Can the post-ruminal urea release impact liver metabolism, and nutritional status of beef cows at late gestation?

We aimed to evaluate the effects of post-ruminal supply of urea (PRU) on nutritional status, and liver metabolism of pregnant beef cows during late gestation. Twenty-four Brahman dams, pregnant from a single sire, and weighing 545 kg ± 23 kg were confined into individual pens at 174 ± 23 d of gestation, and randomly assigned into one of two dietary treatments up to 270 d of gestation: Control (CON, n = 12), consisting of a basal diet supplemented with conventional urea, where the cows were fed with diets containing 13.5 g conventional urea per kg dry matter; and PRU (PRU, n = 12), consisting of a basal diet supplemented with a urea coated to extensively prevent ruminal degradation while being intestinally digestible, where the cows were fed with diets containing 14,8 g urea protected from ruminal degradation per kg dry matter. Post-ruminal supply of urea reduced the urine levels of 3-methylhistidine (P = 0.02). There were no differences between treatments for dry matter intake (DMI; P = 0.76), total digestible nutrient (TDN) intake (P = 0.30), and in the body composition variables, such as, subcutaneous fat thickness (SFT; P = 0.72), and rib eye area (REA; P = 0.85). In addition, there were no differences between treatments for serum levels of glucose (P = 0.87), and serum levels of glucogenic (P = 0.28), ketogenic (P = 0.72), glucogenic, and ketogenic (P = 0.45) amino acids, neither for urea in urine (P = 0.51) as well as urea serum (P = 0.30). One the other hand, enriched pathways were differentiated related to carbohydrate digestion, and absorption, glycolysis, pyruvate metabolism, oxidative phosphorylation, pentose phosphate pathway, and biosynthesis of amino acids of the exclusively expressed proteins in PRU cows. Shifting urea supply from the rumen to post-ruminal compartments decreases muscle catabolism in cows during late gestation. Our findings indicate that post-ruminal urea supplementation for beef cows at late gestation may improve the energy metabolism to support maternal demands. In addition, the post-ruminal urea release seems to be able to trigger pathways to counterbalance the oxidative stress associated to the increase liver metabolic rate.

Further host-genomic characterization of total antibody response to PRRSV vaccination and its relationship with reproductive performance in commercial sows: genome-wide haplotype and zygosity analyses

Background

The possibility of using antibody response (S/P ratio) to PRRSV vaccination measured in crossbred commercial gilts as a genetic indicator for reproductive performance in vaccinated crossbred sows has motivated further studies of the genomic basis of this trait. In this study, we investigated the association of haplotypes and runs of homozygosity (ROH) and heterozygosity (ROHet) with S/P ratio and their impact on reproductive performance.

Results

There was no association (P-value ≥ 0.18) of S/P ratio with the percentage of ROH or ROHet, or with the percentage of heterozygosity across the whole genome or in the major histocompatibility complex (MHC) region. However, specific ROH and ROHet regions were significantly associated (P-value ≤ 0.01) with S/P ratio on chromosomes 1, 4, 5, 7, 10, 11, 13, and 17 but not (P-value ≥ 0.10) with reproductive performance. With the haplotype-based genome-wide association study (GWAS), additional genomic regions associated with S/P ratio were identified on chromosomes 4, 7, and 9. These regions harbor immune-related genes, such as SLA-DOB, TAP2, TAPBP, TMIGD3, and ADORA. Four haplotypes at the identified region on chromosome 7 were also associated with multiple reproductive traits. A haplotype significantly associated with S/P ratio that is located in the MHC region may be in stronger linkage disequilibrium (LD) with the quantitative trait loci (QTL) than the previously identified single nucleotide polymorphism (SNP) (H3GA0020505) given the larger estimate of genetic variance explained by the haplotype than by the SNP.

Conclusions

Specific ROH and ROHet regions were significantly associated with S/P ratio. The haplotype-based GWAS identified novel QTL for S/P ratio on chromosomes 4, 7, and 9 and confirmed the presence of at least one QTL in the MHC region. The chromosome 7 region was also associated with reproductive performance. These results narrow the search for causal genes in this region and suggest SLA-DOB and TAP2 as potential candidate genes associated with S/P ratio on chromosome 7. These results provide additional opportunities for marker-assisted selection and genomic selection for S/P ratio as genetic indicator for litter size in commercial pig populations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-021-00676-5.

Host Genetics of Response to Porcine Reproductive and Respiratory Syndrome in Sows: Reproductive Performance

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.

Host Genetics of Response to Porcine Reproductive and Respiratory Syndrome in Sows: Antibody Response as an Indicator Trait for Improved Reproductive Performance

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.

Genomics of response to porcine reproductive and respiratory syndrome virus in purebred and crossbred sows: antibody response and performance following natural infection vs. vaccination

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.

