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Previous studies have demonstrated evidence for a relationship between the vaginal microbiome and reproductive performance, suggesting the vaginal microbiota may serve as a tool to predict farrowing outcomes in commercial pigs. In this study, we compared the vaginal microbiome in sows with low and high farrowing performance and used it to classify animals with contrasting reproductive outcomes in commercial sows following immune challenge with porcine respiratory and reproductive syndrome (PRRS) vaccination. Eighteen microbes were differentially abundant (q-value Campylobacter, Bacteroides, Porphyromonas, Lachnospiraceae unclassified, Prevotella, and Phascolarctobacterium were also selected in the discriminant and linear regression analyses, and could be used as potential biomarkers for reproductive outcomes. The correct classification rate in the two groups was 100%. In conclusion, this study demonstrates that vaginal microbiota collected after PRRS vaccination could be potentially used to classify sows into having low or high farrowing performance in commercial herds.

Porcine Reproductive and Respiratory Syndrome (PRRS) is historically the most economically important swine disease worldwide that severely affects the reproductive performance of sows. However, little is still known about the genetic basis of reproductive performance in purebred herds during a PRRS outbreak through the comparison of maternal and terminal breeds. Thus, the objective of this work was to explore the host genetics of response to PRRS in purebred sows from two breeds. Reproductive data included 2546 Duroc and 2522 Landrace litters from 894 and 813 purebred sows, respectively, which had high-density genotype data available (29,799 single nucleotide polymorphisms; SNPs). The data were split into pre-PRRS, PRRS, and post-PRRS phases based on standardized farrow-year-week estimates. Heritability estimates for reproductive traits were low to moderate (≤0.20) for Duroc and Landrace across PRRS phases. On the other hand, genetic correlations of reproductive traits between PRRS phases were overall moderate to high for both breeds. Several associations between MARC0034894, a candidate SNP for response to PRRS, with reproductive performance were identified (P-value < 0.05). Genomic analyses detected few QTL for reproductive performance across all phases, most explaining a small percentage of the additive genetic variance (≤8.2%, averaging 2.1%), indicating that these traits are highly polygenic. None of the identified QTL within a breed and trait overlapped between PRRS phases. Overall, our results indicate that Duroc sows are phenotypically more resilient to PRRS than Landrace sows, with a similar return to PRRS-free performance between breeds for most reproductive traits. Genomic prediction results indicate that genomic selection for improved reproductive performance under a PRRS outbreak is possible, especially in Landrace sows, by training markers using data from PRRS-challenged sows. On the other hand, the high genetic correlations with reproductive traits between PRRS phases suggest that selection for improved reproductive performance in a clean environment could improve performance during PRRS, but with limited efficiency due to their low heritability estimates. Thus, we hypothesize that an indicator trait that could be indirectly selected to increase the response to selection for these traits would be desirable and would also improve the reproductive performance of sows during a PRRS outbreak.

Antibody response to porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV) infection, measured as sample-to-positive (S/P) ratio, has been proposed as an indicator trait for improved reproductive performance during a PRRS outbreak in Landrace sows. However, this result has not yet been validated in Landrace sows or evaluated in terminal sire lines. The main objectives of this work were to validate the use of S/P ratio as an indicator trait to select pigs during a PRRS outbreak and to explore the genetic basis of antibody response to PRRSV. Farrowing data included 2,546 and 2,522 litters from 894 Duroc and 813 Landrace sows, respectively, split into pre-PRRS, PRRS, and post-PRRS phases. Blood samples were taken from 1,231 purebred sows (541 Landrace and 690 Duroc) following a PRRS outbreak for subsequent PRRSV ELISA analysis for S/P ratio measurement. All animals had high-density genotype data available (29,799 single nucleotide polymorphisms; SNPs). Genetic parameters and genome-wide association studies (GWAS) for S/P ratio were performed for each breed separately. Heritability estimates (± standard error) of S/P ratio during the PRRS outbreak were moderate, with 0.35 ± 0.08 for Duroc and 0.34 ± 0.09 for Landrace. During the PRRS outbreak, favorable genetic correlations of S/P ratio with the number of piglets born alive (0.61 ± 0.34), number of piglets born dead (−0.33 ± 0.32), and number of stillborn piglets (−0.27 ± 0.31) were observed for Landrace sows. For Duroc, the GWAS identified a major quantitative trait locus (QTL) on chromosome (Chr) 7 (24-15 megabases; Mb) explaining 15% of the total genetic variance accounted for by markers (TGVM), and another one on Chr 8 (25 Mb) explaining 2.4% of TGVM. For Landrace, QTL on Chr 7 (24–25 Mb) and Chr 7 (108–109 Mb), explaining 31% and 2.2% of TGVM, respectively, were identified. Some of the SNPs identified in these regions for S/P ratio were associated with reproductive performance but not during the PRRS outbreak. Genomic prediction accuracies for S/P ratio were moderate to high for the within-breed analysis. For the between-breed analysis, these were overall low. These results further support the use of S/P ratio as an indicator trait for improved reproductive performance during a PRRS outbreak in Landrace sows.

Statistical training is a major component in the education of animal science graduate students (ASGS). Although most graduate courses in animal science require ASGS to take credits in statistics courses, ASGS differ on their educational and professional interest in statistics. Thus, the aim of this study was to identify associations between the overall graduate and statistical training of ASGS with the statistical interest related to their professional career path. Data from a nationwide statistical training survey was used and included information on 381 ASGS from 42 universities. Analyses focused on identifying overall graduate and statistical training factors associated with ASGS’s answers to the following questions: “Gives statistical advices to lab peers” (No/Yes), “Gives statistical advices to others outside the lab” (No/Yes), “Desired career path after graduation” (Academia/Industry/Other), and “Desire to be involved in statistical analysis in desired career path” (No/Somewhat/Yes). Data were analyzed using logistic regression model including 11 fixed effects, such as degree being pursued (MS/PhD), years of graduate education (covariate), previous professional experience (No/Yes), preferred stats software (SAS/R/SAS and R/Other), etc. There were significant associations (P < 0.05) for all four analyses. ASGS were more likely to give statistical advice to lab peers as they had more years of graduate education [odds-ratio (OR)=1.33], had additional training in statistics (OR=1.92), and had analyzed their own dataset (OR=4.46). ASGS with and without previous professional experience had greater desire to go to industry (OR=1.3) and academia (OR=1.23), respectively. ASGS interested in being involved in statistics in their future career had greater years of graduate education (OR=1.31) and credits in stats courses (OR=1.31), had previously completed a graduate degree (OR=1.49), had previous research experience (OR=1.5), and had additional training in statistics (OR=1.54). These results indicate that a variety of experiences prior to and during graduate ASGS education are associated with their interest in statistics.

Experimental design and statistical data analyses are fundamental components of animal science research. Proper design of experiments and adequate sampling permits testing hypotheses raised by researchers and sets the stage for collecting required data and subsequent statistical analysis. When designing experiments, researchers should respect rules of randomization of treatments to avoid statistical bias and permit proper inference to be drawn. Use of sample sizes that result in adequate statistical power to identify the hypothesized differences among factor levels of interest is key and should be driven by formal processes determining such. Best practices for data collection should be performed to obtain high quality data by reducing collection (e.g., mislabeling, improper technique) and measurement errors. With sound data, appropriate and optimal statistical methods should be used to generate valid results. The statistical method deployed should be chosen based on assumptions about residuals (e.g., normality, correlation, and homogeneity) and on the type of data (e.g., quantitative continuous or categorical). The appropriate statistical model used should also be consistent with the experimental design to validate the respective test statistics. The science of statistics is changing rapidly. With the development of high-throughput technologies, the generation of large datasets, high performance and sophisticated models and the interest in Big Data, the training of animal science graduate students in data management and rigorous statistical analyses is more important than ever. In order to meet the demands of current trends, animal science graduate students must be trained in several complex statistical and computational skills to meet the challenges imposed by these complicated, sophisticated and nuanced analytical methods. The livestock production sector will benefit from improved training, use of advanced and appropriate experimental designs, and collection and analysis of quality data in research.

Immunoglobulin G antibody response, measured as sample-to-positive (S/P) ratio, to Porcine Reproductive and Respiratory Syndrome virus (PRRSV) has been proposed as an indicator trait for improved reproductive performance in PRRSV-infected purebred sows and PRRSV-vaccinated crossbred gilts. In this study, we investigated the genetic correlations (rg) of S/P ratio following a PRRSV outbreak and PRRSV-vaccination with performance in non-exposed and PRRSV-exposed sows. PRRSV outbreak phase was defined based on previously described methodologies after the detection of typical clinical signs of PRRSV infection. 541 Landrace sows had S/P ratio measured at ~54 days after the beginning of the PRRSV outbreak (S/Poutbreak), and 906 Landrace x Large White naïve F1 gilts had S/P ratio measured at ~50 days after vaccination with a commercial modified live PRRSV vaccine (S/PVx). 711 and 428 Landrace sows had reproductive performance recorded before and during the PRRSV outbreak, respectively. 811 vaccinated F1 animals had farrowing performance for up to 3 parities. All animals were genotyped for ~28K SNPs. The estimate of rg of S/Poutbreakwith S/PVx was high (rg±SE = 0.72±0.18). Estimates of rg of S/Poutbreak with reproductive performance in F1 sows were low to moderate, ranging from 0.05±0.23 (number stillborn) to 0.30±0.20 (total number born). Estimates of rg of S/PVxwith reproductive performance in non-infected purebred sows were moderate and favorable with number born alive (0.50±0.23), but low (0 to -0.11±0.23) with litter mortality traits. Estimates of rg of S/PVx were moderate and negative (-0.47±0.18) with the number of mummies in PRRSV-infected purebred sows and low with other traits (-0.29±0.18 for total number born to 0.05±0.18 for number stillborn). These results indicate that selection for antibody response following a PRRSV outbreak collected in purebred sows and to PRRSV vaccination collected in commercial crossbred gilts may increase litter size of non-infected and PRRSV-exposed purebred and commercial crossbred sows.

