A method to approximate the inverse of a part of the additive relationship matrix

Single‐step genomic predictions need the inverse of the part of the additive relationship matrix between genotyped animals ( A ₂₂). Gains in computing time are feasible with an algorithm that sets up the sparsity pattern of (SP algorithm) using pedigree searches, when is close to sparse. The objective of this study is to present a modification of the SP algorithm (RSP algorithm) and to assess its use in approximating when the actual is dense. The RSP algorithm sets up a restricted sparsity pattern of by limiting the pedigree search to a maximum number of searched branches. We have tested its use on four different simulated genotyped populations, from 10 000 to 75 000 genotyped animals. Accuracy of approximation is tested by replacing the actual by its approximation in an equivalent mixed model including only genotyped animals. Results show that limiting the pedigree search to four branches is enough to provide accurate approximations of , which contain approximately 80% of zeros. Computing approximations is not expensive in time but may require a great amount of memory (at maximum, approximately 81 min and approximately 55 Gb of RAM for 75 000 genotyped animals using parallel processing on four threads).     

Selecting the hologenome to breed for an improved feed efficiency in pigs—A novel selection index

Most traits in animal breeding, including feed efficiency traits in pigs, are affected by many genes with small effect and have a moderately high heritability between 0.1 and 0.5, which enables efficient selection. Since the microbiota composition in the gastrointestinal tract is also partly heritable and was shown to have a substantial effect on feed efficiency, the host genes affect the phenotype not only directly by altering metabolic pathways, but also indirectly by changing the microbiota composition. The effect of the microbiota composition on the breeding value of an animal is the conditional expectation of its breeding value, given the vector with microbiota frequencies, that is The breeding value of an animal can therefore be decomposed into a heritable contribution that arises from an altered microbiota composition and a heritable contribution that arises from altered metabolic pathways within the animal, so Instead of selecting for breeding value , an index comprising the two components and with appropriate weights, that is , can be used. The present study shows how this breeding strategy can be applied in pig genomic selection breeding scheme for two feed efficiency traits and daily gain.     

Performance of pedigree and various forms of marker-derived relationship coefficients in genomic prediction and their correlations

In recent years, with development and validation of different genotyping panels, several methods have been proposed to build efficient similarity matrices among individuals to be used for genomic selection. Consequently, the estimated genetic parameters from such information may deviate from their counterpart using traditional family information. In this study, we used a pedigree-based numerator relationship matrix ( A ) and three types of marker-based relationship matrices () including two identical by descent, that is and and one identical by state, as well as four Gaussian kernel () similarity kernels with different smoothing parameters to predict yet to be observed phenotypes. Also, we used different kinship matrices that are a linear combination of marker-derived IBD or IBS matrices with A, constructed as , where the weight () assigned to each source of information varied over a grid of values. A Bayesian multiple-trait Gaussian model was fitted to estimate the genetic parameters and compare the prediction accuracy in terms of predictive correlation, mean square error and unbiasedness. Results show that the estimated genetic parameters (heritability and correlations) are affected by the source of the information used to create kinship or the weight placed on the sources of genomic and pedigree information. The superiority of GK -based model depends on the smoothing parameters (θ) so that with an optimum θ value, the GK -based model statistically yielded better performance (higher predictive correlation, lowest MSE and unbiased estimates) and more stable correlations and heritability than the model with IBD, IBS or kinship matrices or any of the linear combinations.     

Semen parameters and testicular dimensions in small breed dogs below ten‐kilogram bodyweight

Because of few available data on semen parameters in small breed dogs, the study aimed to analyse semen and measure testes of dogs ≤10.0 kg bodyweight. Semen was collected from 41 fertile stud dogs, which were divided based on bodyweight: group 1 ≤ 5.0 kg and group 2 between 5.1 and 10.0 kg. Median values for ejaculate volume (group 1: 1.2 ml; group 2: 2.2 ml), total sperm output (group 1: 110.7 × 10⁶; group 2: 215.1 × 10⁶) and testicular volume (group 1: left testicle 2.8 ml, right testicle 2.7 ml; group 2: left testicle 5.5 ml, right testicle 5.0 ml) were lower in group 1 compared to dogs of group 2 (p = .001; p = .001; both testes: p < .001). There was no difference in sperm concentration (p = .985). Based on these results, introduction of an additional weight group to the commonly used reference values is recommended, since values for ejaculate volume, total sperm output and testicular dimensions for dogs ≤5.0 kg bodyweight differed significantly from values of dogs with a bodyweight from 5.1 to 10.0 kg.     