Assessing the statistical training in animal science graduate programs in the United States: survey on statistical training

Statistical analysis of data and understanding of experimental design are critical skills needed by animal science graduate students (ASGS). These skills are even more valuable with the increased development of high-throughput technologies. The objective of this study was to evaluate the perceived statistical training of U.S. ASGS. A survey with 38 questions was shared across U.S. universities, and 416 eligible ASGS from 43 universities participated in this study. The survey included questions on the demographics and overall training, graduate education on statistics, and self-assessment on statistics and career path of ASGS. Several analyses were performed: relationship between perceived received education (PRE; i.e., how ASGS evaluated their graduate education in statistics) and perceived knowledge (PK; i.e., how ASGS evaluated their knowledge in statistics from their education); ranking of statistical topics based on PRE, PK, and confidence in performing statistical analyses (CPSA); cluster analysis of statistical topics for PRE, PK, and CPSA; and factors (demographic, overall training, interest in statistics, and field of study) associated with the overall scores (OS) for PRE, PK, and CPSA. Students had greater (P < 0.05) PRE than PK for most of the statistical topics included in this study. The moderate to high repeatability of answers within statistical topics indicates substantial correlations in ASGS answers between PRE and PK. The cluster analysis resulted in distinct groups of "Traditional" and "Nontraditional" statistical topics. ASGS showed lower (P < 0.05) scores of PRE, PK, and CPSA in "Nontraditional" compared with "Traditional" statistical methods. Several factors were associated (P < 0.05) with the OS of PRE, PK, and CSPA. In general, factors related to greater training and interest in statistics of ASGS were associated with greater OS, such as taking more credits in statistics courses, having additional training in statistics outside the classroom, knowing more than one statistics software, and more. This study provided comprehensive information on the perceived level of education, knowledge, and confidence in statistics in ASGS in the United States. Although objective measurements of their training in statistics are needed, the current study suggests that ASGS have limited statistical training on topics of major importance for the current and future trends of data-driven research in animal sciences.

Phenotypic and genomic relationships between vulva score categories and reproductive performance in first-parity sows

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 < 0.10) for total number born (TNB). There were significant (P ≤ 0.05) pre-defined contrasts of VSC-S versus VSC-M + L on TNB, number born alive (NBA), TND, number of stillborn (NSB), and number of mummies (MUM). Heritability estimates for VSC as a categorical trait (VSCc) and a quantitative trait (VSCq) were 0.40 ± 0.02 and 0.83 ± 0.02, respectively, for across farm, 0.13 ± 0.07 and 0.20 ± 0.10, respectively, for Farm1, 0.07 ± 0.07 and 0.09 ± 0.09, respectively, for Farm2, and 0.20 ± 0.03 and 0.34 ± 0.05, respectively, for Farm3. For across farms, favorable genetic correlations estimates were found for TNB (0.28 ± 0.19) and NBA (0.26 ± 0.17). Within farms, moderate genetic correlations between VSC with reproductive traits were found for TNB (0.61 ± 0.47) and MUM (0.69 ± 0.47) for farm 1, for number of services until first farrow (NS; 0.69 ± 0.38) and unique service with successful first farrow (SFS; − 0.71 ± 0.38) for farm 3. Multiple genomic regions associated with VSC_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 VSC_c and VSC_q. 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.

Dietary nucleotide supplementation as an alternative to in-feed antibiotics in weaned piglets

Nucleotides are important to cell growth and division and are crucial to the rapid proliferation of such cells as the intestinal mucosa and immune cells. Accordingly, the nucleotide requirements of animals are high during periods of rapid growth and periods of stress like post-weaning period. Thus, nucleotide supplementation may be a possible alternative to in-feed antibiotics as growth promoter in this phase. The study aimed to evaluate dietary nucleotide supplementation as an alternative to in-feed antibiotics on performance and gut health of weaned piglets. Ninety-six 21-day-old piglets, weighing 7.44 ± 0.65 kg, were allocated into 1 of 3 treatments (8 pens per treatment; 4 pigs per pen) in a 14-day trial. Dietary treatments consisted of control: corn-soybean meal-based diet; nucleotides: control +2 g/kg of a nutritional additive with purified nucleotides; and antibiotic: control +0.8 g/kg of antibiotic growth promoter based on colistin and tylosin. Performance variables and fecal score were not affected (P > 0.05) by supplementing nucleotide or antibiotic. Nucleotides treatment had similar effect to antibiotic and superior to control (P < 0.05) on enhancing duodenum villus height, jejunum crypt depth, and reduction of Paneth cellular area. Duodenum and ileum of animals supplemented with nucleotides or antibiotics had higher (P < 0.05) number of proliferating cells than did those of control animals, whereas the jejunum of animals that received antibiotic diets presented more (P < 0.05) proliferating cells than either the nucleotides or control animals. Jejunum of nucleotide-treated piglets showed a greater number of apoptotic cells than those fed antibiotic or control diets (P < 0.05). Nucleotides and antibiotic treatments decreased the B lymphocyte counts in duodenum and ileum (P < 0.05) but increased in the jejunum (P < 0.05), when compared to the control treatment. Relative abundance of mitogen-activated protein kinases-6, haptoglobin, and tumor necrosis factor-α mRNA was not influenced (P > 0.05) by treatments. In the ileal, antibiotic supplementation reduced total bacteria quantification compared to nucleotide supplementation or the control (P < 0.05), whereas nucleotides supplementation increased enterobacteria proliferation compared to the antibiotic or control diets (P < 0.05). However, nucleotides and antibiotic reduced (P < 0.05) colon total bacteria quantification when compared to control. These results suggest that the nucleotides source used to weaned piglets improved gut health by modulating the local immune response and modulating intestinal mucosa development, and, therefore, nucleotides may be an alternative to antibiotics as growth promoters.

High-Fat Diets Led to OTU-Level Shifts in Fecal Samples of Healthy Adult Dogs

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.

