The effect of including genomic relationships in the estimation of genetic parameters of functional traits in pigs

The term functionality in animal breeding is used for traits that increase the efficiency of production by lowering the input cost, such as animal health and leg weakness related to longevity. The main objective of the study was to investigate the impact of genomic information, in a multivariate variance component analysis, on some of these traits. In addition, the effect of the inclusion was studied by testing the model's prediction ability based on best linear unbiased estimates for fixed and random effects. The material in this study consists of phenotypes from 76 683 animals, of which 4933 animals are genotyped. The heritabilities for front leg conformation, stayability, osteochondrosis and arched back, estimated using the traditional pedigree, were found to be between 0.12 and 0.29. When using the combined genomic and pedigree relationship matrix, the heritabilities were between 0.14 and 0.36. The results show that the combined relationship matrix can be used for the estimation of (co)variance components, and that the predictive ability of the model in this study marginally increases with the inclusion of genomic information.     

Use of genomic recursions and algorithm for proven and young animals for single‐step genomic BLUP analyses – a simulation study

The purpose of this study was to examine accuracy of genomic selection via single‐step genomic BLUP (ssGBLUP) when the direct inverse of the genomic relationship matrix ( G ) is replaced by an approximation of G ^?1 based on recursions for young genotyped animals conditioned on a subset of proven animals, termed algorithm for proven and young animals (APY). With the efficient implementation, this algorithm has a cubic cost with proven animals and linear with young animals. Ten duplicate data sets mimicking a dairy cattle population were simulated. In a first scenario, genomic information for 20k genotyped bulls, divided in 7k proven and 13k young bulls, was generated for each replicate. In a second scenario, 5k genotyped cows with phenotypes were included in the analysis as young animals. Accuracies (average for the 10 replicates) in regular EBV were 0.72 and 0.34 for proven and young animals, respectively. When genomic information was included, they increased to 0.75 and 0.50. No differences between genomic EBV (GEBV) obtained with the regular G ^?1 and the approximated G ^?1 via the recursive method were observed. In the second scenario, accuracies in GEBV (0.76, 0.51 and 0.59 for proven bulls, young males and young females, respectively) were also higher than those in EBV (0.72, 0.35 and 0.49). Again, no differences between GEBV with regular G ^?1 and with recursions were observed. With the recursive algorithm, the number of iterations to achieve convergence was reduced from 227 to 206 in the first scenario and from 232 to 209 in the second scenario. Cows can be treated as young animals in APY without reducing the accuracy. The proposed algorithm can be implemented to reduce computing costs and to overcome current limitations on the number of genotyped animals in the ssGBLUP method.     

The role of head computed tomography in equine practice

This retrospective study describes the computed tomography (CT) findings in 59 horses presented with diseases of the head over 8 years that underwent CT examination of this region, including dental or sinonasal diseases (Group A) (n = 42), osseous and/or articular diseases (Group B) (n = 11) and soft tissue diseases (Group C) (n = 6). For Group A, radiographic and CT findings comparison was possible. Computed tomography had higher sensitivity (100%) and specificity (96.7%) than radiography in diagnosing dental disease. Compared to CT, radiographic identification of sinus involvement was less sensitive, particularly for ventral conchal and sphenopalatine sinuses and presented an overall sensitivity of 43.5 and 16.7%, respectively. In Group B CT allowed identification of a higher number of bone fragments and fractures in the maxillary, lacrimal, sphenoidal, temporal and zygomatic bones not identified radiographically. Accurate identification of CT changes in the temporomandibular joint and temporohyoid articulation was also possible. Group C included both intra‐ and extra‐cranial disease, retrobulbar masses being the most representative pathology (n = 3). In this group, CT was considered the gold standard for detection of periorbital diseases. We conclude that CT is an imaging technique with high diagnostic value for evaluating the equine head, yielding additional information over multiple radiographic views, which may alter the outcome of the case. Additionally, this paper reports several conditions not previously described using CT.     

Effects of different rearing systems on muscle and meat quality traits of slow- and medium-growing male chickens

1. This experiment was conducted to evaluate the effect of production system on the meat quality of slow- and medium-growing chickens. A total of 1075 1-d-old male chicks were equally divided into 6 experimental groups, represented by three strains (SG: TETRA-H, MG1: TETRA HB Color, MG2: Shaver Farm) and were reared in a poultry house in floor pens (12 males/m²).