Production of N2 and N2O from nitrate ingested by sheep

Supplementing ruminants with nitrate reduces their enteric methane (CH₄) emissions; however, the greenhouse gas (GHG) mitigation achieved can be partially offset by small emissions of nitrous oxide (N₂O), a more potent GHG. Sheep were dosed intraruminally with ¹⁵ to investigate whether dietary is a precursor of N₂O and/or di‐nitrogen gas (N₂), and to quantify the amounts of recovered as N₂O and N₂ in gas emissions from sheep adapted or not adapted to dietary . Ruminally cannulated sheep were adapted to a hay diet supplemented with (n = 3; 10 g /kg DM) or urea (n = 3; 5.3 g urea/kg DM). On the day of the experiment all sheep were dosed intraruminally with ¹⁵ and quickly moved into gas‐tight chambers to enable recovery of ¹⁵N in N₂O and N₂ to be measured. Measurements of gases accumulating in the chambers were made over 10 successive 50 min periods; this enabled the amount of N₂O produced, and the recovery of ¹⁵‐N in N₂O and N₂ to be determined over a total of 10 hr. Only 0.04% of labelled ‐N was recovered as N₂O, and this was not dependent (p > .05) on whether or not the animals had been adapted to dietary . Approximatively 3% of ¹⁵‐N was recovered as ¹⁵N₂, which was also not dependent (p > .05) on whether sheep had been adapted to . Because the kinetics of rumen ammonia (NH₃) were uncertain, the recovery of ¹⁵N from in rumen NH₃ could not accurately be quantified, but our results suggest that approximately 76% of dietary was converted to NH₃ in the rumen. We conclude that the small amount of recovered in N₂ was evidence of denitrification, previously thought not to occur in the rumen.     

Interplay between heritability,genetic correlation and economic weighting in a selection index with and without genomic information

The availability of genomic information demands proper evaluation on how the kind (phenotypic versus genomic) and the amount of information influences the interplay of heritability (h²), genetic correlation () and economic weighting of traits with regard to the standard deviation of the index (σ_I). As σ_I is directly proportional to response to selection, it was the chosen parameter for comparing the indices. Three selection indices incorporating conventional and genomic information for a two trait (i and j) breeding goal were compared. Information sources were chosen corresponding to pig breeding applications. Index I incorporating an own performance in trait j served as reference scenario. In index II, additional information in both traits was contributed by a varying number of full‐sibs (2, 7, 50). In index III, the conventional own performance in trait j was combined with genomic information for both traits. The number of animals in the reference population (N_P = 1000, 5000, 10 000) and thus the accuracy of GBVs were varied. With more information included in the index, σ_I became more independent of , and relative economic weighting. This applied for index II (more full‐sibs) and for index III (more accurate GBVs). Standard deviations of index II with seven full‐sibs and index III with N_P = 1000 were similar when both traits had the same heritability. If the heritability of trait j was reduced ( = 0.1), σ_I of index III with N_P = 1000 was clearly higher than for index II with seven full‐sibs. When enhancing the relative economic weight of trait j, the decrease in σ_I of the conventional full‐sib index was much stronger than for index III. Our results imply that N_P = 1000 can be considered a minimum size for a reference population in pig breeding. These conclusions also hold for comparing the accuracies of the indices.     

Meta‐analysis of the energy and protein requirements of hair sheep raised in the tropical region of Brazil

The objective of this study was to estimate, through mathematical models, energy and protein requirements for maintenance and gain of hair sheep raised in the tropical region of Brazil. To determine the equation parameters, a meta‐analysis of seven independent experiments of nutrient requirements was performed, comprising a total of 243 experimental units (animals), which were conducted under tropical conditions, using hair sheep in growing and finishing phases and endowed of the following quantitative data for each animal: body weight (BW ), empty body weight (EBW ), average daily gain (ADG ), empty body gain (EBG ), heat production (HP ), metabolizable energy intake (MEI ), retained energy (RE ), metabolizable protein intake (MPI ) and body protein content. The regression equations generated were as follows: for Net Energy for maintenance, (NE _m): ; for Net Energy for gain, (NE _g): ; for Metabolizable Protein for maintenance,(MP _m): MPI _(g/day) = 24.8470 (±7.3646) + 560.28 (±99.6582) × EBG _(kg/day); for Net Protein for gain, (NP _g): . The NE _m requirement was 0.246 MJ EBW^?0.75 day^?1. The metabolizable energy for maintenance requirement was 0.391 MJ EBW^?0.75 day^?1. Considering an ADG of 100 g, the NE _g requirement ranged from 0.496 to 1.701 MJ/day for animals with BW ranging from 10 to 40 kg respectively. The efficiencies of use of the metabolizable energy for maintenance and gain were 0.63 and 0.36 respectively. The MP _m requirement was 3.097 g EBW^?0.75 day^?1. Considering an ADG of 100 g, the NP _g requirement ranged from 12.4 to 10.5 g/day for animals with BW ranging from 10 to 40 kg respectively. The total metabolizable energy and protein requirements were lower than those reported by the NRC and AFRC systems. Thus, our results support the hypothesis that nutrient requirements of hair sheep raised in tropical regions differ from wool sheep raised in temperate regions. Therefore, the use of the equations designed in this study is recommended.     