Genomic Analysis of IgG Antibody Response to Common Pathogens in Commercial Sows in Health-Challenged Herds

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 (r _G ) of Ab response to IAV with MH, PCV2, PRRSV, and APP_mean (average Ab responses for all serotypes of APP) were positive (>0.29) at entry. APP_mean 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.

Evaluation of a commercial genetic test for fescue toxicosis in pregnant Angus beef cattle

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.

Genetic Analysis of Antibody Response to Porcine Reproductive and Respiratory Syndrome Vaccination as an Indicator Trait for Reproductive Performance in Commercial Sows

We proposed to investigate the genomic basis of antibody response to porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV) vaccination and its relationship to reproductive performance in non-PRRSV-infected commercial sows. Nine hundred and six F1 replacement gilts (139 ± 17 days old) from two commercial farms were vaccinated with a commercial modified live PRRSV vaccine. Blood samples were collected about 52 days after vaccination to measure antibody response to PRRSV as sample-to-positive (S/P) ratio and for single-nucleotide polymorphism (SNP) genotyping. Reproductive performance was recorded for up to 807 sows for number born alive (NBA), number of piglets weaned, number born mummified (MUM), number of stillborn (NSB), and number of pre-weaning mortality (PWM) at parities (P) 1-3 and per sow per year (PSY). Fertility traits such as farrowing rate and age at first service were also analyzed. BayesC0 was used to estimate heritability and genetic correlations of S/P ratio with reproductive performance. Genome-wide association study (GWAS) and genomic prediction were performed using BayesB. The heritability estimate of S/P ratio was 0.34 ± 0.05. High genetic correlations (r _g) of S/P ratio with farrowing performance were identified for NBA P1 (0.61), PWM P2 (-0.70), NSB P3 (-0.83), MUM P3 (-0.84), and NSB PSY (-0.90), indicating that genetic selection for increased S/P ratio would result in improved performance of these traits. A quantitative trait locus was identified on chromosome 7 (∼25 Mb), at the major histocompatibility complex (MHC) region, explaining ∼30% of the genetic variance for S/P ratio, mainly by SNPs ASGA0032113, H3GA0020505, and M1GA0009777. This same region was identified in the bivariate GWAS of S/P ratio and reproductive traits, with SNP H3GA0020505 explaining up to 10% (for NBA P1) of the genetic variance of reproductive performance. The heterozygote genotype at H3GA0020505 was associated with greater S/P ratio and NBA P1 (P = 0.06), and lower MUM P3 and NSB P3 (P = 0.07). Genomic prediction accuracy for S/P ratio was high when using all SNPs (0.67) and when using only those in the MHC region (0.59) and moderate to low when using all SNPs excluding those in the MHC region (0.39). These results suggest that there is great potential to use antibody response to PRRSV vaccination as an indicator trait to improve reproductive performance in commercial pigs.

Beef cattle that respond differently to fescue toxicosis have distinct gastrointestinal tract microbiota

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. The objective of this study was to identify bacterial and fungal communities associated with fescue toxicosis tolerance. 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 amplicon sequencing to compare the fecal microbiota of the two tolerance groups. This study reveals significantly (q<0.05) 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.

Genetic and genomic characterization of vulva size traits in Yorkshire and Landrace gilts

BACKGROUND

Reproductive 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.

RESULTS

Heritability 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 on Sus scrofa chromosome (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.

CONCLUSIONS

Our 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.

Beginning to offer drinking water at birth increases the species richness and the abundance of Faecalibacterium and Bifidobacterium in the gut of preweaned dairy calves

We previously demonstrated that dairy calves having access to drinking water since birth (W0) achieved greater body weight, fiber digestibility, and feed efficiency than those that first received drinking water at 17 d of age (W17). Since gut microbiota composition could be linked to growth and development of animals, the objective of this study was to examine the effect of offering drinking water to newborn calves on composition of bacteria in the gut using a fecal microbiota analysis. Fresh feces were collected directly from the rectum of calves in W0 (n = 14) and W17 (n = 15) at 2, 6, and 10 wk of age. All of the calves were fed pasteurized waste milk, weaned at 7 wk of age, and offered tap water according to the treatment. The DNA was sequenced using 16S rRNA gene-amplicon sequencing on an Illumina MiSeq system (Illumina Inc., San Diego, CA). The sequences were clustered into operational taxonomic units (OTU) with a 99% similarity threshold. Treatment effects on α-diversity indices and relative abundance of the 10 most abundant genera were analyzed using GLIMMIX procedure of SAS (SAS Institute Inc., Cary, NC). Statistical significance (q-value) of treatment effects on the 50 most abundant OTU was determined with a false discovery rate analysis. At 2 wk of age, W0 had a greater number of observed OTU (5,908 vs. 4,698) and species richness (Chao 1 index) than W17. The number of OTU and richness indices increased from wk 2 to 6, but the increment of W17 was greater than that of W0. The Shannon and inverse-Simpson indices increased linearly with age, but no difference was observed between W0 and W17 at any time point. The Firmicutes to Bacteroidetes ratios were also similar at every time point but decreased markedly when calves were weaned. The relative abundance of genera Faecalibacterium and Bacteroides was greater in W0 than W17 at 2 wk of age. The genus Faecalibacterium continued to be more abundant in W0 than W17 at 6 wk of age but had similar abundance 3 wk after weaning (10 wk of age). The abundance of Faecalibacterium at wk 6 was positively correlated with apparent total-tract digestibility of acid detergent fiber at 10 wk of age. Calves receiving water since birth had greater abundance of OTU related to Faecalibacterium prausnitzii, and Bifidobacterium breve at 6 wk of age (q < 0.085). These species are known to improve growth in preweaned calves. The abundance of none of the genera and OTU was different between W0 at W17 at 10 wk of age (q > 0.100). Overall, beginning to offer drinking water at birth has a potential to modulate gut microbiota composition and thereby positively affect performance of young dairy heifer calves (≤10 wk of age).

