Identify known and novel candidate genes associated with backfat thickness in Duroc pigs by large-scale genome-wide association analysis

Backfat thickness (BFT) is complex and economically important traits in the pig industry, since it reflects fat deposition and can be used to measure the carcass lean meat percentage in pigs. In this study, all 6,550 pigs were genotyped using the Geneseek Porcine 50K SNP Chip to identify SNPs related to BFT and to search for candidate genes through genome-wide association analysis in two Duroc populations. In total, 80 SNPs, including 39 significant and 41 suggestive SNPs, and 6 QTLs were identified significantly associated with the BFT. In addition, 9 candidate genes, including a proven major gene MC4R, 3 important candidate genes (RYR1, HMGA1 and NUDT3) which were previously described as related to BFT, and 5 novel candidate genes (SIRT2, NKAIN2, AMH, SORCS1 and SORCS3) were found based on their potential functional roles in BFT. The functions of candidate genes and gene set enrichment analysis indicate that most important pathways are related to energy homeostasis and adipogenesis. Finally, our data suggests that most of the candidate genes can be directly used for genetic improvement through molecular markers, except that the MC4R gene has an antagonistic effect on growth rate and carcass lean meat percentage in breeding. Our results will advance our understanding of the complex genetic architecture of BFT traits, and laid the foundation for additional genetic studies to increase carcass lean meat percentage of pig through marker-assisted selection and/or genomic selection.

Predicting Metabolizable Energy from Digestible Energy for Growing and Finishing Beef Cattle and Relationships to Prediction of Methane

Reliable predictions of metabolizable energy (ME) from digestible energy (DE) are necessary to prescribe nutrient requirements of beef cattle accurately. A previously developed database that included 87 treatment means from 23 respiration calorimetry studies has been updated to evaluate the efficiency of converting DE to ME by adding 47 treatment means from 11 additional studies. Diets were fed to growing-finishing cattle under individual feeding conditions. A citation-adjusted linear regression equation was developed where dietary ME concentration (Mcal/kg of dry matter [DM]) was the dependent variable and dietary DE concentration (Mcal/kg) was the independent variable: ME = 1.0001 × DE – 0.3926; r 2 = 0.99, root mean square prediction error [RMSPE] = 0.04, P < 0.01 for the intercept and slope). The slope did not differ from unity (95% CI = 0.936 to 1.065); therefore, the intercept (95% CI = -0.567 to -0.218) defines the value of ME predicted from DE. For practical use, we recommend ME = DE – 0.39. Based on the relationship between DE and ME, we calculated the citation-adjusted loss of methane, which yielded a value of 0.2433 Mcal/kg of DMI (SE = 0.0134). This value was also adjusted for the effects of dry matter intake (DMI) above maintenance, yielding a citation-adjusted relationship: CH4, Mcal/kg = 0.3344 – 0.05639 × multiple of maintenance; r 2 = 0.536, RMSPE = 0.0245, P < 0.01 for the intercept and slope). Both the 0.2433 value and the result of the intake-adjusted equation can be multiplied by DMI to yield an estimate of methane production. These two approaches were evaluated using a second, independent database comprising 129 data points from 29 published studies. Four equations in the literature that used DMI or intake energy to predict methane production also were evaluated with the second database. The mean bias was substantially greater for the two new equations, but slope bias was substantially less than noted for the other DMI-based equations. Our results suggest that ME for growing and finishing cattle can be predicted from DE across a wide range of diets, cattle types, and intake levels by simply subtracting a constant from DE. Mean bias associated with our two new methane emission equations suggests that further research is needed to determine whether coefficients to predict methane from DMI could be developed for specific diet types, levels of DMI relative to body weight, or other variables that affect the emission of methane.

Development of genomic predictions for Angus cattle in Brazil incorporating genotypes from related American sires