2. On d 49, 150 healthy birds (50/genotype) were placed in a free-range family farm while the rest of the birds remained indoors. All birds were fed ad libitum and consumed the same diet. On d 70, 20 birds of each experimental group were slaughtered and muscle samples were taken from the left breast and thigh muscles.

3. Thigh muscle of SG males kept on free range was darker (L* = 75.12 vs. 78.33) with lower frying loss (45.9% vs. 55.9%) compared with the indoor group. Similar results were obtained from the MG1 group. Free-range MG2 males had lighter thigh meat (L* = 50.7 vs. 57.8) and lower frying loss compared to the indoor group.

4. In general, the indoor treatment had a lower impact on breast meat than the outdoor system. Regardless of the rearing system, genotypic differences were more pronounced in thigh than in breast muscle.

     

Colostrogenesis during an induced lactation in dairy cattle

Colostrum immunoglobulin G (IgG) is of major importance for the newborn calf because epitheliochorial placentae do not provide transport in utero. The formation of colostrum occurs in the later stages of pregnancy. Our objectives were to induce lactation in non‐pregnant dairy cows and (i) to determine the changes of IgG in serum and mammary secretions during the induction process and (ii) to establish α‐lactalbumin (αLA) and prolactin (Prl) alterations to monitor the changing mammary epithelial tight junction status and development pattern. Estradiol‐17β (E2) and progesterone (P4) injections in a 1–7 days series were combined with a 3‐day injection series (day 21–23) of dexamethasone (DEX). Blood and both front quarter secretion samples were collected daily. Milking started 24 days after the start of the experiment. Results show that the mammary secretory IgG1 was increased at >7 days after the start of steroid injections and depicted a bimodal pattern reaching a high of 16 mg/ml at 21 day compared with 3.2 mg/ml in the serum. There was a small increase in secretory IgG2 that did not correlate with tight junction status, but never reached the serum concentration. The injections of DEX resulted in constriction of tight junctions. Secretory αLA was immediately increased with steroid injections, dropped precipitously after 7 days and then began a steady increase until the start of milking. Changes in serum αLA are related to mammary tight junctions while serum Prl gradually increased from 30 to >60 ng/ml after the steroid injections stopped. These results provide insights into the mechanisms and timing of colostrogenesis during an induced lactation protocol.     

Influence of race and crossbreeding on casein micelles size

Casein (CN) micelles are colloidal aggregates of protein dispersed in milk, the importance of which in the dairy industry is related to functionality and yield in dairy products. The objective of this work was to investigate the correlation of milk CN micelles diameter from Holstein and Zebu crossbreds with milk composition (protein, fat, lactose, total and nonfat solids and milk urea nitrogen), somatic cell count (SCC), age, lactation stage and production. Average casein micelles diameters of milk samples obtained from 200 cows were measured using photon correlation spectroscopy and multiple regression analysis was used to find relationship between variables. CN micelle diameter, SCC and nonfat solids were different between animals with different Holstein crossbreed ratios, which suggests influence of genetic factors, mammary gland health and milk composition. Overall, results indicate the potential use of CN micelle diameter as a tool to select animals to produce milk more suitable to cheese production.     

Prevalence of Type VI Secretion System in Spanish Campylobacter jejuni Isolates

Infections from Campylobacter jejuni pose a serious public health problem and are now considered the leading cause of foodborne bacterial gastroenteritis throughout the world. Sequencing of C. jejuni genomes has previously allowed a number of loci to be identified, which encode virulence factors that aid survival and pathogenicity. Recently, a Type VI secretion system (T6SS) consisting of 13 conserved genes was described in C. jejuni strains and recognised to promote pathogenicity and adaptation to the environment. In this study, we determined the presence of this T6SS in 63 Spanish C. jejuni isolates from the food chain and urban effluents using whole‐genome sequencing. Our findings demonstrated that nine (14%) strains harboured the 13 ORFs found in prototype strain C. jejuni 108. Further studies will be necessary to determine the prevalence and importance of T6SS‐positive C. jejuni strains.     