A Vision for Development and Utilization of High-Throughput Phenotyping and Big Data Analytics in Livestock

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.

Investigating the relationship between vaginal microbiota and host genetics and their impact on immune response and farrowing traits in commercial gilts

Our objectives were to evaluate the interaction between host genetics and vaginal microbiota and their relationships with antibody (Ab) response to porcine reproductive and respiratory syndrome virus (PRRSV) vaccination and farrowing performance in commercial gilts. The farrowing performance traits were number born alive, number weaning (NW), total number born, number born dead, stillborn, mummies and preweaning mortality (PWM). The vaginal microbiota was collected on days 4 (D4) and 52 (D52) after vaccination for PRRSV. Blood samples were collected on D52 for Ab measurement. Actinobacteria, Bacterioidetes, Firmicutes, Proteobacteria and Tenericutes were the most abundant Phyla identified in the vaginal microbiota. Heritability ranged from ~0 to 0.60 (Fusobacterium) on D4 and from ~0 to 0.63 (Terrisporobacter) on D52, with 43 operational taxonomic units (OTUs) presenting moderate to high heritability. One major QTL on chromosome 12 was identified for 5 OTUs (Clostridiales, Acinetobacter, Ruminococcaceae, Campylobacter and Anaerococcus), among other 19 QTL. The microbiability for Ab response to PRRSV vaccination was low for both days (<0.07). For farrowing performance, microbiability varied from <0.001 to 0.15 (NW on D4). For NW and PWM, the microbiability was greater than the heritability estimates. Actinobacillus, Streptococcus, Campylobacter, Anaerococcus, Mollicutes, Peptostreptococcus, Treponema and Fusobacterium showed different abundance between low and high Ab responders. Finally, canonical discriminant analyses revealed that vaginal microbiota was able to classify gilts in high and low Ab responders to PRRSV vaccination with a misclassification rate of <0.02. Although the microbiota explained limited variation in Ab response and farrowing performance traits, there is still potential to explore the use of vaginal microbiota to explain variation in traits such as NW and PWM. In addition, these results revealed that there is a partial control of host genetic over vaginal microbiota, suggesting a possibility for genetic selection on the vaginal microbiota.

375 Identification of QTL associated with antibody response to common infectious diseases in commercial sows

The objective of this study was to perform genome-wide association studies (GWAS) to identify Quantitative Trait Loci (QTL) associated with 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 pig diseases, following the standard acclimation procedures with an average of 53 animals per entry group (CG). Serum was used to quantify antibody response to swine influenza virus (SIV), Mycoplasma hyopneumoniae (MH), porcine circovirus type-2 (PCV2), and 8 serotypes of Actinobacillus pleuropneumoniae (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. GWAS was performed using BayesB (pi=0.99), with the fixed effect of CG and the random effects of SNPs in the model. For APP, QTL were only identified at S/PAcclimation; on SSC14 (2Mb) for APP3, APP7, APP10, and APP13 that explained 5.6, 4.7, 2.8, and 3.6% of the genetic variance, respectively. A gene within this QTL region is SYK, involved in the control of immune-receptors. For APP5, a QTL that explained 4.2% of the genetic variance was identified on SSC4 (105Mb), which co-localizes with two genes associated with immune-response: SIKE1and NRAS. For SIV, no QTL was identified. A QTL on SSC7 (130-131Mb) was identified for MH (S/PParity1, 5.1%) and PCV2 (S/PEntry, 34%; S/PAcclimation, 43.4%). These results provide new information on the genetic basis of response to infectious diseases in sows. The identified QTL have the potential to be used to select for improved immune response. The authors thanks PigGen Canada, Genome Canada, and the Canadian Swine Health Board for financial support, and the late Dr. Stephen Bishop for his scientific contributions.

PSIII-5 Accuracy of genomic prediction of antibody response to common infectious diseases in commercial sows

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.

PSIII-3 Genes and functions associated with tolerance to fescue toxicosis in Angus cows