Genomic prediction has become the new standard for genetic improvement programs, and currently, there is a desire to implement this technology for the evaluation of Angus cattle in Brazil. Thus, the main objective of this study was to assess the feasibility of evaluating young Brazilian Angus (BA) bulls and heifers for 12 routinely recorded traits using single-step genomic BLUP (ssGBLUP) with and without genotypes from American Angus (AA) sires. The second objective was to obtain estimates of effective population size (Ne) and linkage disequilibrium (LD) in the Brazilian Angus population. The dataset contained phenotypic information for up to 277,661 animals belonging to the Promebo® breeding program, pedigree for 362,900, of which 1,386 were genotyped for 50k, 77k, and 150k SNP panels. After imputation and quality control, 61,666 SNP were available for the analyses. In addition, genotypes from 332 American Angus (AA) sires widely used in Brazil were retrieved from the AA Association database to be used for genomic predictions. Bivariate animal models were used to estimate variance components, traditional EBV, and genomic EBV (GEBV). Validation was carried out with the linear regression method (LR) using young-genotyped animals born between 2013 and 2015 without phenotypes in the reduced dataset and with records in the complete dataset. Validation animals were further split into progeny of BA and AA sires to evaluate if their progenies would benefit by including genotypes from AA sires. The Ne was 254 based on pedigree and 197 based on LD, and the average LD (±SD) and distance between adjacent SNPs across all chromosomes was 0.27 (±0.27) and 40743.68 bp, respectively. Prediction accuracies with ssGBLUP outperformed BLUP for all traits, improving accuracies by, on average, 16% for BA young bulls and heifers. The GEBV prediction accuracies ranged from 0.37 (total maternal for weaning weight and tick count) to 0.54 (yearling precocity) across all traits, and dispersion (LR coefficients) fluctuated between 0.92 and 1.06. Inclusion of genotyped sires from the AA improved GEBV accuracies by 2%, on average, compared to using only the BA reference population. Our study indicated that genomic information could help to improve GEBV accuracies and hence genetic progress in the Brazilian Angus population. The inclusion of genotypes from American Angus sires heavily used in Brazil just marginally increased the GEBV accuracies for selection candidates.

Concentration and heritability of immunoglobulin G and natural antibody immunoglobulin M in dairy and beef colostrum along with serum total protein in their calves

Immunoglobulin (Ig) G and natural antibody (NAb) IgM are passively transferred to the neonatal calf through bovine colostrum. Maternal IgG provides pathogen- or vaccine-specific protection and comprises about 85 percent of colostral Ig. Natural antibody IgM is less abundant but provides broad and non-specific reactivity, potentially contributing to protection against the dissemination of pathogens in the blood (septicemia) in a calf’s first days of life. In the dairy and beef industries, failure of passive transfer (FPT) of colostral Ig (serum total protein (STP) <5.2 g/dL) is still a common concern. The objectives of this study were to, i) compare colostral IgG concentrations and NAb-IgM titers between dairy and beef cows; ii) assess the effect of beef breed on colostral IgG; iii) compare passive transfer of colostral Ig in dairy and beef calves; and iv) estimate the heritability of colostral IgG and NAb-IgM. Colostrum was collected from Holstein dairy (n=282) and crossbred beef (n=168) cows at the University of Guelph dairy and beef research centres. Colostral IgG was quantified by radial immunodiffusion and NAb-IgM was quantified by an enzyme-linked immunosorbent assay. In dairy (n=308) and beef (n=169) calves, STP was estimated by digital refractometry. Beef cows had significantly greater colostral IgG (146.5 ± 9.5 SEM g/L) than dairy cows (92.4 ± 5.2 g/L, p <0.01). Beef cows with a higher proportion of Angus ancestry had significantly lower colostral IgG (125.5 ± 5.8 g/L) than cows grouped as “Other” (142.5 ± 4.9 g/L, p= 0.02). Using the FPT cut-off, 13% of dairy and 16% of beef calves had FPT; still, beef calves had a significantly larger proportion with excellent passive transfer (STP ≥6.2 g/dL, p <0.01). The heritability of colostral IgG was 0.04 (± 0.14) in dairy and 0.14 (± 0.32) in beef. Colostral NAb-IgM titers in dairy (12.12 ± 0.22, log2 (reciprocal of titer)) and beef cows (12.03 ± 0.19) did not differ significantly (p=0.71). The range of NAb-IgM titers was 9.18 to 14.60, equivalent to a 42-fold range in antibody concentration. The heritability of colostral NAb was 0.24 (± 0.16) in dairy and 0.11 (± 0.19) in beef cows. This study is the first to compare colostral NAb-IgM between dairy and beef cows. Based on the range in NAb-IgM titers and the heritability, selective breeding may improve colostrum quality and protection for neonatal calves in the early days of life.