Antibody response, measured as sample-to-positive (S/P) ratio, to porcine reproductive and respiratory syndrome virus (PRRSV) following a PRRSV-outbreak (S/POutbreak) in a purebred nucleus and following a PRRSV-vaccination (S/PVx) in commercial crossbred herds have been proposed as genetic indicator traits for improved reproductive performance in PRRSV-infected purebred and PRRSV-vaccinated crossbred sows, respectively. In this study, we investigated the genetic relationships of S/POutbreak and S/PVx with performance at the commercial (vaccinated crossbred sows) and nucleus level (non-infected and PRRSV-infected purebred sows), respectively, and tested the effect of previously identified SNP for these indicator traits. Antibody response was measured on 541 Landrace sows ~54 d after the start of a PRRSV outbreak, and on 906 F1 (Landrace × Large White) gilts ~50 d after vaccination with a commercial PRRSV vaccine. Reproductive performance was recorded for 711 and 428 Landrace sows before and during the PRRSV outbreak, respectively, and for 811 vaccinated F1 animals. The estimate of the genetic correlation (rg) of S/POutbreak with S/PVx was 0.72 ± 0.18. The estimates of rg of S/POutbreak with reproductive performance in vaccinated crossbred sows were low to moderate, ranging from 0.05 ± 0.23 to 0.30 ± 0.20. The estimate of rg of S/PVx with reproductive performance in non-infected purebred sows was moderate and favorable with number born alive (0.50 ± 0.23) but low (0 ± 0.23 to −0.11 ± 0.23) with piglet mortality traits. The estimates of rg of S/PVx were moderate and negative (−0.38 ± 0.21) with number of mummies in PRRSV-infected purebred sows and low with other traits (−0.30 ± 0.18 to 0.05 ± 0.18). Several significant associations (P0 > 0.90) of previously reported SNP for S/P ratio (ASGA0032063 and H3GA0020505) were identified for S/P ratio and performance in non-infected purebred and PRRSV-exposed purebred and crossbred sows. Genomic regions harboring the major histocompatibility complex class II region significantly contributed to the genetic correlation of antibody response to PRRSV with most of the traits analyzed. These results indicate that selection for antibody response in purebred sows following a PRRSV outbreak in the nucleus and for antibody response to PRRSV vaccination measured in commercial crossbred sows are expected to increase litter size in purebred and commercial sows.

Vitamin B and trace minerals are crucial molecular signals involved in many biological pathways of energy metabolism and their bioavailability is compromised in high-producing ruminant animals. Despite the current knowledge of the effects of vitamin B complex and trace minerals on animal performance, their use as a rumen-protected form and its impact on liver metabolism in finishing beef cattle is poorly known. The present study aimed to assess the effects of ruminally protected B-vitamin blend (Trouw Nutrition, Italy) and hydroxy trace minerals (Cu and Zn; Micronutrients Inc., Indianapolis, IN) on hepatic proteome. A total of 20 non-castrated Nellore males with 353 ± 43 kg of initial BW were submitted in a high supplementation (1.7% of BW) in pasture and randomly assigned to one of the following treatments: CTRL – inorganic trace minerals without supplementation of vitamin B blend; SUP – supplementation of hydroxy trace minerals (Cu and Zn) and vitamin B blend (B5, B6, B7, B9, and B12). All animals were fed the same level of the experimental diet for 106 days and liver biopsy was performed at the end of the experimental period. We use shotgun proteomics combined with biological and network analyses of the protein differentially abundant between treatments, showing 37 proteins differentially abundant (P < 0.10) between treatment groups, where all proteins were up-regulated in the SUP treatment. These proteins were related to protein folding (P = 0.0456), oxidoreductase complex (P = 0.0155), mitochondrial respiratory chain complex IV (P = 0.0132), chaperonin-containing T-complex 2 (P = 0.0132), glutathione metabolism (P = 0.00026) and other linked to oxidative stress regulation. These results indicate that ruminal-protected vitamin B and hydroxy trace minerals supplementation during the finishing phase cause positive changes in the abundance of proteins related to oxidative metabolism and response to oxidative damage.

A total of 96 genetically lean immunocastrated male pigs were used in a 98-day study to evaluate the effects of including 3% soybean oil (SO), canola oil (CO), or fish oil (FO) in the diets vs. feeding a standard commercial diet with 1.5% SO (control) on growth performance, carcass and meat quality traits, consumer acceptability, and intramuscular fatty acid composition of the longissimus lumborum (LL) muscle. Pigs were blocked by initial body weight (BW; 28.44 ± 2.95 kg) and assigned to one of four treatments, with six replicate pens per treatment and four pigs per pen. Pig BW and pen feed disappearance were recorded weekly. At the conclusion of the study, pigs were slaughtered, carcass characteristics were measured, and a sample of the LL was removed for meat quality assessment, fatty acid composition analysis, and overall liking evaluation. Dietary treatments had no effect on overall growth performance and pig carcasses. Although loins from pigs fed diets containing either 3% SO or CO had decreased (P = 0.05) Warner-Bratzler shear force, only the addition of 3% SO to pig diets resulted in loin chops that were rated higher (P

Fescue toxicosis is a multifaceted syndrome common in cattle grazing endophyte-infected tall fescue, however, varying symptomatic responses potentially imply genetic tolerance to the syndrome. It was hypothesized that a subpopulation of animals within a herd would develop tolerance to ergot alkaloid toxicity. Therefore, the goals of this study were to develop selection criteria to identify tolerant and susceptible animals within a herd based on animal performance, and then examine responsive phenotypic and cytokine profiles to fescue toxicosis. Angus cows grazed endophyte-infected tall fescue at two locations for 13 weeks starting in mid-April 2016. Forage measurements were collected to evaluate ergot alkaloid exposure during the study. A post hoc analysis of animal performance was utilized to designate cattle into either tolerant or susceptible groups, and weekly physiological measurements and blood samples were collected to evaluate responses to chronic exposure to endophyte-infected tall fescue. Findings from this study support the proposed fescue toxicosis selection method formulated herein, could accurately distinguish between tolerant and susceptible animals based on the performance parameters in cattle chronically exposed to ergot alkaloids, and provides evidence to warrant additional analysis to examine the impact of ergot alkaloids on immune responsiveness in cattle experiencing fescue toxicosis.

High fat diets have been reported to negatively affect the microbiota in both mice and humans. However, there is a lack of studies in canine models. The variation among the gastrointestinal (GI) tract anatomy/physiology and typical diet compositions of these animal species may lead to vastly different results. Due to the large inclusion rate of dietary fat in pet food, it is critical to understand its effects in a canine model. Therefore, the study objective was to report the effects of high fat, low carbohydrate diets on the fecal microbiota in healthy adult dogs. Eight adult beagles were randomly assigned to one of four dietary treatments within each 15-day period of a replicated 4x4 Latin Square design. Diets contained 32% (T1), 37% (T2), 42% (T3), and 47% (T4) fat. T2, T3, and T4 were created by adding increasing levels of canola oil to T1, a commercially manufactured canned canine diet, which served as the control diet. Fresh fecal samples were collected during the last 5 days of each period for microbial analysis. DNA was extracted from fecal samples and paired-end 16S rRNA gene amplicon sequencing was performed using the Illumina MiSeq platform. When comparing whole microbial communities using PERMANOVA, no significant differences were observed among treatments (P = 0.735). Individual OTUs were analyzed using the GLIMMIX procedure of SAS with fixed effects of diet and room, and the random effects of period and animal. Out of the 100 most abundant individual OTUs, 36 showed significant differences in abundance based on treatment (q < 0.05). Overall, OTUs assigned to genera related to fat digestion increased while OTUs assigned to genera involved in carbohydrate digestion decreased. In conclusion, the microbial community adapted to dietary intervention without jeopardizing the health of the animals, evaluated by body condition score, fecal characteristics, and blood parameters.

Training in statistical analysis is essential to Animal Science graduate student curricula. Recently, with the increased use of high-throughput technologies in Animal Science fields, graduate students need certain statistical competencies to manage and analyze so-called “Big Data.” The objective of this study was to identify the current statistical competencies associated with graduate students’ perceived confidence to perform statistical analyses. Data from a comprehensive survey of students enrolled in Animal Science-related graduate programs (n = 354; 125 M.S. and 229 Ph.D. students), representing 42 U.S. universities, were used. Students scored their competencies in 32 topics, such as analyzing ANOVA, mixed models, non-normal data, etc., using a 6-point scale: from 0 to 5, representing no to high knowledge, respectively. Confidence in performing statistical analysis (CPSA) was calculated as the sum of the scores across all topics. Participant’s CPSA scores ranged from 12 to 151, averaging 80.3±28.6. Two backward regression analyses were performed to identify factors associated with CPSA, based on the evaluation of self-perceived competencies on 30 topics covered in statistics courses: one based on their perceived received education (PRE) and one on their perceived knowledge (PK). Thirteen topics were selected (P < 0.15) in each analysis, with 7 overlapping, resulting in R-squareds of 56.9% (PRE) and 71.4% (PK). Overlapping topics included descriptive statistics, heterogeneous variances, linear regression, mean separation, mixed models, normality, and observational studies. The only topic with a negative effect on CPSA was the PK of Negative Binomial analysis, indicating graduate students with greater perceived knowledge for this topic had a lower CPSA. The perceived confidence in performing statistical analyses of Animal Science graduate students seems to increase with their perceived training and knowledge in common statistical methods, whereas statistical competencies needed in the “Big Data” era (e.g. generalized linear and multivariate methods) have limited impact or are not covered.