The objective of this study was to identify differentially expressed genes (DEG) and functions associated with tolerance to fescue toxicosis (FT). Forty pregnant purebred Angus cows were selected based on their growth at two locations in North Carolina (Butner Beef Cattle Field Laboratory, BBFCL; Upper Piedmont Research Station, UPRS) and classified as either high tolerant (HT) or low tolerant (LT) to FT with 20 cows in each group balanced by location. Blood samples were collected on weeks 1, 5, 9, and 13 for RNA sequencing. Counts were analyzed using a negative binomial model including the effects of genetic group, location, time, all possible interactions of these effects, flow cell, covariate of RNA integrity number, and normalized library size as offset. Genotype-by-location-by-time interaction was evident with a high number (4,453) of DEG (q-value<0.1) between genetic groups on week 5 at UPRS compared to all other possible interactions. So further analyses were focused on week 5 at UPRS. The most significant upregulated genes in LT and HT animals were ENPP6 and MESP2, respectively, with log2 fold changes of 1.90 [95% confidence interval = 0.89, 2.92] q-value=0.005) and 0.91 [0.35, 1.47] (q-value=0.01), respectively. Other top 5 upregulated genes for HT animals were CTBS, CLDN19, SPDYC, HEYL, and SDC2, and for LT animals were OLIG1, IL13, ANXA13, ENSBTAG00000024188and CXCL13. Enrichment analysis (P < 0.05) showed that DEG between genetic groups have general functions, such as metabolic, biosynthetic, and catabolic processes, as well as DNA and RNA-related functions, such as translation, transcription, and repair. These findings helped characterizing the genetic basis of tolerance to FT in cattle. In addition, we identified genes that may serve as potential biomarkers for tolerance to FT

68 Genomic prediction accuracies of vulva size traits in Landrace and Yorkshire gilts

Recent results indicated that vulva size measured prior to puberty may be predictive of reproductive performance in sows. Therefore, the objective of this study was to estimate genomic prediction accuracies for vulva size traits in purebred gilts. A total of 1,185 Landrace (n = 477) and Yorkshire (n = 708) gilts originated from two different lines were used in this study. All animals had vulva size measurements taken at an average 21.5 weeks of age (SD = 5.8). Measurements included vulva width (VW), vulva height (VH), and vulva area (VA). Genotype data (Geneseek GGP-HD) was available for all animals, for ~40K SNPs. Marker allele substitution effects were estimated using Bayes-B (pi = 0.99) in a model including the fixed effects of contemporary group, line, breed (for multi-breed analysis only) and body weight (covariate), and the random effect of SNPs. Genomic prediction accuracies were estimated using three training and validation strategies: between-breed, within-breed (4 and 6 cross-validation folds for Landrace and Yorkshire, respectively), and multi-breed (10-fold cross-validation, using one-fold per breed for validation at a time). Between-breed accuracies were low and consistently negative, with -0.02, -0.10, and -0.05 in Landrace and -0.05, -0.04 and -0.03 in Yorkshire, for VW, VH, and VA, respectively. Within Landrace, these were moderate, with 0.35 (VW), 0.42 (VH), and 0.56 (VA), whereas lower accuracies were obtained for Yorkshire, with 0.07 (VW), 0.20 (VH), and 0.14 (VA). Multi-breed accuracies were low with 0.14 (VW), 0.14 (VH), and 0.24 (VA) for Landrace, and 0.03 (VW), 0.16 (VH), and 0.09 (VA) for Yorkshire. These results indicate that genomic selection for vulva size traits is possible in Landrace, but limited in Yorkshire gilts. The low between- and multi-breed results suggest that QTL for these traits are in opposite phases between breeds and/or do not segregate in both breeds. Financial support from the Iowa Pork Industry Center is appreciated.

PSIII-8 Genomic prediction of reproductive performance of commercial sows in health challenged herds

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.

Effect of maternal feed restriction in dairy goats at different stages of gestation on skeletal muscle development and energy metabolism of kids at the time of births

The aim was to determine effects of maternal feed restriction in dairy goats at gestational different stages on skeletal muscle development and energy metabolism in kids at birth. Six pregnant goats were fed 50% of total digestible nutrients (TDN) and crude protein (CP) (NRC, 2007) recommendations in the first half of gestation and then fed to 100% of the recommendations in the second half of gestation (treatment R-M). In the other group, eight pregnant goats were fed 100% of TDN and CP in the first half of gestation and 50% of a restricted diet the second half of gestation (treatment M-R). Birth weight, blood glucose concentration, muscle fiber number, and size of kids at birth were not affected by maternal feed restriction. The mRNA and protein abundance of myogenic, adipogenic and fibrogenic markers were not affected (P > 0.05) by maternal diet. With regard to values for variables in kid energy metabolism, mRNA abundance of the glycolic enzyme HKII was less (P = 0.03) in the M-R group. In conclusion, maternal feed restriction in the first or second half of gestation had no affect mRNA abundance on myogenic, adipogenic, and fibrogenic markers nor were there changes in skeletal muscle mesenchymal stem cell population of kids at the time of birth. There, however, may be detrimental effects on energy metabolism by reducing HKII gene expression in skeletal muscle of dairy goat kids at the time of birth.

The effect of a porcine reproductive and respiratory syndrome outbreak on genetic parameters and reaction norms for reproductive performance in pigs1