Effect of amino acid blend as alternative to antibiotics for growing pigs

This study aimed to evaluate the effect of supplementing arginine (Arg) + glutamine (Gln) replacing antibiotics on performance, immune response, and antioxidant capacity of pigs in the growing phase. One hundred and fifty 63-d-old pigs with initial body weight (BW) of 25.0 ± 1.46 kg were distributed in a randomized block design, with three treatments and ten replicates. The three diets were control; antibiotic, control + 100 mg/kg tiamulin and 506 mg/kg oxytetracycline; amino acid, control + 10 g/kg Arg and 2 g/kg Gln. Dietary treatments were fed from 63 to 77 d. Following the treatment period, all pigs were fed the control diet from 77 to 90 d. Data were analyzed using GLIMMIX and UNIVARIATE in SAS 9.4. From 63 to 70 d, pigs fed diets with antibiotics had improved (P < 0.05) average daily feed intake (ADFI), average daily weight gain (ADG), gain to feed ratio (G:F), and 70 d BW compared to those fed control or amino acid diets. From 70 to 77 d, including antibiotics in the diet increased (P < 0.05) ADG and 77 d BW. From 77 to 90 d, pigs fed the amino acid diet had greater (P < 0.05) ADG and ADFI than those fed an antibiotic diet. From 63 to 90 d, although pig performance was not affected (P > 0.05), growth curve of pigs fed the antibiotic diets was different (P < 0.05) from those fed the control and amino acids diets. At 70 d, serum tumor necrosis factor-α and diamine oxidase (DAO) were lower (P < 0.05) in pigs fed the antibiotic diet than the control diet, and pigs fed the amino acid diet had intermediate results. Ferric reducing antioxidant power (FRAP) was lower (P < 0.05) in pigs fed the amino acid diet than the antibiotic diet, and pigs fed the control diet had intermediate results. At 70 and 77 d, serum urea nitrogen was higher (P < 0.05) in pigs fed the amino acid diet. At 77 d, DAO and serum immunoglobulin G was lower (P < 0.05) in pigs fed the antibiotic diet. FRAP was lower (P < 0.05) in pigs fed the amino acid and control diets. Serum malondialdehyde was higher (P < 0.05) in pigs fed the amino acid diet than those fed the control diet, and pigs fed the antibiotic diet had intermediate results. At 90 d, antibiotics or amino acids did not affect (P > 0.05) serum parameters. Amino acid blend supplementation at the selected doses in this study did not positively affect growing pigs. Although from 63 to 77 d, antibiotics improved performance, when considering the overall study period, growing pigs did not benefit from a diet containing antibiotics.

Correlations of gestational hemoglobin, placental mineral elements and reproductive performances in pregnant sows

Iron status of sows has a great influence on reproductive performance. Iron deficiency reduces reproductive performance and newborn piglet survival rate of sow. The hemoglobin is a potential predictor for iron status of sows and is convenient for rapid detection in pig farms. However, the relationship between iron status, hemoglobin, placental trace elements and reproductive performance remains unclear. In this study, the hemoglobin and reproductive performance of more than 500 sows with 1 st to 6 th parities at different gestation stages (25, 55, 75, 95, 110 days of gestation) in two large-scale sow farms were collected, and content of placental Fe, Zn, Mn and Cu was analyzed. The results show hemoglobin of sows during pregnancy (d 75, d 95, d 110) decreased significantly (P < 0.001). As the parity increases, the hemoglobin levels of sows at d 25, d 55 of gestation and placental mineral element contents included Fe, Zn, Mn and Cu at delivery decreased (P < 0.05), while the litter size, birth alive and litter weights increased gradually (P < 0.001). Furthermore, hemoglobin during pregnancy had a negative linear correlation with litter weight and average weight (P < 0.05), higher hemoglobin at d 25 of gestation may reduce the number of stillbirths (P = 0.05), but higher hemoglobin at d 110 of gestation was tend to be benefit for the birth (P = 0.01). And there was a significant positive linear correlation between hemoglobin at d 110 of gestation and placental Fe and Mn levels (P = 0.002, P = 0.013). There was also a significant positive linear correlation among Fe, Zn, Mn and Cu in the placenta (P < 0.001). The levels of Fe, Zn, and Mn in placental at delivery were positive related to the average weight of the fetus (P = 0.048, P = 0.027, P = 0.047), and placental Cu was linearly correlated with litter size (P = 0.029). Our research revealed the requirements for iron during gestation were varied in different gestation periods and parities. The feeds should be adjusted according to the gestation periods, parities or iron status to meet the iron requirements of sows and fetal pigs.

