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Interest in selection for improved feed efficiency is increasing, but before any steps are taken toward selecting for feed efficiency, correlations with other economically important traits must first be quantified. The objective of this study was to quantify the genetic associations between feed efficiency measured during performance testing and linear type traits, BW, live animal value, and carcass traits recorded in commercial herds. Feed efficiency data were available on 2,605 bulls from 1 performance test station. There were between 10,384 and 93,442 performance records on type traits, BW, animal value, or carcass traits from 17,225 commercial herds. (Co)variance components were estimated using linear mixed animal models. Genetic correlations between the muscular type traits in commercial animals and feed conversion ratio (-0.33 to -0.25), residual feed intake (RFI; -0.33 to -0.22), and residual BW gain (RG; 0.24 to 0.27) suggest that selection for improved feed efficiency should increase muscling. This is further evidenced by the genetic correlations between carcass conformation of commercial animals and feed conversion ratio (-0.46), RFI (-0.37), and residual BW gain (0.35) measured in performance-tested animals. Furthermore, the genetic correlations between RFI and both ultrasonic fat depth and carcass fat score (0.39 and 0.33, respectively) indicated that selection for improved RFI will result in leaner animals. It can be concluded from the genetic correlations estimated in this study that selection for feed efficiency will have no unfavorable effects on the performance traits measured in this study and will actually lead to an improvement in performance for some traits, such as muscularity, animal price, and carcass conformation. Conversely, this suggests that genetic selection for traits such as carcass quality, muscling traits, and animal value might also be indirectly selecting for more efficient animals.

Background Here, we jointly summarise scientific evidence for genetic variation in resistance to infection with Mycobacterium bovis, the primary agent of bovine tuberculosis (TB), provided by two recent and separate studies of Holstein-Friesian dairy cow populations in Great Britain (GB) and Ireland. Methods The studies quantified genetic variation within archived data from field and abattoir surveillance control programmes within each country. These data included results from the single intradermal comparative tuberculin test (SICTT), abattoir inspection for TB lesions and laboratory confirmation of disease status. Threshold animal models were used to estimate variance components for responsiveness to the SICTT and abattoir confirmed M. bovis infection. The link functions between the observed 0/1 scale and the liability scale were the complementary log-log in the GB, and logit link function in the Irish population. Results and discussion The estimated heritability of susceptibility to TB, as judged by responsiveness to the SICTT, was 0.16 (0.012) and 0.14 (0.025) in the GB and Irish populations, respectively. For abattoir or laboratory confirmation of infection, estimates were 0.18 (0.044) and 0.18 (0.041) from the GB and the Irish populations, respectively. Conclusions Estimates were all significantly different from zero and indicate that exploitable variation exists among GB and Irish Holstein Friesian dairy cows for resistance to TB. Epidemiological analysis suggests that factors such as variation in exposure or imperfect sensitivity and specificity would have resulted in underestimation of the true values.

There have been considerable recent advancements in animal breeding and genetics relevant to disease control in cattle, which can now be utilised as part of an overall programme for improved cattle health. This review summarises the contribution of genetic makeup to differences in resistance to many diseases affecting cattle. Significant genetic variation in susceptibility to disease does exist among cattle suggesting that genetic selection for improved resistance to disease will be fruitful. Deficiencies in accurately recorded data on individual animal susceptibility to disease are, however, currently hindering the inclusion of health and disease resistance traits in national breeding goals. Developments in 'omics' technologies, such as genomic selection, may help overcome some of the limitations of traditional breeding programmes and will be especially beneficial in breeding for lowly heritable disease traits that only manifest themselves following exposure to pathogens or environmental stressors in adulthood. However, access to large databases of phenotypes on health and disease will still be necessary. This review clearly shows that genetics make a significant contribution to the overall health and resistance to disease in cattle. Therefore, breeding programmes for improved animal health and disease resistance should be seen as an integral part of any overall national disease control strategy. Deposited by bulk import

peer-reviewed Insulin-like growth factor 1 (IGF-1) has been shown to be associated with fertility, growth, and development in cattle. The aim of this study was to (1) identify novel single nucleotide polymorphisms (SNPs) in the bovine IGF-1 gene and alongside previously identified SNPs (2) determine their association with traits of economic importance in Holstein-Friesian dairy cattle. Nine novel SNPs were identified across a panel of 22 beef and dairy cattle by sequence analysis of the 5′ promoter, intronic, and 3′ regulatory regions, encompassing ∼5 kb of IGF-1. Genotyping and associations with daughter performance for milk production, fertility, survival, and measures of body size were undertaken on 848 Holstein-Friesian AI sires. Using multiple regression analysis nominal associations (P < 0.05) were identified between six SNPs (four novel and two previously identified) and milk composition, survival, body condition score, and body size. The C allele of AF017143 a previously published SNP (C-512T) in the promoter region of IGF-1 predicted to introduce binding sites for transcription factors HSF1 and ZNF217 was associated (P < 0.05) with increased cow carcass weight (i.e., an indicator of mature cow size). Novel SNPs were identified in the 3′ region of IGF-1 were associated (P < 0.05) with functional survival and chest width. The remaining four SNPs, all located within introns of IGF-1 were associated (P < 0.05) with milk protein yield, milk fat yield, milk fat concentration, somatic cell score, carcass conformation, and carcass fat. Results of this study further demonstrate the multifaceted influences of IGF-1 on milk production and growth related traits in cattle. Irish Dairy Research Trust; Department of Agriculture and Food (Ireland) Research Stimulus Fund (RSF-06-0353; RSF-06-0409). Michael Paul Mullen’s contribution was funded by a Science Foundation Ireland grant (07/SRC/B1156).

Molecular genetics (MG) is a scientific discipline concerned with the structure and function of genes at the molecular level and includes the technique of genetic engineering, which can be defined as the direct manipulation of an organism’s genome. MG has enormous potential to impact both within and outside the farm gate. Outside the farm gate, MG has been used to generate tailor-made bacterial cultures with many applications in the dairy food industry, including cultures with the capacity to produce copious amounts of desirable compounds such as acid and flavor compounds. MG in dairy animals has enabled scientists to endow transgenic animals with traits that could not be achieved through standard breeding strategies. For example, high-value proteins such as human lactoferrin have been expressed in transgenic cows. Inside the farm gate, MG has a huge role to play in animal breeding. Indeed, MG is being applied to identify causative mutations or linked genetic markers that give rise to differences in phenotypes (i.e., the performance of the animal as observed in the field). The end objective of this approach, as for any breeding program, is to effectively and efficiently disseminate the superior genetics into the commercial population.

Background Mastitis, an inflammation of the mammary gland, is a major source of economic loss on dairy farms. The aim of this study was to quantify the associations between two previously identified polymorphisms in the bovine toll-like receptor 2 (TLR2) and chemokine receptor 1 (CXCR1) genes and mammary health indictor traits in (a) 246 lactating dairy cow contemporaries representing five breeds from one research farm and (b) 848 Holstein-Friesian bulls that represent a large proportion of the Irish dairy germplasm. To expand the study, a further 14 polymorphisms in immune genes were included for association studies in the bull population. Results TLR4-2021 associated (P < 0.05) with both milk protein and fat percentage in late lactation (P < 0.01) within the cow cohort. No association was observed between this polymorphism and either yield or composition of milk within the bull population. CXCR1-777 significantly associated (P < 0.05) with fat yield in the bull population and tended to associate (P < 0.1) with somatic cell score (SCS) in the cows genotyped. CD14-1908 A allele was found to associate with increased (P < 0.05) milk fat and protein yield and also tended to associate with increased (P < 0.1) milk yield. A SERPINA1 haplotype with superior genetic merit for milk protein yield and milk fat percentage (P < 0.05) was also identified. Conclusion Of the sixteen polymorphisms in seven immune genes genotyped, just CXCR1-777 tended to associate with SCS, albeit only in the on-farm study. The lack of an association between the polymorphisms with SCS in the Holstein-Friesian data set would question the potential importance of these variants in selection for improved mastitis resistance in the Holstein-Friesian cow.