The objective of this study was to estimate genetic parameters of antibody response and reproductive traits after exposure to porcine reproductive and respiratory syndrome virus. Blood samples were taken approximately 60 d after the outbreak. Antibody levels were quantified as the sample-to-positive ratio (S/P ratio) using a fluorescent microsphere assay. Reproductive traits included total number born (TNB), number born alive (NBA), number stillborn (NSB), number mummified (NBM), and number born dead (NBD). Mortality traits were log transformed for genetic analyses. Data were split into prior, during, and after the disease outbreak phases using visual appraisal of the estimates of farm-year-week effects for each reproductive trait. For NBA, data from all phases were combined into a reaction norm analysis with regression on estimates of farm-year-week effects for NBA. Heritability for S/P ratio was estimated at 0.17 ± 0.05. Heritability estimates for reproduction traits were all low and were lower during the outbreak for NBA but greater for mortality traits. TNB was not greatly affected during the outbreak, as many sows that farrowed during the outbreak were mated prior to the outbreak. Heritability for TNB decreased from 0.13 (prior) to 0.08 (after). Genetic correlation estimates between prior to and during the outbreak were high for TNB (0.86 ± 0.23) and NBA (0.98 ± 0.38) but lower for mortality traits: 0.65 ± 0.43, −0.42 ± 0.55, and 0.29 ± 1.39 for LNSB, LNBM, and LNBD, respectively. TNB prior to and after the outbreak had a lower genetic correlation (0.32 ± 0.33). In general, genetic correlation estimates of S/P ratio with reproductive performance during the outbreak were below 0.20 in absolute value, except for LNSB (−0.73 ± 0.29). Based on the reaction norm model, estimates of genetic correlations between the intercept and slope terms ranged from 0.24 ± 0.50 to 0.54 ± 0.35 depending on the parameterization used, indicating that selection for the intercept may result in indirect selection for steeper slopes, and thus, less resilient animals. In general, estimates of genetic correlations between farm-year-week effect classes based on the reaction norm model resembled estimates of genetic correlations from the multivariate analysis. Overall, compared to previous studies, antibody S/P ratios showed a lower heritability (0.17 ± 0.05) and low genetic correlations with reproductive performance during a porcine reproductive and respiratory syndrome outbreak, except for the LNSB.

Evaluating phosphorus release by phytase in diets fed to growing pigs that are not deficient in phosphorus

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.

Genetic analysis of reproductive performance in sows during porcine reproductive and respiratory syndrome (PRRS) and porcine epidemic diarrhea (PED) outbreaks

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 < 0.05) for all traits analyzed except for total piglets born. Heritability estimates for traits during Clean (without any disease), PRRS, and PED ranged from 0.01 (number of mummies; Clean and PED) to 0.41 (abortion; PED). Genetic correlations between traits within disease statuses ranged from −0.99 (proportion born dead with number weaned; PRRS) to 0.99 (number born dead with born alive; Clean). Within trait, between disease statuses, estimates ranged from − 0.17 (number weaned between PRRS and PED) to 0.99 (abortion between Clean and PRRS).

Conclusion

Results indicate that selection for improved performance during PRRS and PED in commercial sows is possible and would not negatively impact performance in Clean environments.

Impact of energy restriction during late gestation on the muscle and blood transcriptome of beef calves after preconditioning

Background

Maternal nutrition has been highlighted as one of the main factors affecting intra-uterine environment. The increase in nutritional requirements by beef cows during late gestation can cause nutritional deficiency in the fetus and impact the fetal regulation of genes associated with myogenesis and immune response.

Methods

Forty days before the expected calving date, cows were assigned to one of two diets: 100% (control) or 70% (restricted group) of the daily energy requirement. Muscle samples were collected from 12 heifers and 12 steers, and blood samples were collected from 12 steers. The objective of this work was to identify and to assess the biological relevance of differentially expressed genes (DEG) in the skeletal muscle and blood of beef calves born from cows that experienced [or not] a 30% energy restriction during the last 40 days of gestation.

Results

A total of 160, 164, and 346 DEG (q-value< 0.05) were identified in the skeletal muscle for the effects of diet, sex, and diet-by-sex interaction, respectively. For blood, 452, 1392, and 155 DEG were identified for the effects of diet, time, and diet-by-time interaction, respectively. For skeletal muscle, results based on diet identified genes involved in muscle metabolism. In muscle, from the 10 most DEG down-regulated in the energy-restricted group (REST), we identified 5 genes associated with muscle metabolism and development: SLCO3A1, ATP6V0D1, SLC2A1, GPC4, and RASD2. In blood, among the 10 most DEG, we found genes related to response to stress up-regulated in the REST after weaning, such as SOD3 and INO80D, and to immune response down-regulated in the REST after vaccination, such as OASL, KLRF1, and LOC104968634.

Conclusion

In conclusion, maternal energy restriction during late gestation may limit the expression of genes in the muscle and increase expression in the blood of calves. In addition, enrichment analysis showed that a short-term maternal energy restriction during pregnancy affects the expression of genes related to energy metabolism and muscle contraction, and immunity and stress response in the blood. Therefore, alterations in the intra-uterine environment can modify prenatal development with lasting consequences to adult life.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5089-8) contains supplementary material, which is available to authorized users.

Chromium, CLA, and ractopamine for finishing pigs

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 ( < 0.001) final BW and ADG. Pigs fed CrY + RAC had greater ( < 0.001) G:F than pigs within the other groups, except for those fed RAC. Pigs fed CrY + RAC and RAC had similar G:F, both greater ( < 0.001) than pigs fed CON. Average daily feed intake was similar ( = 0.83) for all diets. Pigs fed CrY + RAC had greater LM area ( = 0.01) and carcass yield ( < 0.02) than pigs fed CON, CrY, CLA, and CrY + CLA. Loin muscle area and carcass yield of pigs fed RAC were not different from pigs fed the others diets. Pigs fed CON diets had greater BF ( = 0.02) than pigs fed CLA diet. Additives did not affect ( > 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.