Antibody response, measured as sample-to-positive ratio (S/P), to porcine reproductive and respiratory syndrome (PRRS) after PRRS outbreaks has been proposed as an indicator trait to improve reproductive performance in PRRS-infected sows. However, waiting for a PRRS outbreak to occur and having different relationships in healthy pigs may limit the use of this trait. Thus, we proposed to investigate if this relationship also occurs between S/P to PRRS vaccination and reproductive performance in sows without exposure to PRRS. Nine hundred six F1 replacement gilts (139□17 days old) from two commercial farms were vaccinated with a commercial modified live PRRS virus vaccine. Blood samples were collected at 52 days after vaccination to measure S/P to PRRS and SNP genotyping. Reproductive performance included: number born alive (NBA), number of piglets weaned, number born mummified (MUM), number stillborn (NSB), and pre-weaning mortality (PWM) at parities (P) 1 to 3. Average performance was calculated for each trait per sow per year (PSY). Farrowing rate and age at first service were also analyzed. BayesC0 was used to estimate genetic correlations between S/P and reproductive performance. Bivariate genome-wide association studies of antibody response and reproductive traits were performed using BayesB. High genetic correlations between S/P and farrowing performance were identified for NBA_P1 (0.61±0.16), PWM_P2 (-0.64±0.15), PWM_P2 (-0.63±0.20), NSB_P3 (-0.84±0.05), MUM_P3 (-0.83±0.11), and NSB_PSY (-0.90±0.05). A QTL was identified on chromosome 7 (MHC region) for these reproductive traits and for S/P, explaining from 1.2% (PWM_P2) to 22.4% (S/P) of the genetic variance. SNP H3GA0020505 explained most of the variance in this region for these traits. Heterozygote animals for this SNP had overall better performance: greater S/P (P = 0.001), greater (P = 0.06) NBA_P1, and lesser (P = 0.06) MUM_P3 than other genotypes. These results suggest that antibody response to PRRS vaccination may be used as a genetic indicator to improve reproductive performance in commercial pigs.

The current study aimed to identify differentially expressed genes and their biological process in the skeletal muscle of newborn goats as a function of maternal feed restriction during different stages of gestation. A total of 14 pregnant dams were randomly divided into one of the follow dietary treatments: Animals fed at 50% of maintenance requirement from 8-84 d of gestation and then fed at 100% of maintenance requirement from day 85 of gestation to parturition (RM, n = 6), and animals fed at 100% of maintenance requirement from 8-84 d of gestation and then fed at 50% of maintenance requirement from day 85 of gestation to parturition (MR, n = 8). At birth, all male offspring were euthanized and a sample of Logissimus muscle was collected for total RNA extraction and sequencing. Cuffdiff tool (Cufflinks 2.2.1) was used to count reads, normalize transcript expression (FPKM), and identify differentially expressed genes (DEG) between treatments. Network analysis was performed with String 11.0 using the available genome from the closest specie (Ovis aries). A total of 66 DEG (q-value < 0.05) were identified, with 6 up-regulated genes in skeletal muscle of RM compared to MR newborn goats. These genes are related to tissue development, such as CYTL1, UGT8, and NPNT. The 60 down-regulated genes in skeletal muscle of RM compared with MR newborn goats are related to transcription factors (TF) complex. Among the TF, FOS and JUNB families forms heterodimers in response to several stimuli (cytokines,growth factors, stress), and play key roles controlling a number of cellular processes, including signal transduction, cell proliferation, differentiation and apoptosis. In conclusion, maternal feed restriction at different stages of gestation affects tissue development and changes the transcription pattern in the skeletal muscle of newborn goats, which may lead to negative consequences in animal growth and performance.

Antibody response to Porcine Reproductive and Respiratory Syndrome (PRRS) vaccination and infection has been shown to be highly heritable in gilts and sows. This trait, measured as sample-to-positive (S/P) ratio, has been proposed as a selection tool for improved reproductive performance in sows. However, this novel trait has not yet been explored in growing pigs. Therefore, the objective of this study was to estimate genetic parameters for S/P in PRRS-challenged nursery pigs. A total of 854 PRRS-naïve crossbred barrows and gilts (51.9±4.8 d and 17.8±4.6 kg) were randomly allocated to 54 pens in two rooms and vaccinated with a modified live virus PRRS vaccine. Twenty-eight days later (d0), all animals were experimentally inoculated with a highly virulent strain of PRRS virus. Body weight (BW), S/P, and clinical signs of disease were recorded at this time and again at d13. Average daily gain (ADG) was calculated and used in combination with clinical signs to create two distinct groups, robust (R) and susceptible (S), with ~230 animals each. At d42, S/P was measured only in these classified animals. Genetic parameters and effect of classification were estimated for S/P for each collection day. Heritability estimates for S/P were 0.07±0.06, 0.52±0.09, and 0.43±0.28, for d0, d13, and d42, respectively. Genetic correlation estimates were high between collection days, ranging from 0.91±0.31 (d0 and d42) to 0.98±0.03 (d13 and d42). There was an effect of classification for S/P only at d13 (P=0.024), with R showing greater S/P (1.7±0.03) than S (1.64±0.03). These results indicate that, in PRRS-challenged growing pigs, S/P is highly heritable at later collection days, and differences in S/P exist between robust and susceptible animals.

Losses due to infectious diseases are one of the main factors affecting productivity in the swine industry, motivating the investigation of disease resilience-related traits for genetic selection. However, these traits are not expected to be expressed in the nucleus herds, where selection is performed. One alternative is to use information from the commercial level to identify and select nucleus animals genetically superior for coping with pathogen challenges. In this study, we analyzed the genetic basis of antibody (Ab) response to common infectious pathogens in health-challenged commercial swine herds as potential indicator traits for disease resilience, including Ab response to influenza A virus of swine (IAV), Mycoplasma hyopneumoniae (MH), porcine circovirus (PCV2), and Actinobacillus pleuropneumoniae (APP; different serotypes). Ab response was measured in blood at entry into gilt rearing, post-acclimation (∼40 days after entering the commercial herd), and parities 1 and 2. Heritability estimates for Ab response to IAV, MH, and PCV2 ranged from 0 to 0.76. Ab response to APP ranged from 0 to 0.40. The genetic correlation (rG) of Ab response to IAV with MH, PCV2, PRRSV, and APPmean (average Ab responses for all serotypes of APP) were positive (>0.29) at entry. APPmean was negatively correlated with PCV2 and MH at entry and parity 2 but positively correlated with MH at post-acclimation and parity 1. Genomic regions associated with Ab response to different APP serotypes were identified on 13 chromosomes. The region on chromosome 14 (2 Mb) was associated with several serotypes of APP, explaining up to 4.3% of the genetic variance of Ab to APP7 at entry. In general, genomic prediction accuracies for Ab response were low to moderate, except average Ab response to all infectious pathogens evaluated. These results suggest that genetic selection of Ab response in commercial sows is possible, but with variable success depending on the trait and the time-point of collection. Future work is needed to determine genetic correlations of Ab response with disease resilience, reproductive performance, and other production traits.

Most tall fescue [Lolium arundinaceum (Schreb.) Darbysh] in the Southeastern United States contains an endophyte that causes fescue toxicosis (FT) in grazing animals, a serious disease that causes approximately $1 billion in economic losses to the animal industries in the United States. Recently, a genetic test called T-Snip (AgBotanica, LCC, Columbia, MO), was developed with the objective of identifying animals with genetic variation for FT tolerance. The aim of this study was to validate the use of this genetic test in mature, pregnant cows. Over 13 wk, weekly phenotypic data, including body weight, rectal temperatures, hair coat scores, hair shedding scores, and body condition scores, were collected on 148 pregnant purebred Angus cows at 2 locations in NC where infected fescue was the primary source of feed. Birth weights (cBW) and 205-d adjusted weaning weights (adjWW) from these cow’s calves were recorded. All cows were genotyped for T-Snip. At the end of the trial, each phenotypic trait was calculated as the slope of the linear regression of performance on weeks. The effect of T-Snip rating genotypes (4 levels) on slope traits was tested using a linear model also including the fixed-effects of location, parity, and the initial measurement for each trait (covariate). For cBW and adjWW, the model also included the sex of the calf and the month of birth as categorical effects. Associations of T-Snip genotypes were observed for body weight gain (aBWd) of pregnant cows (P = 0.15; interaction with location), change in body condition score (aBCSd; P = 0.13), and adjWW (P = 0.06; interaction with location). For aBWd and adjWW, associations were found just within one location (P = 0.017 and 0.047, respectively), which was the location with higher endophyte infection rate. For all associations, the direction of the T-Snip genotypes was the same and as expected: the greater the genotype score, the better performance. No associations were found for the other traits (P > 0.10). These results indicate that the T-Snip test may be predictive of cow performance (aBWd, aBCSd, and adjWW) in an endophyte-infected tall fescue environment.