The imprinted insulin-like growth factor 2 gene (IGF2) encodes a fetal mitogenic hormone protein (IGF-II) and has previously been shown to be associated with performance in dairy cattle. In this study we assessed genotype-phenotype associations between four single nucleotide polymorphisms (SNPs) located within the bovineIGF2locus on chromosome 29 and a range of performance traits related to milk production, animal growth and body size, fertility and progeny survival in 848 progeny-tested Irish Holstein-Friesian sires. Two of the four SNPs (rs42196909andIGF2.g-3815A>G), which were in strong linkage disequilibrium (r2=0·995), were associated with milk yield (P⩽0·01) and milk protein yield (P⩽0·05); thers42196901SNP was also associated (P⩽0·05) with milk fat yield. Associations (P⩽0·05) with milk fat percentage and milk protein percentage were observed at thers42196901andIGF2.g-3815A>GSNPs, respectively. Thers42196909andIGF2.g-3815A>GSNPs were also associated with progeny carcass conformation (P⩽0·05), while an association (P⩽0·01) with progeny carcass weight was observed at thers42194733SNP locus. None of the four SNPs were associated with body size, fertility and progeny survival. These findings support previous work which suggests that theIGF2locus is an important biological regulator of milk production in dairy cattle and add to an accumulating body of research showing that imprinted genes influence many complex performance traits in cattle.

Previous studies show that DNA sequence variation within the mammalian DLK1-DIO3 imprinted domain influences production traits in domestic livestock, most notably the ovine callipyge phenotype. We assessed genotype-phenotype associations between 7 single nucleotide polymorphisms (SNPs) within the orthologous bovine DLK1-DIO3 domain and performance traits in 848 progeny-tested Holstein-Friesian dairy sires. One SNP (MEG3_01) located proximal to the maternally expressed 3 (MEG3/Gtl2) gene was associated with milk yield, subcutaneous fat levels, and progeny carcass conformation (P < 0.01) and also tended to be associated with milk fat and protein yield (P < 0.10). A single SNP (CLPG_01) within the putative CLPG1 locus was associated with progeny carcass fat (P < 0.05), whereas a single SNP (PEG11_01) located proximal to the paternally expressed 11 (PEG11/Rtl) gene was associated with progeny carcass weight (P < 0.05). The MEG3_01 SNP together with an additional 2 SNPs (MEG8_01 and MEG8_02) located proximal to the putative maternally expressed 8 (MEG8/Rian) ortholog were associated (P < 0.05) with perinatal mortality. Finally, one SNP (MEG3_03) was associated (P < 0.05) with gestation length, whereas both the CLPG_01 and MEG8_01 SNPs also tended to be associated with calving interval (P < 0.10). Linkage disequilibrium analysis suggests that some phenotypic associations observed at these loci are independent. To our knowledge, this is one of the first studies demonstrating associations between the bovine DLK1-DIO3 domain and milk, carcass, fertility and, health traits in cattle. This imprinted domain may serve as a potential target for future genetic selection strategies.

peer-reviewed Background: Leptin modulates appetite, energy expenditure and the reproductive axis by signalling via its receptor the status of body energy stores to the brain. The present study aimed to quantify the associations between 10 novel and known single nucleotide polymorphisms in genes coding for leptin and leptin receptor with performance traits in 848 Holstein-Friesian sires, estimated from performance of up to 43,117 daughter-parity records per sire. Results: All single nucleotide polymorphisms were segregating in this sample population and none deviated (P > 0.05) from Hardy-Weinberg equilibrium. Complete linkage disequilibrium existed between the novel polymorphism LEP-1609, and the previously identified polymorphisms LEP-1457 and LEP-580. LEP-2470 associated (P < 0.05) with milk protein concentration and calf perinatal mortality. It had a tendency to associate with milk yield (P < 0.1). The G allele of LEP-1238 was associated (P < 0.05) with reduced milk fat concentration, reduced milk protein concentration, longer gestation length and tended to associate (P < 0.1) with an increase in calving difficulty, calf perinatal mortality and somatic cells in the milk. LEP-963 exhibited an association (P < 0.05) with milk fat concentration, milk protein concentration, calving difficulty and gestation length. It also tended to associate with milk yield (P < 0.1). The R25C SNP associated (P < 0.05) with milk fat concentration, milk protein concentration, calving difficulty and length of gestation. The T allele of the Y7F SNP significantly associated with reduced angularity (P < 0.01) and reduced milk protein yield (P < 0.05). There was also a tendency (P < 0.1) for Y7F to associate with increased body condition score, reduced milk yield and shorter gestation (P < 0.1). A80V associated with reduced survival in the herd (P < 0.05). Conclusions Several leptin polymorphisms (LEP-2470, LEP-1238, LEP-963, Y7F and R25C) associated with the energetically expensive process of lactogenesis. Only SNP Y7F associated with energy storage. Associations were also observed between leptin polymorphisms and calving difficulty, gestation length and calf perinatal mortality. The lack of an association between the leptin variants investigated with calving interval in this large data set would question the potential importance of these leptin variants, or indeed leptin, in selection for improved fertility in the Holstein-Friesian dairy cow. Department of Agriculture, Food and Fisheries, Ireland - Research Stimulus Fund (RSF-06-0353; RSF-06-0409); Irish Dairy Research Trust; Teagasc Walsh Fellowship

A successful outcome to a given service is a combination of both male and female fertility. Despite this, most national evaluations for fertility are generally confined to female fertility with evaluations for male fertility commonly undertaken by individual breeding organisations and generally not made public. The objective of this study was to define a pertinent male fertility trait for seasonal calving production systems, and to develop a multiple regression mixed model that may be used to evaluate male fertility at a national level. The data included in the study after editing consisted of 361,412 artificial inseminations from 206,683 cow-lactations (134,911 cows) in 2,843 commercial dairy and beef herds. Fixed effects associated with whether a successful pregnancy ensued (pregnant = 1) or not (pregnant = 0) from a given service were year by month of service, day of the week, days since calving, cow parity, level of calving difficulty experienced, whether or not the previous calving was associated with perinatal mortality, and age of the service bull at the date of insemination. Non-additive genetic effects such as heterosis and recombination loss as well as inbreeding level of the service bull, dam or mating were not associated with a successful pregnancy; there was no difference in pregnancy rate between fresh or frozen semen. Random effects included in the model were the additive genetic effect of the cow, as well as a within lactation and across lactation permanent environmental effect of the cow; pedigree group effects based on cow breed were also included via the relationship matrix. Temporal differences in the AI technician and service bull were also included as random effects. A difference in five percentage units in male fertility was evident between the average effects of different dairy and beef breeds. The correlation between raw pregnancy rates for bulls with more than 100 services (n = 431) and service bull solutions from the mixed model analysis was 0.66. The correlation between the raw pregnancy rates of 288 technicians with more than 100 services and their respective solutions from the mixed model was 0.35. These low to moderate correlations suggest considerable re-ranking among both service bulls and technicians and suggest possibly a benefit of using a statistical model to better estimate the performance of both service bulls and technicians.