Effect of Intravenously Administered Crystalloid Solutions on Acid‐Base Balance in Domestic Animals

Intravenous fluid therapy can alter plasma acid‐base balance. The Stewart approach to acid‐base balance is uniquely suited to identify and quantify the effects of the cationic and anionic constituents of crystalloid solutions on plasma pH. The plasma strong ion difference (SID) and weak acid concentrations are similar to those of the administered fluid, more so at higher administration rates and with larger volumes. A crystalloid's in vivo effects on plasma pH are described by 3 general rules: SID > [] increases plasma pH (alkalosis); SID < [] decreases plasma pH (alkalosis); and SID = [] yields no change in plasma pH. The in vitro pH of commercially prepared crystalloid solutions has little to no effect on plasma pH because of their low titratable acidity. Appreciation of IV fluid composition and an understanding of basic physicochemical principles provide therapeutically valuable insights about how and why fluid therapy can produce and correct alterations of plasma acid‐base equilibrium. The ideal balanced crystalloid should (1) contain species‐specific concentrations of key electrolytes (Na⁺, Cl^?, K⁺, Ca⁺⁺, Mg⁺⁺), particularly Na⁺ and Cl^?; (2) maintain or normalize acid‐base balance (provide an appropriate SID); and (3) be isosmotic and isotonic (not induce inappropriate fluid shifts) with normal plasma.     

Founder representation and effective population size in old versus young breeds—genetic diversity of Finnish and Nordic Spitz

Finnish Spitz is 130‐year‐old breed and has been highly popular in Finland throughout its history. Nordic Spitz is very similar to Finnish Spitz by origin and use, but is a relatively recent breed with much smaller population size. To see how breed age and breeding history have influenced the current population, we performed comprehensive population genetic analysis using pedigree data of 28,119 Finnish and 9,009 Nordic Spitzes combined with genomewide single nucleotide polymorphism (SNP) data from 135 Finnish and 110 Nordic Spitzes. We found that the Finnish Spitz has undergone repeated male bottlenecks resulting in dramatic loss of genetic diversity, reflected by 20 effective founders (f_a) and mean heterozygosity (Hz) of 0.313. The realized effective population size in the breed based on pedigree analysis () is 168, whereas the genetic effective population size (N_eg) computed the decay of linkage disequilibrium (r²) is only 57 individuals. Nordic Spitz, although once been near extinction, has not been exposed to similar repeated bottlenecks than Finnish Spitz and had f_a of 27 individuals. However, due to the smaller total population size, the breed has also smaller effective population size than Finnish Spitz ( = 98 and N_eg = 49). Interestingly, the r² data show that the effective population size has contracted dramatically since the establishment of the breed, emphasizing the role of breed standards as constrains for the breeding population. Despite the small population size, Nordic Spitz still maintains SNP heterozygosity levels similar to mixed breed dogs (mean Hz = 0.409). Our study demonstrates that although pedigree analyses cannot provide estimates of the present diversity within a breed, the effective population sizes inferred from them correlate with the genotyping results. The genetic relationships of the northern Spitz breeds and the benefits of the open breed registry are discussed.     

Using heart rate to predict energy expenditure in large domestic dogs

The aim of this study was to establish heart rate as a measure of energy expenditure in large active kennel dogs (28 ± 3 kg bw). Therefore, the heart rate (HR)–oxygen consumption () relationship was analysed in Foxhound‐Boxer‐Ingelheim‐Labrador cross‐breds (FBI dogs) at rest and graded levels of exercise on a treadmill up to 60–65% of maximal aerobic capacity. To test for effects of training, HR and were measured in female dogs, before and after a training period, and after an adjacent training pause to test for reversibility of potential effects. Least squares regression was applied to describe the relationship between HR and . The applied training had no statistically significant effect on the HR– regression. A general regression line from all data collected was prepared to establish a general predictive equation for energy expenditure from HR in FBI dogs. The regression equation established in this study enables fast estimation of energy requirement for running activity. The equation is valid for large dogs weighing around 30 kg that run at ground level up to 15 km/h with a heart rate maximum of 190 bpm irrespective of the training level.     