Most tall fescue [Lolium arundinaceum (Schreb.) Darbysh] in the Southeastern United States contains an endophyte that causes fescue toxicosis (FT) in grazing animals, a serious disease that causes approximately $1 billion in economic losses to the animal industries in the United States. Recently, a genetic test called T-Snip (AgBotanica, LCC, Columbia, MO), was developed with the objective of identifying animals with genetic variation for FT tolerance. The aim of this study was to validate the use of this genetic test in mature, pregnant cows. Over 13 wk, weekly phenotypic data, including body weight, rectal temperatures, hair coat scores, hair shedding scores, and body condition scores, were collected on 148 pregnant purebred Angus cows at 2 locations in NC where infected fescue was the primary source of feed. Birth weights (cBW) and 205-d adjusted weaning weights (adjWW) from these cow’s calves were recorded. All cows were genotyped for T-Snip. At the end of the trial, each phenotypic trait was calculated as the slope of the linear regression of performance on weeks. The effect of T-Snip rating genotypes (4 levels) on slope traits was tested using a linear model also including the fixed-effects of location, parity, and the initial measurement for each trait (covariate). For cBW and adjWW, the model also included the sex of the calf and the month of birth as categorical effects. Associations of T-Snip genotypes were observed for body weight gain (aBWd) of pregnant cows (P = 0.15; interaction with location), change in body condition score (aBCSd; P = 0.13), and adjWW (P = 0.06; interaction with location). For aBWd and adjWW, associations were found just within one location (P = 0.017 and 0.047, respectively), which was the location with higher endophyte infection rate. For all associations, the direction of the T-Snip genotypes was the same and as expected: the greater the genotype score, the better performance. No associations were found for the other traits (P > 0.10). These results indicate that the T-Snip test may be predictive of cow performance (aBWd, aBCSd, and adjWW) in an endophyte-infected tall fescue environment.

Background One of the biggest challenges in the swine industry is to increase female reproductive efficiency. Recently, vulva score categories (VSC), assessed prior to puberty, has been proposed as an indicator trait of efficient reproductive performance in sows. The objective of this study was to validate the use of VSC as an indicator trait for reproductive performance, and to perform genetic and genomic analyses for VSC. Methods The phenotypic relationship of VSC, using a three-point scale: small (VSC-S), medium (VSC-M), and large (VSC-L), on reproductive performance was evaluated on three farms. VSC was measured at 15 weeks of age, for farms 1 and 2, and at 14 weeks of age for farm 3 on 3981 Yorkshire gilts, in which 1083 had genotypes (~ 50 K SNPs). Genetic parameters for VSC with reproductive traits were estimated using ssGBLUP. A Genome-wide association study (GWAS) for VSC was performed using BayesB. Results For the phenotypic analysis of VSC across datasets, differences in performance were identified there was a significant effect (P ≤ 0.05) for the interaction between Farm and VSC for total number dead (TND), and a trend (P c were identified. Of these, a QTL located on chromosome 3 at 33–34 Mb accounted for about 7.1% of the genetic variance for VSCc and VSCq. This region harbors the gene PRM1 that has been associated with early embryonic development in pigs. Conclusions The results support potential of VSC for improved reproductive efficiency on first-parity performance, but the results might depend on the interaction between environmental factors and VSC, as well as potentially additive genetics.

Growth rate is a major component of feed efficiency when estimating residual feed intake (RFI). Quantile regression (QR) methodology can be used to identify animals with different growth trajectories. The objective of this study was to evaluate the use of QR to identify phenotypic and genetic differences in pigs selected for low RFI. Using performance data on 750 Yorkshire pigs selected for low RFI, individual average daily gain (ADG), average daily feed intake (ADFI), RFI and Gompertz growth curve parameters (asymptotic weight (a), inflection point (b) and decay parameter (c)) were estimated for each pig. Using QR methodology, three Gompertz growth curves were estimated for the whole population for three quantiles (0.1, 0.5 and 0.9) of the BW data. Each animal was classified into one of the quantile regression groups (QRG) based on their overall Euclidian distance between each observed and estimated BW from the quantile growth curves. These three curves were also estimated using only part of the data (generations -1 to 3, and -1 to 4) in order to evaluate the agreement classification rate of animals from later generations into QRGs. We evaluated the effect of QRG on growth parameters and performance traits. Genetic parameters were estimated for these traits, as well as for QRG. In addition, genetic trends for each QRG were estimated. Three distinct growth curves were observed for animals classified into either quantiles 0.1 (QRG0.1), 0.5 (QRG0.5) or 0.9 (QRG0.9). When only part of the data was used to estimate quantile growth curves, all animals from QRG0.1 were correctly classified in their group. Animals in QRG0.1 had significantly lower ADFI, ADG and RFI, and greater a, b and c than animals in the other groups. Quantile regression groups analysed as a trait was highly heritable (0.41) and had high (0.8) and moderate (0.46) genetic correlations with ADG and RFI, respectively. Selection for reduced RFI increased the number of animals classified as QRG0.1 in the population. Overall, downward genetic trends were observed for all traits as a function of selection for reduced RFI. However, QRG0.1 was the only group that had a positive genetic trend for ADG. Altogether, these results indicate that selection for reduced RFI changes the shape of growth curves in Yorkshire in pigs, and that QR methodology was able to identify animals having different genetic potential for feed efficiency, bringing a new opportunity to improve selection for reduced RFI.

BackgroundReproductive performance is critical for efficient swine production. Recent results indicated that vulva size (VS) may be predictive of reproductive performance in sows. Study objectives were to estimate genetic parameters, identify genomic regions associated, and estimate genomic prediction accuracies (GPA) for VS traits.ResultsHeritability estimates of VS traits, vulva area (VA), height (VH), and width (VW) measurements, were moderately to highly heritable in Yorkshire, with 0.46 ± 0.10, 0.55 ± 0.10, 0.31 ± 0.09, respectively, whereas these estimates were low to moderate in Landrace, with 0.16 ± 0.09, 0.24 ± 0.11, and 0.08 ± 0.06, respectively. Genetic correlations within VS traits were very high for both breeds, with the lowest of 0.67 ± 0.29 for VH and VW for Landrace. Genome-wide association studies (GWAS) for Landrace, reveled genomic region associated with VS traits onSus scrofachromosome (SSC) 2 (154–157 Mb), 7 (107–110 Mb), 8 (4–6 Mb), and 10 (8–19 Mb). For Yorkshire, genomic regions on SSC 1 (87–91 and 282–287 Mb) and 5 (67 Mb) were identified. All regions explained at least 3.4% of the genetic variance. Accuracies of genomic prediction were moderate in Landrace, ranging from 0.30 (VH) to 0.61 (VA), and lower for Yorkshire, with 0.07 (VW) to 0.11 (VH). Between-breed and multi-breed genomic prediction accuracies were low.ConclusionsOur findings suggest that VS traits are heritable in Landrace and Yorkshire gilts. Genomic analyses show that major QTL control these traits, and they differ between breed. Genomic information can be used to increase genetic gains for these traits in gilts. Additional research must be done to validate the GWAS and genomic prediction results reported in our study.

Tall fescue (Lolium arundinaceum) is a widely used forage grass which shares a symbiosis with the endophytic fungus Epichloë coenophiala. The endophyte produces an alkaloid toxin that provides herbivory, heat and drought resistance to the grass, but can cause fescue toxicosis in grazing livestock. Fescue toxicosis can lead to reduced weight gain and milk yields resulting in significant losses to the livestock industry. In this trial, 149 Angus cows across two farms were continuously exposed to toxic, endophyte-infected, fescue for a total of 13 weeks. Of those 149 cows, 40 were classified into either high (HT) or low (LT) tolerance groups according to their growth performance (weight gain). 20 HT and 20 LT cattle balanced by farm were selected for 16S rRNA gene and ITS1 region Illumina MiSeq amplicon sequencing to compare the fecal microbiota of the two tolerance groups. This study reveals significantly (P) different bacterial and fungal microbiota between HT and LT cattle, and indicates that fungal phylotypes may be important for an animal’s response to fescue toxicosis: We found that fungal phylotypes affiliating to the Neocallimastigaceae, which are known to be important fiber-degrading fungi, were consistently more abundant in the HT cattle. Whereas fungal phylotypes related to the genus Thelebolus were more abundant in the LT cattle. This study also found more pronounced shifts in the microbiota in animals receiving higher amounts of the toxin. We identified fungal phylotypes which were consistently more abundant either in HT or LT cattle and may thus be associated with the respective animal’s response to fescue toxicosis. Our results thus suggest that some fungal phylotypes might be involved in mitigating fescue toxicosis. The results of our study provide a basis for investigating the functional role of the gastrointestinal microbiota in fescue toxicosis in more detail in the future.