Effect of lower-energy, higher-fiber diets on pigs divergently selected for residual feed intake when fed higher-energy, lower-fiber diets

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) ADFI (-12%), energy intake (-12%), ADG (-6%), and backfat depth (-12%); similar (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.

Genomic prediction of piglet response to infection with one of two porcine reproductive and respiratory syndrome virus isolates

Background

Genomic prediction of the pig’s response to the porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV) would be a useful tool in the swine industry. This study investigated the accuracy of genomic prediction based on porcine SNP60 Beadchip data using training and validation datasets from populations with different genetic backgrounds that were challenged with different PRRSV isolates.

Results

Genomic prediction accuracy averaged 0.34 for viral load (VL) and 0.23 for weight gain (WG) following experimental PRRSV challenge, which demonstrates that genomic selection could be used to improve response to PRRSV infection. Training on WG data during infection with a less virulent PRRSV, KS06, resulted in poor accuracy of prediction for WG during infection with a more virulent PRRSV, NVSL. Inclusion of single nucleotide polymorphisms (SNPs) that are in linkage disequilibrium with a major quantitative trait locus (QTL) on chromosome 4 was vital for accurate prediction of VL. Overall, SNPs that were significantly associated with either trait in single SNP genome-wide association analysis were unable to predict the phenotypes with an accuracy as high as that obtained by using all genotyped SNPs across the genome. Inclusion of data from close relatives into the training population increased whole genome prediction accuracy by 33% for VL and by 37% for WG but did not affect the accuracy of prediction when using only SNPs in the major QTL region.

Conclusions

Results show that genomic prediction of response to PRRSV infection is moderately accurate and, when using all SNPs on the porcine SNP60 Beadchip, is not very sensitive to differences in virulence of the PRRSV in training and validation populations. Including close relatives in the training population increased prediction accuracy when using the whole genome or SNPs other than those near a major QTL.

Genomic regions associated with host response to porcine reproductive and respiratory syndrome vaccination and co-infection in nursery pigs

BACKGROUND

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.

METHODS

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.

RESULTS

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.

CONCLUSIONS

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.

Effect of a major quantitative trait locus for porcine reproductive and respiratory syndrome (PRRS) resistance on response to coinfection with PRRS virus and porcine circovirus type 2b (PCV2b) in commercial pigs, with or without prior vaccination for PRRS

A major QTL for host response to porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV) infection was identified in a previous study. Single nucleotide polymorphism WUR10000125 (WUR), which is in complete linkage disequilibrium with the putative causative mutation, can be used as a tag SNP for the QTL. However, the effect of WUR following PRRS vaccination and/or coinfection with other pathogens is not known. Therefore, objectives of this study were to estimate the effect of WUR on host response following PRRS vaccination and coinfection of PRRSV with porcine circovirus type 2b (PCV2b), to estimate genetic parameters for host response to vaccination and coinfection, and to estimate the effect of previously identified candidate SNP under PRRSV-only or PCV2b-only infection on host response to coinfection. Data from 2 trials, comprising a total of 396 commercial crossbred nursery pigs from a single genetic source, were used for all analyses. Pigs were preselected based on WUR genotype: approximately half AA and half AB, where B is the favorable and dominant allele. At weaning, pigs were shipped to Kansas State University, where half of the pigs were vaccinated with a PRRS modified live virus vaccine. Four weeks later, all pigs were coinfected with field strains of PRRSV and PCV2b and followed for 42 d. Body weight and serum viremia measurements were collected following vaccination and coinfection to calculate ADG and viral load (VL), respectively. Average heritability estimates for PRRS VL, PCV2b VL, and ADG were 0.29, 0.09, and 0.40, respectively. After vaccination, AB pigs had lower vaccination VL ( = 0.03) and faster gain ( = 0.004) than AA pigs, as expected. After coinfection, AB pigs had lower PRRSV VL ( < 0.001) but did not significantly differ from AA pigs in growth rate ( = 0.86). For PCV2b VL, suggestive evidence of an interaction between vaccination and WUR genotype ( = 0.11) was detected, where AB pigs had significantly lower PCV2b VL when vaccinated ( = 0.007) but not when they were not vaccinated ( = 0.87). In addition to WUR, several PRRS-associated SNP and a PCV2b-associated SNP had significant effects on host response to coinfection. In conclusion, marker-assisted selection based on WUR genotype alone, or along with other candidate SNP for PRRSV and PCV2b infection, is a promising strategy to select for improved host response to not just PRRS but also coinfection of PRRSV with PCV2b and perhaps other pathogens.

Regularized quantile regression for SNP marker estimation of pig growth curves

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.

Effects of distillers' dried grains with solubles and soybean oil on dietary lipid, fiber, and amino acid digestibility in corn-based diets fed to growing pigs

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.