An insight into population structure and gene flow within pure‐bred cats

Investigation of genetic structure on the basis of pedigree information requires indicators adapted to the specific context of the populations studied. On the basis of pedigree‐based estimates of diversity, we analysed genetic diversity, mating practices and gene flow among eight cat populations raised in France, five of them being single breeds and three consisting of breed groups with varieties that may interbreed. When computed on the basis of coancestry rate, effective population sizes ranged from 127 to 1406, while the contribution of founders from other breeds ranged from 0.7 to 16.4%. In the five breeds, F_IS ranged between 0.96 and 1.83%, with this result being related to mating practices such as close inbreeding (on average 5% of individuals being inbred within two generations). Within the three groups of varieties studied, F_IT ranged from 1.59 to 3%, while values were estimated between 0.04 and 0.91%, which was linked to various amounts of gene exchanges between subpopulations at the parental level. The results indicate that cat breeds constitute populations submitted to low selection intensity, contrasting with relatively high individual inbreeding level caused by close inbreeding practices.     

Across breed multi‐trait random regression genomic predictions in the Nordic Red dairy cattle

The current study evaluates reliability of genomic predictions in selection candidates using multi‐trait random regression model, which accounts for interactions between marker effects and breed of origin in the Nordic Red dairy cattle (RDC). The population structure of the RDC is admixed. Data consisted of individual animal breed proportions calculated from the full pedigree, deregressed proofs (DRP) of published estimated breeding values (EBV) for yield traits and genotypic data for 37 595 single nucleotide polymorphic markers. The analysed data included 3330 bulls in the reference population and 812 bulls that were used for validation. Direct genomic breeding values (DGV) were estimated using the model under study, which accounts for breed effects and also with GBLUP, which assume uniform population. Validation reliability was calculated as a coefficient of determination from weighted regression of DRP on DGV (), scaled by the mean reliability of DRP. Using the breed‐specific model increased the reliability of DGV by 2 and 3% for milk and protein, respectively, when compared to homogeneous population GBLUP. The exception was for fat, where there was no gain in reliability. Estimated validation reliabilities were low for milk (0.32) and protein (0.32) and slightly higher (0.42) for fat.     

Evaluation criterion for response to selection with constraint

The aims of the present study are to represent the concept of restricted breeding values algebraically and to propose a criterion for evaluating the genetic responses achieved by using a restricted selection procedure. An additive genetic mixed model characterized by multiple traits with constraints was assumed. If the random errors approach zero and the fixed effects can be completely estimated correctly in the model, the restricted best linear unbiased predictor of breeding values ( u _R) is equal to , where G ₀, C ₀, and u are the additive genetic variance‐covariance matrix for the q traits, the matrix for restriction, and the vector of breeding values, respectively. Therefore, if we want to evaluate the response to restricted selection, such as by a stochastic computer simulation study with known breeding values, we can use u _R as only one criterion.     

Estimation of genetic parameters for non‐return rate (NRR) in German herdbook Pietrain and Landrace AI boars

Between January 1993 and May 2000, 95 136 artificial insemination (AI) records of 445 Bavarian boars were recorded by three Bavarian AI stations. The analysis of the non‐return rate (NRR) was based on AI matings performed by AI technicians. The animal models applied for estimation of variance components for NRR included the fixed effects of AI station, breed of boar, first and subsequent insemination, type of insemination, duration of breeding period of the sow, and AI technician. Herd–year–season and permanent environment of the sow as well as the paternal additive genetic effects were taken into account as random effects. The estimation procedures employed for the described model were both linear and non‐linear. Genetic variances for the NRR (33‐55‐77 days after insemination) were small. Estimates of paternal heritability for NRR were low with (NRR33), (NRR55) as well as (NRR77) using the non‐linear model, and (NRR33), (NRR55) as well as (NRR77) employing the linear model. Due to the low heritabilities genetic progress on mating success for AI boars may be only possible, if sufficiently large numbers of observations are available.     