Microbial phytase is widely used to enhance digestibility of phytate-P. By tradition, diets with P content well below requirement are used to quantify phytate-P release by phytase, but P-adequate diets may be more physiologically relevant. The objective of this study was to investigate the effects of phytase on P digestion and metabolism and develop a P release curve for phytase in P-adequate diets (above requirement according to NRC, 2012), and to compare these effects in a P-deficient diet. Three replicates of 24 barrows each (BW = 23.0 ± 1.8 kg) were randomly assigned to 1 of 8 dietary treatments, housed in individual pens for 21 d, then moved to metabolism crates for 5 d urine and fecal collections. A basal corn-soybean meal diet (P-adequate, A) was formulated at 0.36% standardized total tract digestible (STTD) P and total Ca:STTD P of 1.83. Phytase was added to A at 200 (A200), 400 (A400), 600 (A600), and 800 (A800) phytase units (FTU)/kg. A positive control diet (PC) was formulated using monocalcium phosphate (MCP) to increase STTD P by 0.16% to 0.52%, the expected STTD P release of 800 FTU/kg. A P-deficient diet (D) was formulated by reducing MCP to achieve 0.21% STTD P, and 200 FTU phytase/kg was added to D for D200. Pig was the experimental unit, and replicate and dietary treatment were fixed effects. Orthogonal polynomial contrasts were used to test linear and quadratic effects of phytase within A, A200, A400, A600, and A800. Phytase increased percent apparent total tract digestibility (ATTD) and STTD of P (quadratic P < 0.001), and quantity of absorbed P (linear P < 0.001; quadratic P = 0.069). Urinary P increased linearly with phytase (P < 0.001) and retained P also increased (linear P = 0.001, quadratic P = 0.094). Phytate-P release was estimated to be 0.049, 0.080, 0.093, and 0.09% STTD P for 200, 400, 600, and 800 FTU/kg, respectively. It appears that the effect of phytase may be lower in P-adequate diets as compared to P-deficient diets, given that there was a 12% improvement for A200 versus A, and a 28% improvement in STTD P for D200 versus D. In conclusion, phytase improved P digestibility and retention in P-adequate diets, and P digestibility was used to estimate the quantity of P released by phytase. Further research investigating P release by phytase in P-adequate diets, rather than P-deficient diets, may be preferable.

Residual feed intake (RFI) is the difference between observed and predicted feed intake of an animal, based on growth and maintenance requirements. In Yorkshire pigs, divergent selection for increased (Low RFI) and decreased (High RFI) RFI was carried out over 10 generations (G) while feeding a corn- and soybean-meal-based, higher-energy, lower-fiber (HELF) diet. In G8 to G10, representing 4 replicates, barrows and gilts (n = 649) of the RFI lines were fed the HELF diet and a diet incorporating coproducts that were lower in energy and higher in dietary fiber (LEHF). The diets differed in ME, 3.32 vs. 2.87 Mcal/kg, and in neutral detergent fiber (NDF), 9.4% vs. 25.9%, respectively. The impact of the LEHF diet on 1) performance and growth, 2) diet digestibility, 3) genetic parameter estimates, and 4) responses to selection for RFI, when fed the HELF, was assessed. In general, the LEHF diet reduced the performance of both lines. When fed the HELF diet, the Low RFI pigs had lower (P 0.05) loin muscle area (LMA; +5%); and greater (P < 0.05) feed efficiency (i.e., 8% higher G:F and 7% lower RFI) than the High RFI line. These patterns of line differences were still present under the LEHF diet but differences for ADFI (-11%), energy intake (-10%), G:F (+2%), and RFI (-6%) were reduced compared to the HELF diet. Apparent total tract digestibility (ATTD) of the HELF and LEHF diets was assessed using 116 barrows and gilts from G8. When fed the HELF diet, ATTD of DM, GE, N, and NDF were similar between lines (P ≥ 0.27), but when fed the LEHF diet, the Low RFI pigs had greater digestibility (7%, 7%, 10%, and 32%) than the High RFI line (P ≤ 0.04). To measure responses to selection for RFI and estimate genetic parameters, data from all 10 generations were used (HELF; n = 2,310; LEHF, n = 317). Heritability estimates of performance traits ranged from 0.19 to 0.63, and genetic correlations of traits between diets were high and positive, ranging from 0.87 (RFI) to 0.99 (LMA). By G10, RFI in the Low RFI line was 3.86 and 1.50 genetic SD lower than in the High RFI line when fed the HELF and LEHF diets, respectively. Taken together, the results of this study demonstrate that responses to selection for RFI when fed a HELF diet are not fully realized when pigs are fed an extremely LEHF diet. Thus, feeding diets that differ from those used for selection may not maximize genetic potential for feed efficiency.

Previous studies on genomics of antibody response, measured as sample-to-positive (S/P) ratio, to Porcine Reproductive and Respiratory Syndrome virus (PRRSV) have reported a major quantitative trait locus (QTL) on the major histocompatibility complex (MHC) on chromosome 7, explaining ~25% of the genetic variance of this trait. S/P ratio following modified live PRRSV vaccination in crossbred commercial gilts has been proposed as genetic indicator for reproductive performance in non-infected purebred sows and PRRSV-vaccinated crossbred sows. This motivated further genomic study for this trait by performing haplotype-based genome-wide association study (GWAS). 906 naïve F1 (Landrace x Large White) had blood samples taken at ~50d after vaccination for measuring PRRSV ELISA S/P ratio and genotyping. Haplotype-based GWAS identified 8 genomic regions on chromosomes 4 (108 Mb), 7 (15, 21, and 24–27 Mb), and 9 (33 Mb) that were associated (q-value < 0.07) with S/P ratio. From those, only the MHC region (chromosome 7; 24 – 26 Mb) had been identified in the SNP based GWAS. The main SNP identified in the SNP based GWAS (H3GA0020505) was not in LD with the haplotype; thus, we added this SNP to the haplotype model. We observed that the haplotype explained more of the genetic variance compared to the H3GA0020505 SNP, indicating that the MHC haplotype is in stronger LD with the QTL than the H3GA0020505 SNP. All the significant regions associated with S/P ratio included immune-related candidate genes, such as SLA-DOB, TAP2, TAPBP, TMIGD3, and ADORA. This study validated the QTL identified on the MHC region, narrowing the search for causal genes in this region, and identified new genomic regions, along with candidate genes associated with S/P ratio. Identifying novel genomic regions provides more resources for marker-assisted selection and genomic prediction of S/P ratio in purebred and commercial pig populations.

Previous studies proposed the use of antibody response to Porcine Reproductive and Respiratory Syndrome virus (PRRSV), measured as sample-to-positive (S/P) ratio, as a potential indicator trait to improve the reproductive performance of PRRSV-infected Landrace sows. However, this indicator trait has not yet been validated in Landrace sows or evaluated in a terminal sire line, such as Duroc. The main objective of this work was to perform host-genetic analyses of S/P ratio and reproductive traits during a PRRSV outbreak in maternal and terminal breeds. The data consisted of 690 Duroc and 541 Landrace multiparous sows (1.9±1.2 and 2.3±1.5, respectively) with S/P ratio collected at approximately 54 days after the predicted beginning of the outbreak. Of these, 644 Duroc and 528 Landrace sows also had reproductive data recorded during the PRRSV outbreak comprising number of piglets born alive (NBA), stillborn piglets (NSB), mummified piglets (NBM), number born dead (NBD; sum of NSB and NBM), total number born (TNB; sum of NBA and NBD), and number weaned (NW). All animals had genotype data on ~30K SNPs common across both breeds. Heritability estimates (± standard error) of S/P ratio during the PRRSV outbreak were moderate, with 0.33±0.06 for Duroc and 0.28±0.07 for Landrace. Reproductive traits during the PRRSV outbreak had overall low heritability estimates (≤0.18). Favorable genetic correlations of S/P ratio with NBA (0.65±0.33), in accordance with previous studies, and NBD (-0.33±0.28) were observed for Landrace sows only. Estimates of genetic correlation with other traits were -0.21±0.30 (NBM), -0.12±0.29 (NSB), 0.10±0.38 (NW), and 0.54±1.29 (TNB) for Landrace. For Duroc, these estimates were weaker: -0.33±0.40 (NBA), 0.26±0.27 (NBA), and 0.28±0.30 (NW), with convergence issues for mortality traits. These results further support the use of S/P ratio as an indicator trait for improved reproductive performance during a PRRSV outbreak in Landrace sows.

Studies on differences in resilience to porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV) between breeds are scarce in the literature. Thus, the objective of this work was to assess PRRSV resilience in PRRSV wild-type infected sows from two breeds. Farrowing data included 2546 and 2522 litters from 894 Duroc and 813 Landrace sows, respectively, which were housed together and experienced the same PRRSV outbreak. Traits used for this study were number of piglets born alive (NBA), number born dead (NBD), total number born (TNB), and number weaned (NW). The impact of PRRSV infection was evaluated by comparing the reproductive performance of breeds between PRRS phases (pre-PRRS, PRRS, and post-PRRS). PRRS phases were defined based on the reproductive performance data. NBA, NBD, and NW were analyzed as a proportion of TNB using a Poisson mixed model. Pre-defined contrasts were used to evaluate the effect of breed on PRRSV resilience and on return to PRRSV-free performance, representing the differences between breeds for the difference between pre-PRRS and PRRS phases, and pre-PRRS and post-PRRS phases, respectively. There was a significant (P ≤ 0.003) interaction between PRRS phase and breed for all traits, as shown in Table 1. In general, reproductive performance reduced from pre-PRRS to PRRS, and then increased from PRRS to post-PRRS, as expected. The resilience contrast was significant for all traits (P ≤ 0.003). In all cases, the drop in percent reproductive performance from pre-PRRS to PRRS was lower for Duroc than for Landrace, indicating that Duroc sows have greater PRRSV resilience than Landrace sows. The return to PRRSV-free performance contrast had a trending effect for NBD (P = 0.055), and it was not significant for the other traits (P ≥ 0.515). These results indicate that Duroc sows have overall greater phenotypic PRRSV resilience for reproductive performance than Landrace sows.