There is a paucity of estimates of genetic variation for secondary sex ratio (i.e., sex ratio at birth) in dairy cattle. The objective of this study was to estimate the direct and maternal genetic variance as well as maternal permanent environmental variance for offspring sex in dairy herds. The data consisted of 77,508 births from 61,963 dams and 2,859 sires in 1,369 Irish dairy herds across the years 2003 to 2008, inclusive. Mixed models were used to estimate all parameters. Significant genetic variation in sex ratio existed, with a heritability for secondary sex ratio estimated at 0.02; the genetic standard deviation was 0.07 percentage units. No maternal genetic effects on secondary sex ratio were identified but the proportion of phenotypic variance in secondary sex ratio attributable to maternal permanent environmental effects was similar to that attributable to the additive genetic variance (i.e., 0.02). These results, therefore, suggest that the paternal (genetic) influence on secondary sex ratio is just as large as the maternal (non-genetic) influence, both of which are biologically substantial. The results from this study will be useful in generating a sample population of divergent animals for inclusion in a controlled experiment to elucidate the physiological mechanism underpinning differences in secondary sex ratio.

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.

The influence of genetic selection on the milk fatty acid profile of spring calving dairy cows S Mc Parland, D.P. Berry, J Coleman, R.F. Veerkamp, H Soyeurt Teagasc Moorepark Dairy Production Research Centre, Fermoy, Co. Cork, Ireland, Gembloux AgroBioTech University of Liege, Animal Science Unit, Gembloux, Belgium, National Fund for Scientific Research, Brussels, Belgium, Wageningen University and Research Centre, Animal Breeding and Genomics, P.O. Box 65, 8200 AB Lelystad, Netherlands Email: sinead.mcparland@teagasc.ie

Background Studies in mice and humans have shown that imprinted genes, whereby expression from one of the two parentally inherited alleles is attenuated or completely silenced, have a major effect on mammalian growth, metabolism and physiology. More recently, investigations in livestock species indicate that genes subject to this type of epigenetic regulation contribute to, or are associated with, several performance traits, most notably muscle mass and fat deposition. In the present study, a candidate gene approach was adopted to assess 17 validated single nucleotide polymorphisms (SNPs) and their association with a range of performance traits in 848 progeny-tested Irish Holstein-Friesian artificial insemination sires. These SNPs are located proximal to, or within, the bovine orthologs of eight genes (CALCR, GRB10, PEG3, PHLDA2, RASGRF1, TSPAN32, ZIM2 and ZNF215) that have been shown to be imprinted in cattle or in at least one other mammalian species (i.e. human/mouse/pig/sheep). Results Heterozygosities for all SNPs analysed ranged from 0.09 to 0.46 and significant deviations from Hardy-Weinberg proportions (P ≤ 0.01) were observed at four loci. Phenotypic associations (P ≤ 0.05) were observed between nine SNPs proximal to, or within, six of the eight analysed genes and a number of performance traits evaluated, including milk protein percentage, somatic cell count, culled cow and progeny carcass weight, angularity, body conditioning score, progeny carcass conformation, body depth, rump angle, rump width, animal stature, calving difficulty, gestation length and calf perinatal mortality. Notably, SNPs within the imprinted paternally expressed gene 3 (PEG3) gene cluster were associated (P ≤ 0.05) with calving, calf performance and fertility traits, while a single SNP in the zinc finger protein 215 gene (ZNF215) was associated with milk protein percentage (P ≤ 0.05), progeny carcass weight (P ≤ 0.05), culled cow carcass weight (P ≤ 0.01), angularity (P ≤ 0.01), body depth (P ≤ 0.01), rump width (P ≤ 0.01) and animal stature (P ≤ 0.01). Conclusions Of the eight candidate bovine imprinted genes assessed, DNA sequence polymorphisms in six of these genes (CALCR, GRB10, PEG3, RASGRF1, ZIM2 and ZNF215) displayed associations with several of the phenotypes included for analyses. The genotype-phenotype associations detected here are further supported by the biological function of these six genes, each of which plays important roles in mammalian growth, development and physiology. The associations between SNPs within the imprinted PEG3 gene cluster and traits related to calving, calf performance and gestation length suggest that this domain on chromosome 18 may play a role regulating pre-natal growth and development and fertility. SNPs within the bovine ZNF215 gene were associated with bovine growth and body conformation traits and studies in humans have revealed that the human ZNF215 ortholog belongs to the imprinted gene cluster associated with Beckwith-Wiedemann syndrome--a genetic disorder characterised by growth abnormalities. Similarly, the data presented here suggest that the ZNF215 gene may have an important role in regulating bovine growth. Collectively, our results support previous work showing that (candidate) imprinted genes/loci contribute to heritable variation in bovine performance traits and suggest that DNA sequence polymorphisms within these genes/loci represents an important reservoir of genomic markers for future genetic improvement of dairy and beef cattle populations.

Mycobacterium bovis is the primary agent of tuberculosis (TB) in cattle. The failure of Ireland and some other countries to reach TB-free status indicates a need to investigate complementary control strategies. One such approach would be genetic selection for increased resistance to TB. Previous research has shown that considerable genetic variation exists for susceptibility to the measures of M. bovis infection, confirmed M. bovis infection, and M. bovis-purified protein derivative (PPD) responsiveness. The objective of this study was to estimate the genetic and phenotypic correlations between economically important traits and these measures of M. bovis infection. A total of 20,148 and 17,178 cows with confirmed M. bovis infection and M. bovis-PPD responsiveness records, respectively, were available for inclusion in the analysis. First- to third-parity milk, fat, and protein yields, somatic cell count, calving interval, and survival, as well as first-parity body condition score records, were available on cows that calved between 1985 and 2007. Bivariate linear-linear and threshold-linear sire mixed models were used to estimate (co)variance components. The genetic correlations between economically important traits and the measures of M. bovis infection estimated from the linear-linear and threshold-linear sire models were similar. The genetic correlations between susceptibility to confirmed M. bovis infection and economically important traits investigated in this study were all close to zero. Mycobacterium bovis-PPD responsiveness was positively genetically correlated with fat production (0.39) and body condition score (0.36), and negatively correlated with somatic cell score (-0.34) and survival (-0.62). Hence, selection for increased survival may indirectly reduce susceptibility to M. bovis infection, whereas selection for reduced somatic cell count and increased fat production and body condition score may increase susceptibility to M. bovis infection.

peer-reviewed Equations for predicting the meat, fat and bone proportions in beef carcasses using the European Union carcass classification scores for conformation and fatness, and hindquarter composition were developed and their accuracy was tested using data from 662 cattle. The animals included bulls, steers and heifers, and comprised of Holstein–Friesian, early- and late-maturing breeds x Holstein–Friesian, early-maturing X early-maturing, late-maturing X early-maturing and genotypes with 0.75 or greater late-maturing ancestry. Bulls, heifers and steers were slaughtered at 15, 20 and 24 months of age, respectively. The diet offered before slaughter includes grass silage only, grass or maize silage plus supplementary concentrates, or concentrates offered ad libitum plus 1 kg of roughage dry matter per head daily. Following the slaughter, carcasses were classified mechanically for conformation and fatness (scale 1 to 15), and the right side of each carcass was dissected into meat, fat and bone. Carcass conformation score ranged from 4.7 to 14.4, 5.4 to 10.9 and 2.0 to 12.0 for bulls, heifers and steers, respectively; the corresponding ranges for fat score were 2.7 to 11.5, 3.2 to 11.3 and 2.8 to 13.3. Prediction equations for carcass meat, fat and bone proportions were developed using multiple regression, with carcass conformation and fat score both included as continuous independent variables. In a separate series of analyses, the independent variable in the model was the proportion of the trait under investigation (meat, fat or bone) in the hindquarter. In both analyses, interactions between the independent variables and gender were tested. The predictive ability of the developed equations was assed using cross-validation on all 662 animals. Carcass classification scores accounted for 0.73, 0.67 and 0.71 of the total variation in carcass meat, fat and bone proportions, respectively, across all 662 animals. The corresponding values using hindquarter meat, fat and bone in the model were 0.93, 0.87 and 0.89, respectively. The bias of the prediction equations when applied across all animals was not different from zero, but bias did exist among some of the genotypes of animals present. In conclusion, carcass classification scores and hindquarter composition are accurate and efficient predictors of carcass meat, fat and bone proportions.

