ireland were derived and used to define selection sub-indexes. The intention of the sub-indexes was to simplify selection decisions by commercial bull and semen buyers for situations where all of the resulting progeny are slaughtered, or when some female progeny are kept as replacement breeding cows. Separate sets of economic values for calving ease and gestation length are proposed for use in separate calving sub-indexes depending on whether dairy cows or beef cows are to be mated. Proposed economic values for calf quality, growth, calving and reproduction sub-indexes were assumed to be independent of the breed of cow to be mated. It was also recommended that separate total indexes for dairy cow and beef cow matings be constructed as simple linear functions of the sub-indexes.

Two studies were conducted to examine the effects of selection for milk-fat yield on pancreatic responses to exogenous glucose, as measured by circulating insulin concentrations following an intravenous glucose load, in heifer calves. The first study involved 6-month-old Friesian heifers, eight each from the Massey University high breeding index (HBI) and low breeding index (LBI) lines. Average breeding indices (BI) for milk-fat yield of the calves based on ancestry BI were 136 (s.d. 2) and 112 (s.d. 2), respectively. Oestrous cycling of the heifers was controlled by intravaginal insertion of progesterone-impregnated controlled internal drug-releasing devices (CIDRs). Challenges of glucose (0, 75, 150 and 300 mg/kg live weight) and insulin (0, 0·1, 1, and 10 fig/kg live weight) were administered via indwelling jugular cannulas and were followed by serial blood sampling to measure responses. Plasma insulin concentrations immediately following the glucose challenge were significantly (P < 0·05) greater in HBI than in LBI heifers, peak insulin concentrations (above baseline) in the HBI group being approximately twice those in the LBI group. Plasma glucose concentrations were marginally lower in HBI heifers, probably due to the secondary effect of the relatively greater hyperinsulinaemia in this group. Although the exogenous insulin challenge significantly reduced circulating glucose concentrations in all heifers, there was no difference between the lines in the magnitude of insulin-induced hypoglycaemia.The second study was designed to determine whether insulin responses to an exogenous glucose load were influenced by stage of the oestrous cycle in heifers of the two lines. In this study, eight yearling HBI heifers and eight LBI heifers (with BI of 135 (s.d. 4) and 111 (s.d. 1) respectively) were administered an intravenous glucose load (150 mg/kg live weight) on tivo occasions, the first being after 17 days of CIDR treatment (simulating the luteal phase of the oestrous cycle) and the second 46 h after withdrawal of the CIDRs (when the heifers were expected to be in oestrus). HBI heifers again showed significantly greater circulating insulin concentrations than LBI heifers following the glucose challenge but the magnitude of this effect was not influenced by time relative to CIDR withdrawal. It is concluded that heifers selected for high milk-fat yield have an increased pancreatic response to exogenous glucose which is apparently independent of the stage of the oestrous cycle. This difference may provide a useful means of identifying heifers of superior genetic merit for milk-fat production prior to their first lactation.

This study investigated the potential use of blood metabolite and hormone concentrations as genetic markers for milk fat production and their possible interactions with sex and age. Two groups of calves, one from the Massey University high breeding index (HBI) line of dairy cattle (seven males, eight females) and the other from the low breeding index (LBI) line (four males, 11 females), were studied at 3·5 months and 7 months of age. The average breeding indices (BI) of the calves based on ancestry BI were 138 (s.d. 4·4) and 111 (s.d. 2·3) respectively. Serial blood sampling regimens were conducted in relation to feeding (chaffed lucerne hay at 1·3 times maintenance energy requirement), during an intravenous urea load (120 mg/kg live weight) and during fasting (63 h) and refeeding. Urea spaces and fractional decay constants at each age were estimated by a single compartment distribution model based on plasma urea concentrations following the intravenous urea load.Plasma concentrations of urea, creatinine and non-esterified fatty acids (NEFA) were not significantly different between the lines in any of the periods examined and at either age. In contrast, plasma concentrations of glucose and insulin were greater in the HBI calves than in the LBI calves although these differences were restricted mainly to the period immediately after feeding. Urea space at 7 months of age was also greater in the HBI animals than in the LBI animals. Plasma concentrations of all hormones and metabolites except insulin were significantly influenced by sex and/or age.The study does not confirm previous findings that genetic merit for dairying is expressed in terms of plasma levels of urea and NEFA, particularly those during a fast. However, the results of the present study are consistent with previous observations of differences in glucose and insulin metabolism between the tivo Massey University genetic merit lines. These traits may therefore have potential as genetic markers for milk fat production.

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.

Recombinantly derived bovine somatotropin (bST) was administered to 25 Friesian cows by 2-weekly injections of a controlled release formulation at a dose rate equivalent to 25 mg/day. Treatment commenced 7 to 11 weeks after calving and continued for 26 weeks. A comparable group of 25 cows treated only with the slow release vehicle served as a control. During the treatment period, administration of bST increased yields of milk (controls 2358 v. bST 2598 (pooled s.e. = 39·8) kg; P < 0·01), fat (107·4 v. 119·3 (pooled s.e. = 1·9) kg; (P < 0·01) and protein (84·7 v. 93·7 (pooled s.e. = 1·2) kg; (P < 0·001). Magnitude of the treatment effect was strongly influenced by season, being greatest in spring/early summer (weeks 1 to 13 of treatment) and autumn (weeks 19 to 25) but not significant during the intervening summer dry period when herbage yield was low. Voluntary intakes, as measured by indigestible marker techniques at weeks 7 to 8 and 12 to 13 of treatment, were not influenced by bST administration. However, the net loss of body condition experienced by bST-treated cows (0·3 condition score units) was not sufficient to explain their responses in yield of milk and milk components, suggesting that some responses in voluntary intake had occurred. Administration of bST had little effect on milk composition, fatty acid composition of milk fat, live weight, reproductive performance or milk yield in the subsequent lactation.