The objective of this study was to investigate the expression of genes involved in energy metabolism and volatile fatty acids (VFA) and urea transport in rumen epithelium of bulls with different feed efficiency based on residual feed intake (RFI). Twenty-seven Nellore bulls (age = 22.5 ± 0.8 mo; initial body weight = 401 ± 42 kg) were classified as either Low, Medium, and High (n = 9 per group) RFI and finished in individual pens. During the finishing phase animals were fed the same diet formulated to meet the requirements of 1.3 kg daily gain with a target finish weight of 550 kg. At the end of the trial, bulls were slaughtered and ruminal fluid was collected for further VFA analyses. Samples of rumen epithelium from ventral sac were rapidly excised, rinsed with phosphate buffered saline solution (pH = 7.04) and immediately immerged in RNA later solution within 2 mL tubes. After 48 h, rumen epithelium samples were placed at −80 °C until total RNA isolation and qPCR analysis. Data were analyzed using SAS 9.4 with α = 0.05; trends were determined as 0.10 > P > 0.05. The concentrations of total VFA, acetate, propionate, butyrate, valerate, isobutyrate, isovalerate, and acetate: propionate ratio did not differ (P > 0.05) among RFI groups. The mRNA abundance of UQCR10 (P 0.05) among treatments. No differences (P > 0.05) were observed for mRNA abundance of genes associated with ion pumping (ATP1B1, ATP1B2, ATP1B3), protein turnover (IGF1R, MKI67, UBA1), heat production (UCP2), butyrate metabolism (BDH1, BDH2, HMGCL, HMGS1), and VFA (CA7, DRA, NHE2, MCT1, and PAT1) and urea transport (AQP3, AQP7, AQP8, AQP10, and SLC14A1) in rumen epithelium of bulls classified as High, Medium, and Low RFI. These findings may indicate that more efficient animals (Low and Medium RFI) have lower energy expenditure in this tissue, which likely contribute for their better efficiency compared to the less efficient (High RFI) bulls.

The WUR1000125 (WUR) single nucleotide polymorphism (SNP) can be used as a genetic marker for host response to porcine reproductive and respiratory syndrome (PRRS), PRRS vaccination, and co-infection with porcine circovirus type 2b (PCV2b). Objectives of this study were to identify genomic regions other than WUR associated with host response to PRRS vaccination and PRRSV/PCV2b co-infection and regions with a different effect on host response to co-infection, depending on previous vaccination for PRRS. Commercial crossbred nursery pigs were pre-selected for WUR genotype (n = 171 AA and 198 AB pigs) where B is the dominant and favorable allele. Half of the pigs were vaccinated for PRRS and 4 weeks later, all pigs were co-infected with PRRS virus and PCV2b. Average daily gain (ADG) and viral load (VL) were quantified post vaccination (Post Vx) and post co-infection (Post Co-X). Single-SNP genome-wide association analyses were then conducted to identify genomic regions associated with response to vaccination and co-infection. Multiple SNPs near the major histocompatibility complex were significantly associated with PCV2b VL (−log 10 P ≥ 5.5), regardless of prior vaccination for PRRS. Several SNPs were also significantly associated with ADG Post Vx and Post Co-X. SNPs with a different effect on ADG, depending on prior vaccination for PRRS, were identified Post Vx (−log 10 P = 5.6) and Post Co-X (−log 10 P = 5.5). No SNPs were significantly associated with vaccination VL (−log10 P ≤ 4.7) or PRRS VL (−log10 P ≤ 4.3). Genes near SNPs associated with vaccination VL, PRRS VL, and PCV2b VL were enriched (P ≤ 0.01) for immune-related pathways and genes near SNPs associated with ADG were enriched for metabolism pathways (P ≤ 0.04). SNPs associated with vaccination VL, PRRS VL, and PCV2b VL showed overrepresentation of health QTL identified in previous studies and SNPs associated with ADG Post Vx of Non-Vx pigs showed overrepresentation of growth QTL. Multiple genomic regions were associated with PCV2b VL and ADG Post Vx and Post Co-X. Different SNPs were associated with ADG, depending on previous vaccination for PRRS. Results of functional annotation analyses and novel approaches of using previously-reported QTL support the identified regions.

This study aimed to evaluate the effects of dietary chromium, CLA, and ractopamine on performance, carcass traits, and pork quality of finishing pigs slaughtered at 115 kg BW. Ninety-six crossbred barrows (initial BW = 70.21 ± 1.98 kg) were randomly assigned to 1 of 6 dietary treatments. There were 8 replicates per treatment (48 pens; 2 pigs/pen). A diet formulated according to the nutritional requirements was used as the control (CON). The other 5 diets were based on the CON and supplemented as follows: 0.4 mg/kg Cr yeast (CrY); 0.5% CLA; 0.4 mg/kg CrY and 0.5% CLA (CrY + CLA); 20 mg/kg ractopamine (RAC); 0.4 mg/kg CrY and 20 mg/kg RAC (CrY + RAC). Lysine levels on diets containing ractopamine were raised by 20% compared to CON to meet the greater requirements of pigs fed ractopamine. Pigs fed RAC and CrY + RAC were fed CON for the first 17 d, and then the respective diets for the last 28 d on trial. Data were analyzed in a model including the fixed effect of treatment (6 levels) and initial BW as a covariate for all characteristics, with the exception of carcass traits, in which final BW was used as a covariate. Least-squares means were separated using Tukey-Kramer's method. Differences were considered when probability values were lower than 0.05. Pigs fed RAC and CrY + RAC had the greatest ( 0.05) pork quality, except for color. No differences ( > 0.05) were observed for carcasses pH and temperature. The values for pigs fed RAC were greater ( = 0.01) than pigs fed other diets. Pigs fed RAC had lower ( < 0.01) values compared to pigs fed other experimental diets. Serum urea nitrogen concentration (SUN) was lower ( = 0.02) in pigs fed CrY + RAC than in pigs fed CON and RAC and similar to pigs fed the other feeding additives. In summary, it was demonstrated that, when combined, CrY and RAC increase LM area and carcass yield, and reduce SUN, suggesting that chromium could improve nutrient utilization by muscle cells in RAC-fed pigs. Additionally, the additives have no major effects on pork quality.

Background: Genomic growth curves are generally defined only in terms of population mean; an alternative approach that has not yet been exploited in genomic analyses of growth curves is the Quantile Regression (QR). This methodology allows for the estimation of marker effects at different levels of the variable of interest. We aimed to propose and evaluate a regularized quantile regression for SNP marker effect estimation of pig growth curves, as well as to identify the chromosome regions of the most relevant markers and to estimate the genetic individual weight trajectory over time (genomic growth curve) under different quantiles (levels). Results: The regularized quantile regression (RQR) enabled the discovery, at different levels of interest (quantiles), of the most relevant markers allowing for the identification of QTL regions. We found the same relevant markers simultaneously affecting different growth curve parameters (mature weight and maturity rate): two (ALGA0096701 and ALGA0029483) for RQR(0.2), one (ALGA0096701) for RQR(0.5), and one (ALGA0003761) for RQR(0.8). Three average genomic growth curves were obtained and the behavior was explained by the curve in quantile 0.2, which differed from the others. Conclusions: RQR allowed for the construction of genomic growth curves, which is the key to identifying and selecting the most desirable animals for breeding purposes. Furthermore, the proposed model enabled us to find, at different levels of interest (quantiles), the most relevant markers for each trait (growth curve parameter estimates) and their respective chromosomal positions (identification of new QTL regions for growth curves in pigs). These markers can be exploited under the context of marker assisted selection while aiming to change the shape of pig growth curves. Made available in DSpace on 2018-01-03T23:20:13Z (GMT). No. of bitstreams: 1 2017M.DeonJASBRegularized.pdf: 529201 bytes, checksum: f7a0a79c7f5c710e225da410f3ac2a5b (MD5) Previous issue date: 2018-01-03

In the current study we have performed two experiments to evaluate the effects of adipogenic induction media on dedifferentiated fat (DFAT) cells redifferentiation into mature adipocytes. In experiment 1, we aimed to evaluate whether it is necessary to use insulin in the induction media to allow DFAT cells differentiation into mature adipocytes by establishing two experimental treatments where insulin was either withdrawn from the culture medium, after 72 h of a normal induction period (Treatment 1: Insulin - ) or kept in culture media (Treatment 2: Insulin + ) for 16 d. In experiment 2, we aimed to evaluate if the lack of 3-isobutyl-1-methylxanthine (IBMX) in the induction medium would affect the differentiation of DFAT cells into mature adipocytes. For that, DFAT cells were induced to differentiate into lipid assimilating adipocytes using an induction medium containing IBMX (Treatment 1: IBMX + ) or without IBMX (Treatment 2: IBMX - ) during the first 72 h of induction. In both experiments we have evaluated the mRNA expression of lipid metabolism markers and cell morphology through Oil-Red staining as indicators of differentiation of DFAT cells into lipid-assimilating cells. The results of Experiment 1 revealed no differences in mRNA expression for any of the lipid metabolism markers with exception of GLUT4 ( P =0.02), which was greater in Insulin - compared to Insulin + treatment. Similarly, no differences were observed for mRNA expression of adipogenic markers between IBMX + and IBMX - treatments with exception of FABP4 ( P =0.01), which was greater for the IBMX - compared to IBMX + treatment. In both experiments we did not observed any differences in cell morphology among treatments. Our results suggest that neither insulin nor IBMX are required to accelerate redifferentiation process of pig-derived DFAT cells.