Three genetic groups of Holstein-Friesian dairy cows were established from within the Moorepark (Teagasc, Ireland) dairy research herd: LowNA, indicative of the Irish national average-genetic-merit North American Holstein-Friesian; HighNA, high-genetic-merit North American Holstein-Friesian; HighNZ, high-genetic-merit New Zealand Holstein-Friesian. Genetic merit in this study was based on the Irish total merit index, the Economic Breeding Index. Animals from within each genetic group were randomly allocated to 1 of 2 possible post-European Union-milk-quota pasture-based feeding systems (FS): 1) The Moorepark (MP) pasture system (2.64 cows/ha and 500 kg of concentrate supplement per cow per lactation) and 2) a high output per hectare (HC) pasture system (2.85 cows/ha and 1,200 kg of concentrate supplement per cow per lactation). A total of 126, 128, and 140 spring-calving dairy cows were used during the years 2006, 2007, and 2008, respectively. Each group had an individual farmlet of 17 paddocks, and all groups were managed similarly throughout the study. The effects of genetic group, FS, and the interaction between genetic group and FS on reproductive performance, body weight, body condition score, and blood metabolite concentrations were studied using mixed models with factorial arrangements of genetic groups and FS. Odds ratios were used in the analysis of binary fertility traits, and survival analysis was used in the analysis of survival after first calving. When treatment means were compared, the HighNA and HighNZ genotypes (with greater genetic merit for fertility performance) had greater first-service pregnancy rates and had a greater proportion of cows pregnant after 42 d of the breeding season than the LowNA group. Both HighNA and HighNZ genotypes were submitted for artificial insemination earlier in the breeding season and had greater survival than the LowNA genotype. There was no significant FS or genotype by FS interactions for any of the reproductive, blood metabolite, body weight, or body condition score measures. The results demonstrate that increased genetic merit for fertility traits resulted in improved reproductive performance and that the poor reproductive capacity of inferior-genetic-merit animals for fertility was not improved through concentrate supplementation at pasture.

The incidence of and risk factors associated with calving assistance and dystocia in pasture-based dairy herds were determined from analysis of 152,641 records of full-term calvings from Holstein-Friesian dams served by artificial insemination (AI) sires of seven breeds in herds of 20 calvings or more per year over 4 years. The overall incidence of calving assistance and dystocia was 31.1% and 6.8%, respectively. The incidence in primiparae and pluriparae was 40.0% and 28.2% for assistance, and 9.3% and 5.8% for dystocia, respectively. Association analyses were undertaken using generalised estimating equations using a logit link function. The likelihood of calving assistance or dystocia did not change over time but was greatest in autumn and in spring. The likelihood of calving assistance or dystocia was greater for males in primiparae and males sired by Charolais sires. The odds of calving assistance and dystocia were greater in twin calves (OR 2.0 and 2.4; P

peer-reviewed Validation of economic indexes under a controlled experimental environment, can aid in their acceptance and use as breeding tools to increase herd profitability. The objective of this study was to compare intake, growth and carcass traits in bull and steer progeny of high and low ranking sires, for genetic merit in an economic index. The Beef Carcass Index (BCI; expressed in euro (€) and based on weaning weight, feed intake, carcass weight, carcass conformation and fat scores) was generated by the Irish Cattle Breeding Federation as a tool to compare animals on genetic merit for the expected profitability of their progeny at slaughter. A total of 107 male suckler herd progeny, from 22 late-maturing ‘continental’ beef sires of high (n = 11) or low (n = 11) BCI were compared under either a bull or steer production system, and slaughtered at approximately 16 and 24 months of age, respectively. All progeny were purchased after weaning at approximately 6 to 8 months of age. Dry matter (DM) intake and live-weight gain in steer progeny offered grazed grass or grass silage alone, did not differ between the two genetic groups. Similarly, DM intake and feed efficiency did not differ between genetic groups during an ad libitum concentrate-finishing period on either production system. Carcasses of progeny of high BCI sires were 14 kg heavier (P < 0.05) than those of low BCI sires. In a series of regression analyses, increasing sire BCI resulted in increases in carcass weight (P < 0.01) and carcass conformation (P = 0.051) scores, and decreases in carcass fat (P < 0.001) scores, but had no effect on weaning weight or DM intake of the progeny. Each unit increase in sire expected progeny difference led to an increase in progeny weaning weight, DM intake, carcass weight, carcass conformation score and carcass fat score of 1.0 (s.e. = 0.53) kg, 1.1 (s.e. = 0.32) kg, 1.3 (s.e. = 0.31) kg, 0.9 (s.e. = 0.32; scale 1 to 15) and 1.0 (s.e. = 0.25; scale 1 to 15), respectively, none of which differed from the theoretical expectation of unity. The expected difference in profitability at slaughter between progeny of the high and low BCI sires was €42, whereas the observed phenotypic profit differential of the progeny was €53 in favour of the high BCI sires. Results from this study indicate that the BCI is a useful tool in the selection of genetically superior sires, and that actual progeny performance under the conditions of this study is within expectations for both bull and steer beef production systems.

Mastitis is one of the most costly diseases to the dairy farming industry. Conventional antibiotic therapy is often unsatisfactory for successful treatment of mastitis and alternative treatments are continually under investigation. We have previously demonstrated, in two separate field trials, that a probiotic culture,Lactococcus lactisDPC 3147, was comparable to antibiotic therapy to treat bovine mastitis. To understand the mode of action of this therapeutic, we looked at the detailed immune response of the host to delivery of this live strain directly into the mammary gland of six healthy dairy cows. All animals elicited signs of udder inflammation 7 h post infusion. At this time, clots were visible in the milk of all animals in the investigation. The most pronounced increase in immune gene expression was observed inInterleukin(IL)-1β andIL-8, with highest expression corresponding to peaks in somatic cell count. Infusion with a live culture of aLc. lactisleads to a rapid and considerable innate immune response.

The relationship between bulk tank somatic cell count (SCC) and farm management and infrastructure was examined using data from 398 randomly selected, yet representative, Irish dairy farms where the basal diet is grazed grass. Median bulk tank SCC for the farms was 282,887 cells/ml ranging from 82,209 to 773,028 cells/ml. Two questionnaires were administered through face-to-face contact with each farmer. Herd-level factors associated with bulk tank SCC were determined using linear models with annual somatic cell score (i.e., arithmetic mean of the natural logarithm of bulk tank SCC) included as the dependent variable. All herd level factors were analysed individually in separate regression models, which included an adjustment for geographical location of the farm; a multiple regression model was subsequently developed. Management practices associated with low SCC included the use of dry cow therapy, participation in a milk recording scheme and the use of teat disinfection post-milking. There was an association between low SCC and an increased level of hygiene and frequency of cleaning of the holding yard, passageways and cubicles. Herd management factors associated with bulk tank SCC in Irish grazing herds are generally in agreement with most previous studies from confinement systems of milk production. Deposited by bulk import

The body condition score (BCS) of a dairy cow is an assessment of the proportion of body fat that it possesses, and it is recognized by animal scientists and producers as being an important factor in dairy cattle management. The scale used to measure BCS differs between countries, but low values always reflect emaciation and high values equate to obesity. The intercalving profile of BCS is a mirror image of the milk lactation profile. Cows lose condition for 50 to 100 d postcalving, because of homeorhetic changes that occur in the somatotropic axis and the sensitivity of peripheral tissues to insulin, and the upregulation of lipolytic pathways in adipose tissue. Management and feeding have little effect on early postcalving BCS loss (wk 1 to 4 postcalving) until the natural period of insulin resistance has passed and the somatotropic axis has recoupled. There is evidence, however, that management and diet can influence the timing of recoupling of the somatotropic axis and the sensitivity of peripheral tissues to insulin, and gene expression differences in adipose tissue 30 d in milk confirm an effect of energy intake on lipogenic enzymes. The BCS in which a cow calves, nadir BCS, and the amount of BCS she loses postcalving are associated with milk production, reproduction, and health. Body condition score may also be a valid indicator of animal welfare, but further research is required to determine the effect of BCS and BCS change on how a cow “feels.” Although the actual strength of the association may vary, there is relative consistency in the associations among calving and nadir BCS, and BCS change on milk production, postpartum anestrous, the likelihood of a successful pregnancy and days open, the risk of uterine infection, and the risk of metabolic disorders. For many production and health variables, the association with BCS is nonlinear, with an optimum calving BCS of 3.0 to 3.25 (5-point scale); lower calving BCS is associated with reduced production and reproduction, whereas calving BCS ≥3.5 (5-point scale) is associated with a reduction in early lactation dry matter intake and milk production and an increased risk of metabolic disorders. Ongoing research into the automation of body condition scoring suggests that it is a likely candidate to be incorporated into decision support systems in the near future to aid producers in making operational and tactical decisions.