Nano zinc supplementation in goat (Capra hircus) ration improves immunity,serum zinc profile and IGF-1 hormones without affecting thyroid hormones

The trial was aimed at evaluating probable superiority, if any of nano zinc (NZn) over inorganic zinc (Zn) on immunity, serum minerals and T₃, T₄, and IGF-1 hormone profiles in goats. NZn was synthesized by using 0.45 M aqueous solution of Zn nitrate and 0.9 M aqueous solution of sodium hydroxide (average particle size 74 nm). Twenty-four male goats were grouped into four groups as per their body weight and were supplemented with either a basal diet with concentrate and straw at 50:50 ratio (Negative control, NC) alone or supplemented with 50 mg/kg Zn (Control) from inorganic Zn source, that is ZnO (IZn-50), 50 mg/kg Zn from NZn (NZn-50) or 25 mg/kg Zn from NZn (NZn-25). No change was observed in thyroid hormone status on zero and 90th day of experimental feeding, but NZn supplementation improved (p < 0.05) IGF-1 level on 90th day serum samples. Zn supplementation improved the humoral immunity in all the groups irrespective of the source. Similarly, cell-mediated immunity (CMI) measured by skinfold thickness after injecting Con-A, was also improved in Zn supplemented groups than control at 6, 12 and 48 h of incubation. NZn-50 animals showed highest HI (haemagglutination inhibition) titre as well as skin thickness. The (cluster of differentiation in %) was more (p < 0.05) in Zn supplemented groups. NZn-50 showed higher (p < 0.05) count than NC and similar (p > 0.05) to IZn-50 and NZn-25 groups without affecting (p > 0.05) the ratio of , among the treatment groups. Thus, NZn supplementation at 25 mg/kg had similar immunity and serum T₃, T₄ and IGF-1 profiles compared with IZn at 50 mg/kg dose.     

Cover Image,Volume 17, Issue 4

The cover image is based on the SHORT COMMUNICATION Clinical outcomes, ultrastructure and immunohistochemical features of canine high‐grade olfactory neuroblastoma by Molly E. Church et al., https://doi.org/10.1111/vco.12512 .

     

Advanced treatment technique for swine wastewater using two agents: Thermally polymerized amorphous silica and hydrated lime for color and phosphorus removal and sulfur for nitrogen removal

The efficacy of advanced treatment of swine wastewater using thermally polymerized, modified amorphous silica and hydrated lime (M‐CSH‐lime) for color and phosphorus removal and sulfur for nitrogen removal was examined with a demonstration‐scale treatment plant. The color removal rate was approximately 78% at M‐CSH‐lime addition rates of > 0.055 wt/v%. The ‐P removal rate exceeded 99.9% with > 0.023 wt/v%. pH of the effluent from the M‐CSH‐lime reactor increased with the addition rate till a maximum value of 12.7, which was effective in disinfection. The recovered M‐CSH‐lime would be suitable as a phosphorus fertilizer because the total P₂O₅ content was approximately 10%. The nitrogen oxide (NOx‐N) removal rate by sulfur denitrification increased to approximately 80% when the NOx‐N loading rate was around 0.1 kg‐N/ton‐S/day. It was suggested that the combination of the two processes would be effective in the advanced treatment of swine wastewater.     

Cover Image,Volume 17, Issue 3

The cover image is based on the SHORT COMMUNICATION Ultra‐frequent HRAS p.Q61R somatic mutation in canine acanthomatous ameloblastoma reveals pathogenic similarities with human ameloblastoma by Santiago Peralta et al., https://doi.org/10.1111/vco.12487 .

     

Splanchnic net balance of oxygen and metabolites in response to a discontinuous mesenteric vein infusion of ammonium in sheep

To simulate daily episodes of high absorption associated with the intake of diets with high N content, four wethers (42 ± 3.4 kg body weight), fitted with permanent catheters in the femoral artery and splanchnic vessels, were infused with 340 μmol into the mesenteric vein for 3 h, during the morning meal, over seven consecutive days. On the 7th day, mass transfers of , urea, glucose, lactate, ß‐OH‐butyrate and O₂ were measured across portal‐drained viscera (PDV), liver and splanchnic tissues during the last 90 min of the infusion. Measurements were repeated on the following day, at the same time, without the infusion. Plasma concentration in the portal vein (+332 μm ; p = 0.006), portal absorption (+424 μmol/min; p < 0.001), liver uptake (+375 μmol/min; p = 0.003) and urea N production (+338 μmol/min; p = 0.059) were higher during infusion. Mass transfers of urea, glucose, lactate, ß‐OH‐butyrate and O₂ across the PDV, and glucose, lactate, ß‐OH‐butyrate and O₂ across the liver, were not altered by the infusion. Results suggest that a daily, discontinuous increase in portal flow during a meal stimulates liver removal and urea N production but does not significantly affect liver glucose production and O₂ consumption in sheep.