The vaginal microbiome of gilts vaccinated for porcine reproductive and respiratory syndrome (PRRS) has been previously associated with first-parity reproductive performance in absence of PRRS outbreak. However, associations using multiparous sows have not been investigated. The objective of this study was to associate the vaginal microbiota of PRRS-vaccinated gilts with longevity. Vaginal swabs from 251 commercial F1 gilts (Landrace/Large-White) were collected on days 4 and 52 after PRRS vaccination (dpv) for 16S rRNA sequencing. Sequences were clustered into operational taxonomic unit (OTU). Sows were assigned to one of four groups according to the maximum parity reached (number of animals): without parity (13), first-parity (45), second-parity (47), and 3 or more parities (146). A negative binomial mixed model including fixed effects of group, dpv, group*dpv, and collection age (covariate), and random effect of animal, was used to identify OTUs with differential abundance. The false discovery rate method was used for multiple test correction. Canonical discriminant analysis (CDA) was performed to classify animals into the four parity groups by including significant OTUs in stepwise selection (P < 0.05) using the whole data. A leave-one-out-cross-validation was used to assess the predictive ability of OTUs to correctly classify animals into the parity groups. Abundance of five and four OTUs was associated (q < 0.05) with group and with group*dpv (q < 0.05), respectively. In the CDA analysis, 220 OTUs identified in the vaginal microbiome were included (P < 0.05). The first and second canonical variables explained 96.6 and 3.4% of the variation, respectively. All animals were correctly classified into their respective parity groups. This study indicates that the vaginal microbiome composition of gilts collected after PRRS-vaccination may be used to predict longevity in commercial sow herds. This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brazil (Capes) – Finance Code 001.

Reproductive efficiency is critical to maximizing productivity in the swine industry. A recent study indicated that vulva score (VSC) assessed prior to puberty may be predictive of reproductive performance in sows, in which gilts with greater VSC had greater reproductive performance. The objective of this study was to validate the effect of VSC on reproductive performance, to estimate genetic parameters, and to perform genomic analysis of VSC. A total of 5494 phenotypes and 1326 genotypes (~50K SNPs) from two farms were available for this study. Measurements included VSC assessed using a three-point scale: small (VSC-S), medium (VSC-M), and large (VSC-L), at 15 and 14 weeks of age, for Farm 1 and 2, respectively, and subsequent first parity performance. Genetic parameters were estimated using single-step GBLUP. Genome-wide association study (GWAS) was performed for VSC using BayesB (p=0.999). For Farm1, VSC-L was associated with a greater (P-value=0.04) farrow rate (0.68±0.03) than VSC-S (0.53±0.07). For Farm2, VSC-L was associated with greater (P-value=0.04) number of piglets born alive (NBA; 11.4±0.17) and less mummified fetuses (P-value=0.03; 0.09±0.01) than VSC-S (10.9±0.14; 0.14±0.01). Heritability estimates of VSC were 0.35±0.06 for Farm1 and 0.34±0.05 for Farm2. Moderate genetic correlations between VSC with reproductive traits were found for total number born (0.61±0.21) and NBA (0.62±0.19). The GWAS identified multiple genomic regions associated with VSC. Of these, a QTL located on chromosome 1 at 85Mb accounted for >3% of the genetic variance. This region harbors ADAM21, a gene that has been associated with early embryonic development in pigs. These results validated the use of VSC for prediction of first-parity performance, identified genomic regions controlling VSC, and indicate that selection for increased VSC is possible and could improve reproductive efficiency in swine. We are grateful to Fast Genetics for providing the data and the Iowa Pork Industry Center for financial support.

Automated high-throughput phenotyping with sensors, imaging, and other on-farm technologies has resulted in a flood of data that are largely under-utilized. Drastic cost reductions in sequencing and other omics technology have also facilitated the ability for deep phenotyping of livestock at the molecular level. These advances have brought the animal sciences to a cross-roads in data science where increased training is needed to manage, record, and analyze data to generate knowledge and advances in Agriscience related disciplines. This paper describes the opportunities and challenges in using high-throughput phenotyping, "big data," analytics, and related technologies in the livestock industry based on discussions at the Livestock High-Throughput Phenotyping and Big Data Analytics meeting, held in November 2017 (see: https://www.animalgenome.org/bioinfo/community/workshops/2017/). Critical needs for investments in infrastructure for people (e.g., "big data" training), data (e.g., data transfer, management, and analytics), and technology (e.g., development of low cost sensors) were defined by this group. Though some subgroups of animal science have extensive experience in predictive modeling, cross-training in computer science, statistics, and related disciplines are needed to use big data for diverse applications in the field. Extensive opportunities exist for public and private entities to harness big data to develop valuable research knowledge and products to the benefit of society under the increased demands for food in a rapidly growing population.

Previous results indicated that antibody response to PRRSV has moderate genomic prediction accuracy; however, little is known about this for other common infectious diseases. Therefore, the objective of this study was to estimate the accuracy of genomic prediction for antibody response to infectious diseases in commercial sows. A total of 2,848 Large White x Landrace replacement gilts were sourced from 17 high-health multipliers (7 breeding companies; BC) and introduced to 23 commercial farms with a history of common diseases, following standard acclimation procedures. Serum was used to quantify antibody response to swine influenza virus (SIV), Mycoplasma hyopneumoniae (MH), porcine circovirus type 2 (PCV2), and 8 serotypes of Actinobacilluspleuropneumoniae(APP1-3, 5, 7, 10, 12, and 13) at entry (S/PEntry), following acclimation (S/PAcclimation), and during parities 1 (S/PParity1) and 2 (S/PParity2). All animals were genotyped for 38,191 SNPs. Genomic prediction was performed using BayesB (pi=0.99), with the fixed effect of CG and random effects of SNPs included in the model. Training and validation were performed using 7-fold cross-validation, with data from each BC used as the validation dataset in one-fold. In general, prediction accuracies were low: SIV, from 0.13 (S/PAcclimation) to 0.26 (S/PParity1); MH, -0.07 (S/PAcclimation) to 0.13 (S/PParity2); PCV2, 0.04 (S/PParity1) to 0.32 (S/PAcclimation); APP, -0.08 (S/PEntry, APP10) to 0.26 (S/PAcclimation, APP7). At each point, average accuracies were 0.06 for S/PEntry, 0.09 for S/PAcclimationand S/PParity1, and 0.08 for S/PParity2, showing small increases in accuracy after the acclimation period. Among diseases, average accuracies ranged from 0.01 (APP1) to 0.22 (PCV2). Results show that, overall, the accuracy of genomic prediction of antibody response to common infectious diseases in commercial gilts is limited. The authors thank PigGen Canada, Genome Canada, and the Canadian Swine Health Board for financial support, and the late Dr. Stephen Bishop for his scientific contributions.

The objective of this study was to perform genomic predictions for reproductive performance of sows under natural health challenge. Reproductive performance (1 to 4 parities) and genotype (~40K SNPs) were available for 2,604 crossbred sows, for a total of 7,635 farrowing records. Animals from 17 high-health multipliers from 7 breeding companies (PigGen Canada) were shipped to 23 commercial farms with recent history of common infectious diseases. Gilts entered farms with an average of 53 animals per contemporary group (CG). Traits included total number of piglets: born (TB), born alive (NBA), stillborn (SB), mummified (MUM), born dead (NBD), and weaned (NW). Genomic predictions were performed using Bayes-B (pi=0.995) with a seven-fold cross-validation using each company in turn for validation and the others for training. The model included the effects of CG (fixed) and SNP (random), and net number of fosters (covariate) for NW. Genomic predictions were done for animal lifetime performance (sum performance of parities) for each trait and using first parity performance as the training set to predict subsequent parity performance. Accuracy was calculated as the weighted average correlation between GEBV and adjusted phenotype across validation sets divided by the square root of heritability. Lifetime performance accuracies were low to moderate, ranging from 0.11 (TB) to 0.45 (NBD). Accuracies using parity 1 to predict subsequent performance were low, ranging from -0.07 (SB in parity 3) to 0.19 (NBD in parity 2), with average accuracies per trait ranging from 0.04 (SB) to 0.16 (NBD).Although most accuracies were low, the moderately high accuracies for some lifetime performance shows that genomic prediction can be used to improve performance under natural health challenge in sows. We appreciate the financial support of PigGen Canada, Canadian Swine Health Board, Genome Alberta and Swine Innovation Porc, and the late Dr. Stephen Bishop for his scientific contributions.

Background Fescue toxicosis (FT) is the multifaceted syndrome that causes the major loss of revenue in beef industry. Management of FT has been substantial challenge for the beef industry. Little research has been conducted to identify host genetic variation for FT response. Therefore, the objectives of this study were 1) to identify differentially expressed genes (DEG) in animals with contrasting response to fescue toxicosis, 2) to assess the biological relevance of DEG and 3) to investigate the relationships of DEG through gene networks in Angus cows. Results Genotype-by-location-by-time interaction was evident, with one location (2,296) having much greater number of DEG (q-value < 0.1) between HT and LT animals than the other (554). In addition, there was a greater number of DEG (q-value < 0.1) between HT and LT animals on week 5 (3,892) than on weeks 1(1,413), 9 (1,384), and 13 (573). So, further analyses focused on DEG between HT and LT animals on week 5 at the most toxic location. The most significant DEG between HT and LT animals had relevant functions associated with FT: cellular growth (SPDYC, HEYL, ANXA13), cardiovascular function (FGB, HBA, WNT11, BPIFB4, MESP2), protein metabolism (ENPP6, MMP8), and immune response (CTBS, SDC2, CXCL13, IL-13, JAKMIP2). The strongest positive partial correlation (0.99) was between CTBS and CXCL13, where CTBS is involved in carbohydrate metabolism and immune function, and CXCL13 is involved in immune, inflammatory, and defense response, and G-protein coupled pathway. The regulation of the most significant DEG between HT and LT animals on week 5 are highly correlated, indicating a complex interaction between. When all DEG were analyzed, the enriched biological processes associated with fescue toxicosis included immune response, cardiovascular function and development, metabolic, cellular and biological processes, and fertilization. Conclusions These findings provide potential biomarkers that should be evaluated for selection of cattle with greater tolerance to fescue toxicosis which will help to establish the herd with fescue tolerant cows in regions where high endophyte infected pasture is present.