Since 1994, Irish cattle have been exposed to greater risks of acquiring Mycobacterium avium subspecies paratuberculosis (MAP) infection as a consequence of the importation of over 70,000 animals from continental Europe. In recent years, there has been an increase in the number of reported clinical cases of paratuberculosis in Ireland. This study examines the prevalence of factors that promote the introduction and within-herd transmission of Mycobacterium avium subspecies paratuberculosis (MAP) on selected Irish dairy farms in the Cork region, and the association between these factors and the results of MAP screening tests on milk sock filter residue (MFR). A total of 59 dairy farms, selected using non-random methods but apparently free of endemic paratuberculosis, were enrolled into the study. A questionnaire was used to collect data about risk factors for MAP introduction and transmission. The MFR was assessed on six occasions over 24 months for the presence of MAP, using culture and immunomagnetic separation prior to polymerase chain reaction (IMS-PCR). Furthermore, blood samples from all entire male and female animals over one year of age in 20 herds were tested by ELISA. Eighteen (31%) farms had operated as closed herds since 1994, 28 (47%) had purchased from multiple sources and 14 (24%) had either direct or indirect (progeny) contact with imported animals. Milk and colostrum were mixed on 51% of farms, while 88% of farms fed pooled milk. Thirty (51%) herds tested negative to MFR culture and IMS-PCR, 12 (20%) were MFR culture positive, 26 (44%) were IMS-PCR positive and seven (12%) were both culture and IMS-PCR positive. The probability of a positive MFR culture was significantly associated with reduced attendance at calving, and with increased use of individual calf pens and increased (but not significantly) if mulitiple suckling was practised. There was poor agreement between MFR culture and MFR IMS-PCR results, but moderate agreement between MFR culture and ELISA test results. This study highlights a lack of awareness among Irish dairy farmers about the effect of inadequate biosecurity on MAP introduction. Furthermore, within-herd transmission will be facilitated by traditional calf rearing and waste management practices. The findings of viable MAP in the presence of known transmission factors in non-clinically affected herds could be a prelude to long-term problems for the Irish cattle and agri-business generally. Deposited by bulk import

peer-reviewed Recent publications indicate that the prevalence of perinatal mortality has increased in some dairy industries and an increased proportion of this loss is not associated with the traditional risk factors for perinatal mortality. The objectives of this study were to establish the prevalence of perinatal mortality (calf death within 24 h of calving) in Irish dairy herds and to determine the current significance of putative risk factors in pasture-based management systems. A total of 182 026 records of full-term calvings from Holstein-Friesian dams served by artificial insemination (AI) sires of seven breeds in herds of 20 calvings or more per year were available from the Irish national breeding database over 4 years (2002 to 2005). The prevalence of perinatal mortality was 4.29% (7.7% in primiparae and 3.5% in pluriparae). The likelihood of perinatal mortality increased between 2002 and 2005 and was greatest in June and in winter. There was an interaction (P < 0.001) between the effect of calving assistance and parity with the effect of dystocia on perinatal mortality being greater in primiparae. The odds of perinatal mortality were greater in male (OR = 1.12; P < 0.001) and in twin calves (OR = 5.70-13.36; P < 0.001) and in dams that had perinatal mortality at the previous calving (OR = 4.21; P < 0.001). The logit of the probability of perinatal mortality increased by 0.099 per unit increase in sire predicted transmitting ability (PTA) for direct perinatal mortality. The probability of perinatal mortality increased at an increasing rate in primiparae as animals calved at a younger age relative to the median age at first calving. The only herd-level factor examined, herd size did not affect the odds of perinatal mortality. These data indicate that the prevalence of perinatal mortality in this cattle population is similar to that in other pasture-based dairy systems worldwide. The putative exposures and attributes traditionally associated with perinatal mortality were associated with perinatal mortality in this pasture-based dairy cow population. The practical implication of these results is that as many of the significant risk factors are largely not under management control (year of calving, month of calving, twin calving, primiparity, previous perinatal mortality and foetal gender), herd owners must focus on the significant determinants under their control (age at first calving, sire genetic merit for direct perinatal mortality and both the extent of calving supervision and the degree of assistance), in order to reduce the prevalence of perinatal mortality and improve perinatal welfare.

There is a paucity of studies on the effect of intrauterine conditions on subsequent progeny performance in dairy cows. Using a large national data set on Irish Holstein-Friesian dairy cows, the objective of this study was to determine if intrauterine conditions, quantified by a maternal genetic variance component, significantly affected milk production, age at first calving, calving interval, somatic cell score (natural logarithm of somatic cell count) and survival in first-, second-, and third-parity female offspring. Maternal genetic variance for each trait in each parity was estimated in a linear mixed model which included, other than fixed effects, direct additive genetic, maternal genetic, cytoplasmic and permanent environmental effect of the dam, and residual component. A covariance was also estimated between the direct additive and maternal genetic components where possible. Because calves in Irish dairy herds are separated from dams at birth, a significant maternal genetic variance (with all other random effects in the model) indicates a prepartum maternal effect. A significant maternal genetic variance was estimated for 305-d milk yield in first and third lactation, somatic cell score in first lactation, and survival to second lactation from 188,144 lactations on 80,881 animals. Where estimated, a negative correlation existed between the direct additive and maternal genetic components. Regression of maternal mixed model solutions on dam milk production at different stages relative to conception revealed that greater milk yield preconception and during gestation was associated with reduced survival and milk yield and greater somatic cell count in the progeny. This study suggests that offspring survival and performance are affected by prepartum conditions that offspring experience as an oocyte, embryo, or fetus, one of which is mediated through milk production (or factors related to milk production) of the dam.

The objective of this study was to estimate genetic parameters for grass dry matter intake (DMI), energy balance (EB), and cow internal digestibility (IDG) in grazing Holstein-Friesian dairy cows. Grass DMI was estimated up to 4 times per lactation on 1,588 lactations from 755 cows on 2 research farms in southern Ireland. Simultaneously measured milk production and BW records were used to calculate EB. Cow IDG, measured as the ratio of feed and fecal concentrations of the natural odd carbon-chain n-alkane pentatriacontane, was available on 583 lactations from 238 cows. Random regression and multitrait animal models were used to estimate residual, additive genetic and permanent environmental (co)variances across lactations. Results were similar for both models. Heritability for DMI, EB, and IDG across lactation varied from 0.10 [8 days in milk (DIM)] to 0.30 (169 DIM), from 0.06 (29 DIM) to 0.29 (305 DIM), and from 0.08 (50 DIM) to 0.45 (305 DIM), respectively, when estimated using the random regression model. Genetic correlations within each trait tended to decrease as the interval between periods compared increased for DMI and EB, whereas the correlations with IDG in early lactation were weakest when measured midlactation. The lowest correlation between any 2 periods was 0.10, -0.36, and -0.04 for DMI, EB, and IDG, respectively, suggesting the effect of different genes at different stages of lactations. Eigenvalues and associated eigenfunctions of the additive genetic covariance matrix revealed considerable genetic variation among animals in the shape of the lactation profiles for DMI, EB, and IDG. Genetic parameters presented are the first estimates from dairy cows fed predominantly grazed grass and imply that genetic improvement in DMI, EB, and IDG in Holstein-Friesian cows fed predominantly grazed grass is possible.