Methane emissions and δ13C composition from beef steers consuming increasing proportions of sericea lespedeza hay on bermudagrass hay diets

An experiment was conducted to evaluate the effects of different proportions of ‘Au Grazer’ sericea lespedeza [SL, Lespedeza cuneata (Dum. Cours.) G. Don], a legume rich in condensed tannins (CT), on nutrient intake and digestibility, and to estimate methane (CH₄) emissions and ¹³C isotopic composition (δ¹³C_CH4) from beef steers consuming a forage-based diet. Twenty-five Angus-crossbred steers were distributed in a randomized complete block design (344 ± 48 kg initial BW), and randomly assigned to one of five treatments: 0SL, 25SL, 50SL, 75SL, and 100SL, diets containing 0%, 25%, 50%, 75%, and 100% of SL hay, respectively, mixed with ‘Tifton-85’ bermudagrass hay (Cynodon spp.). The study was carried out for two experimental periods of 21-d each. The statistical model included the fixed effect of treatment and random effects of block, experimental period, and their interaction. Apparent total tract digestibility of crude protein, neutral detergent fiber, and acid detergent fiber was linearly decreased (P < 0.001) by the inclusion of SL. No effects were observed for total CH₄ emissions per day, nor for CH₄ relative to organic matter intake or digestible organic matter with the inclusion of SL. However, emission of CH₄ in relation to intake of CT was affected by treatment (P < 0.001). A linear (P < 0.001) decrease and a quadratic effect (P < 0.001) were observed for δ¹³C of diets and gas, respectively, in which diets and enteric CH₄ with greater inclusion of SL were more depleted in ¹³C. Moreover, the difference in δ¹³C between diets and gas (Δδ¹³C) had a linear decrease (P = 0.001) with the inclusion of SL. The model developed to predict the C₃ proportions in the enteric CH₄ fitted to predicted values (P < 0.0001). Therefore, greater proportions of SL resulted in lesser CH₄ emission when CT intake was considered and the isotopic composition from enteric CH₄ was able to predict the contribution of SL in the emissions.     

HPLC separation and NMR structural elucidation of sn-1,2-, 2,3-, and 1,3-diacylglycerols from olive oil as naphthylethylurethane derivatives

In this study, sn-1,2-, sn-2,3-, and sn-1,3-diacylglycerols were isolated from olive oil, and their urethane derivatives (urethanes) were prepared. Normal-phase high-performance liquid chromatography (NP-HPLC) separation of the urethane isomers was performed and the separate classes were studied by nuclear magnetic resonance (NMR). The use of 1H NMR and homo- and heteronuclear 2D techniques provided a great amount of information in a very short time, particularly when a high-field NMR instrument (700 MHz) was used. Particularly diagnostic for this kind of compound was the glyceridic moiety that presents typical chemical shifts both for carbon and hydrogen. These studies show the usefulness of NMR spectroscopy to recognize clearly the sn-1,3- and, moreover, sn-1,2- with respect to sn-2,3-diacylglycerols, although very minor differences occur between them.     

Convenient large-scale purification of yessotoxin from Protoceratium reticulatum culture and isolation of a novel furanoyessotoxin

Yessotoxins from a large-scale culture (226 L) of Protoceratium reticulatum strain CAWD129 were harvested by filtration followed by solid-phase extraction. The extract was purified by column chromatography over basic alumina and reverse-phase flash chromatography to afford pure yessotoxin (193 mg). Isolation of yessotoxin was greatly facilitated by selection of a strain which did not produce analogues that interfered with yessotoxin isolation. In addition to yessotoxin, numerous minor yessotoxins were detected by LC-MS in other fractions. From one of these, an early eluting minor analogue with the same molecular weight as yessotoxin and a similar mass spectrometric fragmentation pattern was isolated. This analogue was identified by NMR and mass spectrometry as a novel yessotoxin analogue containing a furan ring in the side chain. This finding reveals biosynthetic flexibility of the yessotoxin pathway in P. reticulatum and confirms earlier findings of production of many minor yessotoxin analogues by this alga. Production of these analogues appeared to be a constitutive trait of P. reticulatum CAWD129.