The effect of recombinantly derived bovine somatotropin (bST) treatment on milk production and pasture intake was examined in 16 New Zealand Friesian cows from low or high genetic merit (breeding index) selection lines. Recombinantly derived bST was administered by 2-weekly injection of a controlled release formulation for a period of 4 weeks (weeks 16 to 19 of lactation) at a dose rate equivalent to 50 mg/day. During this period the animals were housed for 18 days with food intake being measured over the last 8 days. Treatment with bST resulted in significantly higher yields of milk, fat and protein compared with the controls. Cows from the low breeding index (LBI) line were more responsive to exogenous bST than cows of the high breeding index (HBI) line in both milk and fat yield. Milk composition was not affected by bST treatment. There was a significant increase of proportionately 0·108 in intake of freshly cut pasture between bST-treated and untreated animals during days 16 to 23 of treatment. Thus, no significant difference in calculated energy balance was observed between the bSTtreated and untreated cows. This study indicates that the genetic background of cows may be an important determinant of their response to bST treatment and that such treatment rapidly alters voluntary intake in pasture-fed cows.

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.

Genomics is a technology for increasing the accuracy with which the genetic merit of young potential breeding animals can be determined. It enables earlier selection decisions, thus reducing generation intervals and gives rise to more rapid annual rates of genetic gain. Recently, the cost of genomics has reduced to the point where it enables breeding-program costs to be reduced substantially. Ireland has been a rapid adopter of genomics technology in its dairy-cattle breeding program, with 40% of dairy-cow artificial inseminations in 2010 being from bulls evaluated using genomic information. This rapid adoption has been facilitated by a comprehensive database of phenotypes and genotypes, strong public funding support for applied genomics research, an international network of collaborators, a short path between research and implementation, an overall selection index which farmers use in making breeding decisions, and a motivated and informed breeding industry. The shorter generation interval possible with genomic selection strategies also allows exploitation of the already accelerating rate of genetic progress in Ireland, because elite young dairy bulls are considerably superior to the small numbers of bulls that entered progeny test 6 years ago. In addition, genomics is having a dramatic impact on the artificial-insemination industry by substantially reducing the cost of entry, the cost of operation, and shifting the focus of breeding from bulls to cows. We believe that the current industry structures must evolve substantially if Irish cattle farmers are to realise the full benefits of genomics and be protected from related risks. Our model for future dairy breeding envisages a small number of ‘next generation research herds’, 1000 ‘bull breeder herds’ and an artificial-insemination sector using 30 new genomically selected bulls per year to breed the bulk of replacements in commercial milk-producing herds. Accurate imputation from a low-density to a higher-density chip is a key element of our strategy to enable dairy farmers to afford access to genomics. This model is capable of delivering high rates of genetic gain, realising cost savings, and protecting against the risks of increased inbreeding and suboptimal breeding goals. Our strategy for exploiting genomic selection for beef breeding is currently focussed on genotyping, using a high-density chip, a training population of greater than 2000 progeny-tested bulls representing all the main beef breeds in Ireland. We recognise the need for a larger training population and are seeking collaboration with organisations in other countries and populations.

A model describing the selection of cows to have a second lactation is developed. This model allows for factors independent of milk yield in first lactation to influence the variable upon which selection is based. Under this model a procedure for estimating the biases in best linear unbiased predictors, which assume no selection, is presented. This procedure was used to obtain estimates of biases for 1109 Holstein sires in artificial insemination in the northeastern United States. Estimated biases for assumed selection models were small relative to changes in ranking of bulls from first to second lactations of daughters. Rank correlation was .77 between rank of bulls based on first lactation and rank for second lactations of daughters where selection is ignored.

Four central performance tests of growth in Hereford bulls from about 10 to 19 months of age on pasture were conducted in New Zealand. From the 100 bulls performance tested 63 were representatively sampled, including bulls with high and low performance test rankings, and progeny tested in dairy herds. Crossbred progeny were purchased from the dairy herds at 3 to 4 months of age, assembled in one location and reared together on pasture for 14 to 15 months prior to slaughter. Regressions of progeny growth and carcass traits on a number of different performance traits for growth of their sires were in almost all cases not statistically significant. The effective heritability, from offspring-sire regression, was 0·07 (s.e. 0·05) for final live weight and 009 (s.e. 0·06) for post weaning gain from about 200 to 550 days of age. It is concluded that central performance tests, as presently conducted in New Zealand, are of limited value for ranking breeding values of bulls for growth. Possible reasons for these results are discussed. It is suggested that pre-test environmental effects and age at the start of the central test are critical factors.

The New Zealand Dairy Board, in organising the genetic improvement of dairy cattle, has the objective of maximising net income per farm. For given farm conditions this is achieved by maximising net income per cow. Because of the problems associated with measuring net income for each cow, selection has been based on milkfat production per cow, but other traits are monitored to prevent their deterioration. The genetic studies of dairy cattle in New Zealand are summarised. Evidence of genetic progress in milkfat per cow is reviewed. The evidence includes a controlled experiment conducted at the Ruakura No. 2 dairy farm, the comparison of Premier Sires Service (PSS) progeny with the progeny of other bulls in tested herds, and a comparison between short- and long-term users of PSS using marker bull techniques. Evidence that genetic improvement per cow in milkfat production is being accompanied by improved productive efficiency is found from a comparison of 507 paired herds.