The objective of this study was to quantify the effect of periparturient body condition score (BCS) and body weight (BW) related traits on the incidence of calving dystocia and stillbirths, and to determine any consequent effect of dystocia and stillbirths on BCS, BW, milk production, udder health, and fertility in grazing Holstein-Friesian dairy cows. Up to 2,384 lactation records with data on calving dystocia or stillbirths were available from one research herd across 15 yr. Mixed models and generalized estimating equations were used to quantify all effects. Body condition score or BW 8 wk precalving or at calving, or change precalving did not significantly affect the odds of a difficult calving or stillbirth. Cows that experienced dystocia lost, on average, more BCS and BW between calving and nadir and had significantly reduced nadir BCS and BW. Incidence of stillbirths did not affect BCS in early lactation, although BW loss postpartum was greater following a stillbirth. A dystocia or stillbirth event was associated with reduced 60-d milk yield (42 and 52 kg less milk produced following a difficult calving or a stillbirth, respectively). The effect of stillbirth on milk yield was independent of dystocia. Cows that experienced dystocia had reduced milk concentration of fat, protein, and lactose, whereas average somatic cell score (natural logarithm of somatic cell count) in the first 60-d postpartum was elevated. There was no significant effect of dystocia or stillbirth on clinical mastitis, but pregnancy rates to first service and throughout the 12-wk breeding season were compromised in cows that had experienced difficulty at calving. The significance of the effects of stillbirth on somatic cell score and reduced fertility were mediated through its association with dystocia. In conclusion, periparturient BCS and BW within the range observed in the current study did not significantly affect incidence of dystocia and stillbirth, but these events negatively affected cow performance in early lactation.

The objective of the present study was to determine effects of strain of Holstein-Friesian and feed system on body weight (BW) and body condition score (BCS; scale of 1 to 5) lactation profiles in seasonal-calving, grass-based milk production systems. The 3 strains of Holstein-Friesian compared differed in milk production potential and were high-production North American (HP), high-durability North American (HD), and New Zealand (NZ). The 3 feed systems compared were a high grass allowance feed system typical of spring-calving herds in Ireland (MP); an increased stocking rate system (HS); and an increased concentrate supplementation system (HC), each maintained within a separate farmlet. The data comprised 20,611 weekly BW and 7,920 BCS records assessed every 3 wk across 5 yr on 584 lactations. An exponential function was used to model BW and BCS lactation profiles across feed systems. Across feed systems, the NZ strain was significantly lighter (545 kg) but had greater average BCS (3.10 units) compared with the HP (579.3 kg and 2.76 units, respectively) and HD strains (583.2 kg and 2.87 units, respectively). Across feeding systems, the HD and HP strains exhibited a greater loss of BCS in early lactation (0.27 and 0.29 units, respectively) compared with the NZ strain (0.21 units). The HP strain failed to gain BCS over the entire lactation. Concentrate input did not affect the rate of BCS or BW loss in early lactation or BCS at 60 DIM. This study extends previous research outlining the greater suitability of the NZ strain to the low-cost grass-based system of milk production predominantly operated in Ireland.

Genetics is responsible for approximately half the observed changes in animal performance in well structured breeding programs. Key characteristics of the dairy cow of the future include (1) production of a large quantity of high-value output (i.e. milk and meat), (2) good reproductive performance, (3) good health status, (4) good longevity, (5) no requirement for a large quantity of feed, yet being able to eat sufficient feed to meet its requirements, (6) easy to manage (i.e. easy calving, docile), (7) good conformation (over and above reflective of health, reproductive performance and longevity), (8) low environmental footprint, and (9) resilience to external perturbations. Pertinent and balanced breeding goals must be developed and implemented to achieve this type of animal; excluding any characteristic from the breeding goal could be detrimental for genetic gain in this characteristic. Attributes currently not explicitly considered in most dairy-cow breeding objectives include product quality, feed intake and efficiency, and environmental footprint; animal health is poorly represented in most breeding objectives. Lessons from the past deterioration in reproductive performance in the global Holstein population remind us of the consequences of ignoring or failing to monitor certain animal characteristics. More importantly, however, current knowledge clearly demonstrates that once unfavourable trends have been identified and the appropriate breeding strategy implemented, the reversal of genetic trends is achievable, even for low-heritability traits such as reproductive performance. Genetic variation exists in all the characteristics described. In the genomics era, the relevance of heritability statistics for most traits is less; the exception is traits not amenable to routine measurement in large populations. Phenotyping strategies (e.g. more detailed phenotypes, larger population) will remain a key component of an animal breeding strategy to achieve the cow of the future as well as providing the necessary tools and information to monitor performance. The inclusion of genomic information in genetic evaluations is, and will continue, to improve the accuracy of genetic evaluations, which, in turn, will augment genetic gain; genomics, however, can also contribute to gains in performance over and above support of increased genetic gain. Nonetheless, the faster genetic gain and thus reduced ability to purge out unfavourable alleles necessitates the appropriate breeding goal and breeding scheme and very close monitoring of performance, in particular for traits not included in the breeding goals. Developments in other disciplines (e.g. reproductive technologies), coupled with commercial struggle for increased market share of the breeding industry, imply a possible change in the landscape of dairy-cow breeding in the future.

peer-reviewed Background Excessive maternal weight gain during pregnancy impacts on offspring health. This study focused on the timing of maternal gestational weight gain, using a porcine model with mothers of normal pre-pregnancy weight. Methods Trial design ensured the trajectory of maternal gestational weight gain differed across treatments in early, mid and late gestation. Diet composition did not differ. On day 25 gestation, sows were assigned to one of five treatments: Control sows received a standard gestation diet of 2.3 kg/day (30 MJ DE/day) from early to late gestation (day 25–110 gestation). E sows received 4.6 kg food/day in early gestation (day 25–50 gestation). M sows doubled their food intake in mid gestation (day 50–80 gestation). EM sows doubled their food intake during both early and mid gestation (day 25–80 gestation). L sows consumed 3.5 kg food/day in late gestation (day 80–110 gestation). Offspring body weight and food intake levels were measured from birth to adolescence. Markers of lipid metabolism, hypertrophy and inflammation were investigated in subcutaneous adipose tissue of adolescent offspring. Results The trajectory of gestational weight gain differed across treatments. However total gestational weight gain did not differ except for EM sows who were the heaviest and fattest mothers at parturition. Offspring birth weight did not differ across treatments. Subcutaneous adipose tissue from EM offspring differed significantly from controls, with elevated mRNA levels of lipogenic (CD36, ACACB and LPL), nutrient transporters (FABP4 and GLUT4), lipolysis (HSL and ATGL), adipocyte size (MEST) and inflammation (PAI-1) indicators. The subcutaneous adipose depot from L offspring exhibited elevated levels of CD36, ACACB, LPL, GLUT4 and FABP4 mRNA transcripts compared to control offspring. Conclusions Increasing gestational weight gain in early gestation had the greatest impact on offspring postnatal growth rate. Increasing maternal food allowance in late gestation appeared to shift the offspring adipocyte focus towards accumulation of fat. Mothers who gained the most weight during gestation (EM mothers) gave birth to offspring whose subcutaneous adipose tissue, at adolescence, appeared hyperactive compared to controls. This study concluded that mothers, who gained more than the recommended weight gain in mid and late gestation, put their offspring adipose tissue at risk of dysfunction. This research was funded by Teagasc, under the National Development Plan. LBMcN was in receipt of a Teagasc Walsh Fellowship. Nestle hosted LG on a sabbatical and funded the RT-PCR cost.