Modifying the NRC weight gain model to estimate daily gain for stockers grazing bermudagrass in the southern United States

The energy requirements, feed intake, and performance of grazing animals vary daily due to changes in weather conditions, forage nutritive values, and plant and animal maturity throughout the grazing season. Hence, realistic simulations of daily animal performance can be made only by the models that can address these changes. Given the dearth of simple, user-friendly models of this kind, especially for pastures, we developed a daily gain model for large-frame stockers grazing bermudagrass [Cynodon dactylon (L.) Pers.], a widely-used warm-season perennial grass in the southern United States. For model development, we first assembled some of the classic works in forage-beef modeling in the last 50 years into the National Research Council (NRC, 1984) weight gain model. Then, we tested it using the average daily gain (ADG) data obtained from several locations in the southern United States. The evaluation results showed that the performance of the NRC model was poor as it consistently underpredicted ADG throughout the grazing season. To improve the predictive accuracy of the NRC model to make it perform under bermudagrass grazing conditions, we made an adjustment on the model by adding the daily departures of the modeled values from the data trendline. Subsequently, we tested the revised model against an independent set of ADG data obtained from eight research locations in the region involving about 4,800 animals, using 30 years (1991-2020) of daily weather data. The values of the various measures of fit used, namely the Willmott index of 0.92, the modeling efficiency of 0.75, the R 2 of 0.76, the root mean square error of 0.13 kg d -1, and the prediction error relative to the mean observed data of 24% demonstrated that the revised model mimicked the pattern of observed ADG data satisfactorily. Unlike the original model, the revised model predicted more closely the ADG value throughout the grazing season. The revised model may be useful to accurately reflect the impacts of daily weather conditions, forage nutritive values, seasonality, and plant and animal maturity on animal performance.

Characterizing the effect of incrementally increasing dry bulb temperature on linear and nonlinear measures of heart rate variability in non-pregnant, mid-gestation, and late-gestation sows

Characterizing the sow physiological response to an increased heat load is essential for effective heat stress mitigation. The study objective was to characterize the effects of a 400-min heating episode on sow heart rate variability (HRV) at different reproductive stages. Heart rate variability is a commonly used non-invasive proxy measure of autonomic function. Twenty-seven sows were enrolled in the study according to their gestation stage at time of selection: 1) non-pregnant (NP; n = 7), 2) mid-gestation (MID; 57.3 ± 11.8 d gestation; n = 11), and 3) late-gestation (LATE; 98.8 ± 4.9 d gestation; n = 8). The HRV data utilized in the study were collected from each pig as the dry bulb temperature in the room increased incrementally from 19.84 ± 2.15 °C to 35.54 ± 0.43 °C (range: 17.1 – 37.5 °C) over a 400-min period. After data collection, one 5-min set of continuous heart rate data were identified per pig for each of nine temperature intervals (19 to 20.99, 21 to 22.99, 23 to 24.99, 25 to 26.99, 27 to 28.99, 29 to 30.99, 31 to 32.99, 33 to 34.99, 35 to 36.99 °C). Mean inter-beat interval length (RR), standard deviation of r-r intervals (SDNN), root mean square of successive differences (RMSSD), high frequency spectral power (HF), sample entropy (SampEn), short-term detrended fluctuation analysis (DFAα1), and three measures (%REC, DET, LMEAN) derived from recurrence quantification analysis were calculated for each data set. All data were analyzed using the PROC GLIMMIX procedure in SAS 9.4. Overall, LATE sows exhibited lower RR than NP sows (P < 0.01). The standard deviation of r-r intervals and RMSSD differed between each group (P < 0.01), with LATE sows exhibiting the lowest SDNN and RMSSD and NP sows exhibiting the greatest SDNN and RMSSD. Late-gestation sows exhibited lower HF than both MID and NP sows (P < 0.0001), greater DFA values than NP sows (P = 0.05), and greater DET compared to MID sows (P = 0.001). Late-gestation also sows exhibited greater %REC and LMEAN compared to MID (P < 0.01) and NP sows (all P < 0.01). In conclusion, LATE sows exhibited indicators of greater autonomic stress throughout the heating period compared to MID and NP sows. However, temperature by treatment interactions were not detected as dry bulb increased. Future studies are needed to fully elucidate the effect of gestational stage and increasing dry bulb temperature on sow HRV.