Background Porcine reproductive and respiratory syndrome (PRRS) is one of the most infectious swine diseases in the world, resulting in over 600 million dollars of economic loss in the USA alone. More recently, the USA swine industry has been having additional major economic losses due to the spread of porcine epidemic diarrhea (PED). However, information regarding the amount of genetic variation for response to diseases in reproductive sows is still very limited. The objectives of this study were to identify periods of infection with of PRRS virus (PRRSV) and/or PED virus (PEDV), and to estimate the impact their impact on the phenotypic and genetic reproductive performance of commercial sows. Results Disease (PRRS or PED) was significant (P

Vitamin B and trace minerals are crucial molecular signals involved in many biological pathways, however, their bioavailability is compromised in high-producing ruminant animals. So far, studies have mainly focused on the effects of these micronutrients on animal performance, but their use in a rumen-protected form and their impact on liver metabolism in finishing beef cattle is poorly known. We used a shotgun proteomic approach combined with biological network analyses to assess the effects of a rumen-protected B-vitamin blend, as well as those of hydroxy trace minerals, on the hepatic proteome. A total of 20 non-castrated Nellore males with 353 ± 43 kg of initial body weight were randomly assigned to one of the following treatments: CTRL—inorganic trace minerals without supplementation of a protected vitamin B blend, or SUP—supplementation of hydroxy trace minerals and a protected vitamin B blend. All animals were fed the same amount of the experimental diet for 106 days, and liver biopsies were performed at the end of the experimental period. Supplemented animals showed 37 up-regulated proteins (p &lt, 0.10), and the enrichment analysis revealed that these proteins were involved in protein folding (p = 0.04), mitochondrial respiratory chain complex I (p = 0.01) and IV (p = 0.01), chaperonin-containing T-complex 2 (p = 0.01), glutathione metabolism (p &lt, 0.01), and other aspects linked to oxidative-stress responses. These results indicate that rumen-protected vitamin B and hydroxy trace mineral supplementation during the finishing phase alters the abundance of proteins associated with the electron transport chain and other oxidation–reduction pathways, boosting the production of reactive oxygen species, which appear to modulate proteins linked to oxidative-damage responses to maintain cellular homeostasis.

We investigated how feed restriction at 50% of maintenance requirements during different stages of gestation affects the transcriptome of newborn goats' skeletal muscle. Fourteen pregnant dams were randomly assigned into one of the following dietary treatments: animals fed at 50% of maintenance requirement from 8-84 d of gestation and then fed at 100% of maintenance requirement from day 85 of gestation to parturition (RM, n = 6), and animals fed at 100% of maintenance requirement from 8-84 d of gestation and then fed at 50% of maintenance requirement from day 85 of gestation to parturition (MR, n = 8). At birth, samples of offspring's Longissimus muscle were collected for total RNA extraction and sequencing. Our data showed 66 differentially expressed (DE) genes (FDR < 0.05). A total of 6 genes were upregulated and 60 downregulated (FDR < 0.05) in the skeletal muscle of the newborns resulting from treatment RM compared with MR. Our results suggest that the DE genes upregulated in newborn goats' skeletal muscle from the RM group compared to MR, included genes related to satellite cells, and genes that indicates impaired insulin sensitivity and changes in the composition of intramuscular fat. The DE genes upregulated in newborn goats' skeletal muscle from the MR group compared to RM, are also related to impaired insulin sensitivity, as well as a predominantly oxidative metabolism and cellular oxidative stress. However, protective mechanisms against insulin sensitivity and oxidative stress may have been augmented in the skeletal muscle of offspring from MR treatment compared to RM, in order to maintain cellular homeostasis.

Allocation of treatments to experimental units (EUs) is done at random. In the presence of a concomitant variable (e.g., initial body weight; iBW), one strategy is to block WUs into iBW groups. However, in some scientific manuscripts, EUs are sorted by iBW and then allocated to treatments (e.g., treatments “A” and “B”) based on iBW, such that the lightest EU receives “A,” the second and third lightest receive “B,” etc. Although this strategy guarantees similar iBW between treatments, this ignores the random process required for statistical analysis of the data. We aimed to quantify the impact of lack of randomization on the statistical power and type I error of completely randomized designs (CRD). Data were simulated for ADG using two treatments (“A” having 50 g/d more than “B,” and MSE=1250 g2/d2). Data were simulated for different replicates per treatment (RepsPerTreat; from 3 to 18, every 3). We used two scenarios for the correlations between iBW and ADG (ρ ADG,iBW): 0 and 0.5. Treatments were allocated to EUs at random (CRD) or according to the order of EUs based on iBW (completely non-randomized design; CNRD). The model included the fixed-effects of intercept and treatment. For ρ ADG,iBW=0, results showed that CRD had greater statistical power (POW) than CNRD for RepsPerTreat from 3 to 9, whereas CNRD had greater from 12 to 18. For ρ ADG,iBW=0.5, CNRD had an even greater POW than CRD starting at 9 RepsPerTreat. Although the type I error (ERROR) of CRD were close to 5% across all scenarios with different RepsPerTreat, CNRD had consistently greater and lower ERROR than CRD with =0 and 0.5, respectively. Having ERROR deviating from 5% is not expected. Visual inspection of the F-values of these models when the null hypothesis was true showed that a distribution other than the theoretical F-distribution, indicating that the statistical test is not valid. Sorting EUs by iBW does not guarantee greater statistical power but results in invalid F-tests.

Porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) are two of the most significant pathogens affecting swine. Co-infections are common and result in respiratory disease and reduced weight gain in growing pigs. Although PRRS modified live virus (MLV) vaccines are widely used to decrease PRRS-associated losses, they are generally considered inadequate for disease control. The gut microbiome provides an alternative strategy to enhance vaccine efficacy and improve PRRS control. The objective of this study was to identify gut microbiome characteristics associated with improved outcome in pigs immunized with a PRRS MLV and co-challenged with PRRSV and PCV2b. Twenty-eight days after vaccination and prior to co-challenge, fecal samples were collected from an experimental population of 50 nursery pigs. At 42 days post-challenge, 20 pigs were retrospectively identified as having high or low growth outcomes during the post-challenge period. Gut microbiomes of the two outcome groups were compared using the Lawrence Livermore Microbial Detection Array (LLMDA) and 16S rDNA sequencing. High growth outcomes were associated with several gut microbiome characteristics, such as increased bacterial diversity, increased Bacteroides pectinophilus, decreased Mycoplasmataceae species diversity, higher Firmicutes:Bacteroidetes ratios, increased relative abundance of the phylum Spirochaetes, reduced relative abundance of the family Lachnospiraceae, and increased Lachnospiraceae species C6A11 and P6B14. Overall, this study identifies gut microbiomes associated with improved outcomes in PRRS vaccinated pigs following a polymicrobial respiratory challenge and provides evidence towards the gut microbiome playing a role in PRRS vaccine efficacy.

The use of corn coproducts increases the concentration of fiber and, often, the use of supplemental lipids in swine diets, which may affect energy and nutrient digestibility. An experiment was conducted to determine the effects of reduced-oil distillers' dried grains with solubles (DDGS) and soybean oil (SBO) on dietary AA, acid hydrolyzed ether extract (AEE), and NDF digestibility in corn-based diets fed to growing pigs. Eighteen growing pigs (33.8 ± 2.2 kg BW) were surgically fitted with a T-cannula in the distal ileum and allocated to 1 of 6 dietary treatment groups in a 3-period incomplete Latin square design, with 9 observations per treatment. Six dietary treatments were obtained by adding 0, 20, and 40% DDGS to corn-casein diets formulated with 2 and 6% SBO. Ileal digesta and fecal samples were collected and the apparent ileal digestibility (AID) and apparent total tract digestibility (ATTD) of AEE and NDF and the AID of AA were determined. Apparent values were corrected for endogenous losses of lipids, and true ileal (TID) and true total tract digestibility (TTTD) values of lipids were calculated. Results showed that the AID of Lys decreased (0.001) with the inclusion of DDGS but was not affected ( = 0.63) by the inclusion of SBO. An interaction between DDGS and SBO on the AID ( = 0.002) and ATTD ( = 0.009) of NDF was observed, where the AID and ATTD of NDF decreased with DDGS at 6% SBO but no effect was observed at 2% SBO. The AID of NDF increased with SBO at 0% DDGS, but no effect was observed at 20 or 40% DDGS. An interaction between DDGS and SBO on the AID ( = 0.011) and ATTD ( = 0.008) of AEE was observed, where the AID and ATTD of AEE increased with SBO. The AID and ATTD of AEE increased with DDGS at 2% SBO, but no effect was observed at 6% SBO. Correction by ileal and fecal endogenous loss of AEE (9.5 and 13.6 g/kg of DMI, respectively) showed that increasing dietary AEE had no effect on the TID and TTD of AEE (0.05). In conclusion, the AID of Lys decreased with DDGS and was not affected by lipids from SBO. The greatest AID and ATTD of NDF was observed in diets with a high AEE and low NDF content. Low values of apparent digestibility of AEE in lower-lipid diets are possibly the result of endogenous losses of lipids, because the true digestibility of AEE was not affected by the dietary increase of AEE.