The objective was to quantify the strength of the relationship between body condition score (BCS) and live weight (LW) in pasture-based Holstein-Friesian dairy cattle, and to determine the kg LW per unit BCS. A total of 26021 test-day records with information on both BCS (1–10 scale, where 1 is emaciated and 10 is obese) and LW across 1110 lactations from one research farm were used in the analysis. Correlation and regression analyses were used to determine the degree of association between BCS and LW in different parities, stages of the inter-calving interval and years. Correlations between BCS and LW were relatively consistent, with the mean correlation between BCS and LW across all data of 0·55 implying that differences in BCS explain approximately 30% of the variation in LW. Significantly different regressions of LW on BCS were present within stage of inter-calving interval by parity subclasses. Excluding calving, LW per unit BCS varied from 17 kg (early to mid lactation in parity 1) to 36 kg (early lactation in parity 4 and 5). However, LW per unit BCS was greatest at calving varying from 44 kg in first parity animals to 62 kg in second parity animals. On average, 1 BCS unit equated to 31 kg LW across all data.

The hypothesis for this study was that the prevailing climate around the time of conception was associated with changes in the secondary sex ratio (SSR) in grazing, seasonally bred dairy cattle. Calving date, parity, cow breed, and calf sex were obtained for 8,621 lactations (with single births only) from 1,897 cows between 1970 and 2003 (inclusive). Conception date was estimated by subtracting a gestation length of 282 d from the date at calving. Climatic factors, including maximum and minimum ambient temperature, relative humidity, rainfall, sunlight hours, and evaporation rate, were averaged across the week immediately prior to conception for all lactations. Sun radiation data were available after 1976. Generalized estimating equations, with cow included as a repeated effect, were used to determine the effect of climate around the time of conception on the logit of the probability of a male calf. Breed of cow, year of conception, and parity at conception did not affect the SSR. The odds of a male calf being born were 3.74 times greater when the immediately previous calf born was male. A male calf was more likely to be born following periods of elevated air temperature, greater evaporation, or both. A 1 degrees C increase in average maximum air temperature from the average (18.3 degrees C), during the week immediately prior to conception, was associated with a 1-percentage unit increase in the probability of a male calf being born (i.e., from 52 to 53%). A corresponding 1 degrees C increase in average minimum air temperature was reflected in a 0.5-percentage unit increase in the probability of a male calf being born. The probability of a male calf being born increased by 2.9 percentage units with each additional millimeter of evaporation per day. Results indicate that climatic factors associated with elevated temperatures and greater evaporation may influence the SSR in dairy cattle.

The objective of the present study was to quantify the climatic, animal, and management factors influencing incidence of milk fever (MF) in cows exposed to grazing systems. Data were extracted on 4,469 calvings of multiparous cows in a seasonal calving research herd between 1970 and 2000. Climatic data during the calving period also were extracted for these years. Poisson regression was used to investigate the effect of climate on frequency of MF within year; the offset variable was the number of cows at risk for MF at that time. Generalized estimating equations, with cow included as a repeated effect, were used to quantify the effect of parturition-associated cow and management factors on the logit of the probability of MF. Both univariate and multivariate analyses were performed. Explanatory variables investigated included time of calving relative to the herd-year calving period, parity, body weight, breed of cow, body condition score at calving, weight and gender of the calf, incidence of twin calves, calving inductions, and calving assistance. Odds of recurring MF within cow, as well as the timing of MF relative to day of calving, was quantified using generalized estimating equations with cow included as a repeated effect. Results show significant effects of evaporation, minimum grass temperature, difference between ambient maximum and minimum temperature, and rainfall on the odds of MF occurring, with a greater incidence at greater evaporation, larger diurnal variation in air temperature, greater rainfall, and lesser grass minimum temperature. Cow factors, such as age, excessive or poor body condition score, and requirement for calving assistance increased the odds of MF; a lesser odds ratio was observed in cows hormonally induced to calve and those that had twin births. Results indicate that herd managers may identify the day of greatest risk for MF and cows that are at greatest risk of MF based on climatic, cow, and management factors.

According to the Trivers-Willard hypothesis, maternal condition at or around conception affects the secondary sex ratio in mammals. However, there are little or no data available on indicators of maternal condition in dairy cows on the sex of the resultant offspring. A total of 76,607 body condition score (BCS; scale of 1 to 5) records and 76,611 body weight (BW) records from 3,209 lactations across 1,172 cows were extracted from a research database collated from one research herd between 1986 and 2004, inclusive. Exclusion of multiple births and cows with no information before calving (e.g., nulliparous animals) resulted in 2,029 records with BCS and BW observations from the previous calving, and 2,002 and 1,872 lactations with BCS and BW observations at conception and midgestation, respectively. Change in BCS and BW between calving and conception and between conception and midgestation was calculated per lactation. Generalized estimating equations were used to model the logit of the probability of a male calf, in which cow was included as a repeated effect with a first-order autoregressive correlation structure assumed among records within cow. Of the BCS variables investigated, there was a linear relationship between the logit of the probability of a male calf and BCS change between calving and conception, the rate of BCS change over this period (BCS divided by days in milk), and BCS at the calving event immediately before conception. The birth of a bull calf was 1.85 times more likely in cows that lost no BCS from calving to conception compared with cows that lost one BCS unit from calving to conception. This increase in odds was equivalent to a 14% unit increase in the probability of a male calf (from 54 to 68%). The amount of BW lost between calving and conception and the rate of loss affected the sex of the resultant offspring. Less BW loss or greater BW gain between calving and conception was associated with greater likelihood of a male calf. Results suggested a positive effect of pre-conception BCS and BW change on secondary sex ratio, agreeing with the Trivers-Willard hypothesis that females in good physiological condition are more likely to produce male offspring.

Trends in milk production, calving rates, and survival were monitored on a potential 5580 primiparous and multiparous Holstein-Friesian dairy cows across 14 Irish seasonal spring-calving dairy farms between the years 1990 and 2001. Over this period calving rate to first service (CALV1) reduced by 0·96% per year (55 to 44%;P< 0·001), calving rate to first and second service (CALV12) reduced by 0·84% per year ( 77 to 70%;P< 0·001) and herd average parity number reduced by 0·10 lactation per year (4·3 to 3·5;PPMILK) of the cows increased by 25 kg per year (PPPMILKand reduced calving rates as assessed by CALV1 and CALV12. Increased proportion of NAHF genes exhibited a negative effect on survival (PP

The effect of reducing the frequency of official milk recording and the number of recorded samples per test-day on the accuracy of predicting daily yield and cumulative 305-day yield was investigated. A control data set consisting of 58 210 primiparous cows with milk test-day records every 4 weeks was used to investigate the influence of reduced milk recording frequencies. The accuracy of prediction of daily yield with one milk sample per test-day was investigated using 41 874 testday records from 683 cows. Results show that five or more test-day records taken at 8-weekly intervals (A8) predicted 305-day yield with a high level of accuracy. Correlations between 305-day yield predicted from 4-weekly recording intervals (A4) and from 8-weekly intervals were 0.99, 0.98 and 0.98 for milk, fat and protein, respectively. The mean error in estimating 305-day yield from the A8 scheme was 6.8 kg (s.d. 191 kg) for milk yield, 0.3 kg (s.d. 10 kg) for fat yield, and −0.3 kg (s.d. 7 kg) for protein yield, compared with the A4 scheme. Milk yield and composition taken during either morning (AM) or evening (PM) milking predicted 24-h yield with a high degree of accuracy. Alternating between AM and PM sampling every 4 weeks predicted 305-day yield with a higher degree of accuracy than either all AM or all PM sampling. Alternate AM-PM recording every 4 weeks and AM + PM recording every 8 weeks produced very similar accuracies in predicting 305-day yield compared with the official AM + PM recording every 4 weeks.