Effects of increased ambient temperature and supplemental altrenogest prior to pregnancy establishment in gilts

Heat stress (HS) mitigation strategies are critically needed to combat the substantial economic effects on animal agriculture. The manifestations of seasonal infertility include delayed puberty onset, reduced conception rates, decreased litter size, and increased wean to estrus interval. To assess the effects of HS during early gestation and evaluate a benefit of supplemental altrenogest (ALT) as a mitigation strategy, thirty crossbred post-pubertal gilts (157 ± 11 kg) were subjected to estrous synchronization via 14 d oral administration of ALT. Artificial insemination during estrus was performed and gilts were then placed into one of four treatment groups; heat stress (HS; 35 ± 1 οC for 12h/31.60 ± 1 οC for 12h) with (HSALT, n = 7) or without (HSCON, n = 7) 15 mg/d ALT supplementation or thermal neutral (TN; 20 ± 1 οC) conditions with (TNALT, n = 8) or without (TNCON, n = 8) 15 mg/d ALT supplementation until 12 d post-estrus (dpe). Administrating ALT occurred at 0600 h from 3-12 dpe and rectal temperatures (TR) and respiration rates (RR) were recorded. Blood was collected via jugular venipuncture on 0, 4, 8 and 12 dpe. Gilts were euthanized humanely at 12 dpe followed by collection of ovarian tissue, and uterine flushing for conceptus collection. In HS compared to TN gilts, RR and TR were increased (P < 0.01) but unaffected by ALT supplementation. Feed intake (FI) was reduced (P < 0.01) by HS but unaltered by ALT treatment. Corpora lutea (CL) weight was reduced (P < 0.01) in HSCON gilts when compared to TNCON and HSALT gilts despite progesterone (P4) concentrations in serum and luteal tissue not being affected by treatment (P ≥ 0.10). CL diameter was reduced (P ≤ 0.05) in HSALT gilts compared to other treatments. Interleukin-1β (IL1B) uterine flush concentration was not affected (P > 0.20) by environment or ALT supplementation, although moderate (P = 0.06) interaction between environment and ALT existed, as IL1B concentration in TNALT was increased (P = 0.03) compared to TNCON gilts. While environment did not affect conceptus development (P = 0.90), ALT supplementation advanced conceptus elongation (P < 0.01). Collectively, these data demonstrate that HS may affect luteal development prior to pregnancy establishment, and ALT increases conceptus elongation by12 dpe.

Pulmonary arterial pressure in fattened Angus steers at moderate altitude influences early postmortem mitochondria functionality and meat color during retail display

Pulmonary hypertension is a noninfectious disease of cattle at altitudes > 1524 m (5,000 ft). Mean pulmonary arterial pressures (PAP) are used as an indicator for pulmonary hypertension in cattle. High PAP cattle (≥ 50 mmHg) entering the feedlot at moderate elevations have lower feed efficiency as compared to low PAP cattle (< 50 mmHg). The impact of pulmonary arterial pressure on mitochondrial function, oxidative phosphorylation (OXPHOS) protein abundance, and meat color was examined using longissimus lumborum (LL) from high (98 ± 13 mmHg; n = 5) and low (41 ± 3 mmHg; n = 6) PAP fattened Angus steers (live weight of 588 ± 38 kg) during early postmortem period (2 h and 48 h) and retail display (day 1 to 9), respectively. High PAP muscle had greater (P = 0.013) OXPHOS-linked respiration and proton leak-associated respiration than low PAP muscles at 2 h postmortem but rapidly declined to be similar (P = 0.145) to low PAP muscle by 48 h postmortem. OXPHOS protein expression was higher (P = 0.045) in low PAP than high PAP muscle. During retail display, redness, chroma, hue, ratio of reflectance at 630 nm and 580 nm, and metmyoglobin reducing activity decreased faster (P < 0.05) in high PAP steaks than low PAP. Lipid oxidation significantly increased (P < 0.05) in high PAP steaks but not (P > 0.05) in low PAP. The results indicated that high PAP caused a lower OXPHOS efficiency and a greater fuel oxidation rates under conditions of low ATP demand in premortem beef LL muscle, this could explain the lower feed efficiency in high PAP feedlot cattle compared to low PAP counterparts. Mitochondrial integral function (membrane integrity or/and protein function) declined faster in high PAP than low PAP muscle at early postmortem. LL steaks from high PAP animals had lower color stability than those from the low PAP animals during simulated retail display, which could be partially attributed to the loss of muscle mitochondrial function at early postmortem by ROS damage in high PAP muscle. Pulmonary arterial hypertension could also decrease type I/type II muscle fiber ratio in skeletal muscle, which needs to be investigated further.