The objective of the present study was to determine the distribution of subclincial mastitis and intramammary infection (IMI) across udder quarters and to quantify, if any, the level of interdependence between quarters. Subclinical mastitis was defined as an udder quarter somatic cell count of ≥250,000. Intramammary infection was defined as the presence of pathogens in an udder quarter. The data used in the analyses consisted 6577 test-day records from 2034 lactations with observations on subclinical mastitis and 8428 test-day records from 2575 lactations with observations on IMI; each test-day record consisted data on all four udder quarters. Records were from animals on three research herds in southern Ireland. Observed distributions of IMI were compared to expected distributions, estimated using a binomial probability distribution, assuming independence among quarters. Generally, the observed frequencies deviated significantly from the expected frequencies, indicating some level of interdependence between quarters. Intraclass correlations were estimated from a mixed model including cow and test-day record nested within cow as random effects; fixed effects in the model included herd, year of calving, month of calving, parity, days in milk at sampling and interactions. Intraclass correlations within test-day record ranged from 0.14 to 0.50 for subclinical mastitis and from 0.02 to 0.40 for IMI. Thus, substantial interdependence between quarters exists which should be accounted for when analysing data from experiments across udder quarters. Failure to do so may result in incorrect inferences from statistical tests.

peer-reviewed Differences in conception rate to first service between artificial inseminations (AI) carried out by commercial AI operators (CAI) or do-it-yourself operators (DIY), between natural service (NAT) and AI, between different AI sires, and between fresh and frozen-thawed semen, on Irish commercial dairy farms, were studied using logistic regression. The study comprised 12 933 potential first inseminations from 77 spring-calving dairy herds. The data were recorded during 1999 and 2000. Amongst the total, 4 394 cows had repeated records across the two years. Adjustment variables included: herd, year, parity, calving period, calving to service interval, herd size, proportion of North American Holstein-Friesian genes, peak milk yield, semen fresh or frozen-thawed status, AI sire and a cow history variable to account for the correlation structure that may exist between performance records of cows present in both years of the study. Interactions of interest were tested but were non-significant. No significant association was observed between the category of AI operator and the likelihood of conception rate to first service (PREG1). The variation in PREG1 observed within the category of operator (CAI and DIY) was investigated using the Levene test for homogeneity of variance. There was no difference between the level of variation observed within CAI and DIY operators. There were significant differences in the likelihood of PREG1 between different AI sires. Amongst the 40 most commonly used AI sires, 3 sires had a lower likelihood of PREG1 (P < 0.05) when compared to the reference AI sire (sire with PREG1 similar to the mean of the group). There was a tendency for a reduced likelihood of PREG1 with the use of fresh semen compared to frozen-thawed semen ( , P = 0.067). Amongst the adjustment variables in the model, those significantly associated with the likelihood of PREG1 included the herd, calving period, calving to first service interval and peak milk yield. No significant difference in the likelihood of PREG1 was observed between AI and NAT. AIB Bank; Holstein UK and Ireland; the National AI Co-ops; Dairy Levy Fund (Ireland)

Genetic (co)variances between body condition score (BCS), body weight (BW), milk yield, and fertility were estimated using a random regression animal model extended to multivariate analysis. The data analyzed included 81,313 BCS observations, 91,937 BW observations, and 100,458 milk test-day yields from 8725 multiparous Holstein-Friesian cows. A cubic random regression was sufficient to model the changing genetic variances for BCS, BW, and milk across different days in milk. The genetic correlations between BCS and fertility changed little over the lactation; genetic correlations between BCS and interval to first service and between BCS and pregnancy rate to first service varied from -0.47 to -0.31, and from 0.15 to 0.38, respectively. This suggests that maximum genetic gain in fertility from indirect selection on BCS should be based on measurements taken in midlactation when the genetic variance for BCS is largest. Selection for increased BW resulted in shorter intervals to first service, but more services and poorer pregnancy rates; genetic correlations between BW and pregnancy rate to first service varied from -0.52 to -0.45. Genetic selection for higher lactation milk yield alone through selection on increased milk yield in early lactation is likely to have a more deleterious effect on genetic merit for fertility than selection on higher milk yield in late lactation.

(Co)variance components for body condition score (BCS), body weight (BW), BCS change, BW change, and milk yield traits were estimated. The data analyzed included 6646 multiparous Holstein-Friesian cows with records for BCS, BW, and(or) milk yield at different stages of lactation from 74 dairy herds throughout Southern Ireland. Heritability estimates for BCS ranged from 0.27 to 0.37, while those for BCS change ranged from 0.02 to 0.10. Heritability estimates for BW records varied from 0.39 to 0.50, while heritabilities for BW change were similar to those observed for BCS change (0.03 to 0.09). The genetic correlations between BCS and BW at the same days in milk deviated little from 0.50, and the genetic correlations between BCS change and BW change over the same period ranged from 0.42 to 0.55. BCS and BW directly postpartum were both phenotypically and genetically negatively correlated with both BW change and BCS change in early lactation. The genetic correlations between BCS and milk yield were negative. The results of the present study show that animals that lose most BCS in early lactation tend to gain most BCS in late lactation, a trend also exhibited by BW.

The New Zealand, Australian and Irish dairy industries have used genomic information to enhance their genetic evaluations over the last 2–4 years. The improvement in the accuracy obtained from including genomic information on thousands of animals in the national evaluation system has revolutionised the dairy breeding programs in the three countries. The genomically enhanced breeding values (GEBV) of young bulls are more reliable than breeding values based on parent average, thus allowing the young bulls to be reliably selected and used in the national herd. Traditionally, the use of young bulls was limited and bulls were not used extensively until they were 5 years old when the more reliable progeny test results became available. Using young sires, as opposed to progeny-tested sires, in the breeding program dramatically reduces the generation interval, thereby facilitating an increase in the rate of genetic gain by 40–50%. Young sires have been marketed on their GEBV in the three countries over the last 2–4 years. Initial results show that the genomic estimates were overestimated in both New Zealand and Ireland. Adjustments have since been introduced into their respective national evaluations to reduce the bias. A bias adjustment has been included in the Australian evaluation since it began; however, official genomic evaluations have not been in place as long as in New Zealand and Ireland, so there has been less opportunity to validate if the correction accounts for all bias. Sequencing of the dairy cattle population has commenced in an effort to further improve the genomic predictions and also to detect causative mutations that underlie traits of economic performance.

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.

Impact of genetic selection on feed efficiency on carcass traits in Irish beef cattle J.J. Crowley, R.D. Evans, D.P. Berry Teagasc, Moorepark Dairy Production Research Centre, Fermoy, Cork, Ireland, Irish Cattle Breeding Federation, Bandon, Cork, Ireland, School of Agriculture, Food Science and Veterinary Medicine, College of Life Sciences, University College Dublin, Belfield, Dublin 4, Ireland Email: john.j.crowley@teagasc.ie

0.07(0.246) -0.16(0.046)*** Fat (kg) 0.24(0.277) -0.11(0.045)* Protein (kg) 0.30(0.247) -0.06(0.046) Lactose (kg) 0.00(0.260) -0.20(0.044)*** Fat Percent 0.21(0.305) 0.01(0.045) Protein Percent 0.43(0.191)* 0.26(0.043)*** Lactose Percent -0.37(0.237) -0.30(0.042)*** Urea (kg) -0.31(0.308) -0.09(0.044) Casein (kg) 0.38(0.196)* 0.21(0.045)*** SCS -0.36(0.326) 0.29(0.043)*** ‡ *P