Genomewide association of piglet responses to infection with one of two porcine reproductive and respiratory syndrome virus isolates

Porcine reproductive and respiratory syndrome (PRRS) is a devastating disease in the swine industry. Identification of host genetic factors that enable selection for improved performance during PRRS virus (PRRSV) infection would reduce the impact of this disease on animal welfare and production efficiency. We conducted genomewide association study (GWAS) analyses of data from 13 trials of approximately 200 commercial crossbred nursery-age piglets that were experimentally infected with 1 of 2 type 2 isolates of PRRSV (NVSL 97-7985 [NVSL] and KS2006-72109 [KS06]). Phenotypes analyzed were viral load (VL) in blood during the first 21 d after infection (dpi) and weight gain (WG) from 0 to 42 dpi. We accounted for the previously identified QTL in the region on SSC4 in our models to increase power to identify additional regions. Many regions identified by single-SNP analyses were not identified using Bayes-B, but both analyses identified the same regions on SSC3 and SSC5 to be associated with VL in the KS06 trials and on SSC6 in the NVSL trials ( < 5 × 10); for WG, regions on SSC5 and SSC17 were associated in the NVSL trials ( < 3 × 10). No regions were identified with either method for WG in the KS06 trials. Except for the region on SSC4, which was associated with VL for both isolates (but only with WG for NVSL), identified regions did not overlap between the 2 PRRSV isolate data sets, despite high estimates of the genetic correlation between isolates for traits based on these data. We also identified genomic regions whose associations with VL or WG interacted with either PRRSV isolate or with genotype at the SSC4 QTL. Gene ontology (GO) annotation terms for genes located near moderately associated SNP ( < 0.003) were enriched for multiple immunologically (VL) and metabolism- (WG) related GO terms. The biological relevance of these regions suggests that, although it may increase the number of false positives, the use of single-SNP analyses and a relaxed threshold also increased the identification of true positives. In conclusion, although only the SSC4 QTL was associated with response to both PRRSV isolates, genes near associated SNP were enriched for the same GO terms across PRRSV isolates, suggesting that host responses to these 2 isolates are affected by the actions of many genes that function together in similar biological processes.

Genetic and genomic basis of antibody response to porcine reproductive and respiratory syndrome (PRRS) in gilts and sows

Background

Our recent research showed that antibody response to porcine reproductive and respiratory syndrome (PRRS), measured as sample-to-positive (S/P) ratio, is highly heritable and has a high genetic correlation with reproductive performance during a PRRS outbreak. Two major quantitative trait loci (QTL) on Sus scrofa chromosome 7 (SSC7; QTL_MHC and QTL₁₃₀) accounted for ~40 % of the genetic variance for S/P. Objectives of this study were to estimate genetic parameters for PRRS S/P in gilts during acclimation, identify regions associated with S/P, and evaluate the accuracy of genomic prediction of S/P across populations with different prevalences of PRRS and using different single nucleotide polymorphism (SNP) sets.

Methods

Phenotypes and high-density SNP genotypes of female pigs from two datasets were used. The outbreak dataset included 607 animals from one multiplier herd, whereas the gilt acclimation (GA) dataset included data on 2364 replacement gilts from seven breeding companies placed on health-challenged farms. Genomic prediction was evaluated using GA for training and validation, and using GA for training and outbreak for validation. Predictions were based on SNPs across the genome (SNP_All), SNPs in one (SNP_MHC and SNP₁₃₀) or both (SNP_SSC7) QTL, or SNPs outside the QTL (SNP_Rest).

Results

Heritability of S/P in the GA dataset increased with the proportion of PRRS-positive animals in the herd (from 0.28 to 0.47). Genomic prediction accuracies ranged from low to moderate. Average accuracies were highest when using only the 269 SNPs in both QTL regions (SNP_SSC7, with accuracies of 0.39 and 0.31 for outbreak and GA validation datasets, respectively. Average accuracies for SNP_ALL, SNP_MHC, SNP₁₃₀, and SNP_Rest were, respectively, 0.26, 0.39, 0.21, and 0.05 for the outbreak, and 0.28, 0.25, 0.22, and 0.12, for the GA validation datasets.

Conclusions

Moderate genomic prediction accuracies can be obtained for PRRS antibody response using SNPs located within two major QTL on SSC7, while the rest of the genome showed limited predictive ability. Results were obtained using data from multiple genetic sources and farms, which further strengthens these findings. Further research is needed to validate the use of S/P ratio as an indicator trait for reproductive performance during PRRS outbreaks.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-016-0230-0) contains supplementary material, which is available to authorized users.

Molecular Factors Underlying the Deposition of Intramuscular Fat and Collagen in Skeletal Muscle of Nellore and Angus Cattle

Studies have shown that intramuscular adipogenesis and fibrogenesis may concomitantly occur in skeletal muscle of beef cattle. Thus, we hypothesized that the discrepancy of intramuscular fat content in beef from Nellore and Angus was associated with differences in intramuscular adipogenesis and fibrogenesis during the finishing phase. To test our hypothesis, longissimus muscle samples of Nellore (n = 6; BW = 372.5 ± 37.3 kg) and Angus (n = 6; BW = 382.8 ± 23.9 kg) cattle were collected for analysis of gene and protein expression, and quantification of intramuscular fat and collagen. Least-squares means were estimated for the effect of Breed and differences were considered at P ≤ 0.05. A greater intramuscular fat content was observed in skeletal muscle of Angus compared to Nellore cattle (P≤0.05). No differences were observed for mRNA expression of lipogenic and lipolytic markers ACC, FAS, FABP4, SERBP–1, CPT–2, LPL, and ACOX (P > 0.05) in skeletal muscle of Nellore and Angus cattle. Similarly, no differences were observed in mRNA expression of adipogenic markers Zfp423, PPARγ, and C/EBPα (P>0.05) However, a greater PPARγ protein content was observed in skeletal muscle of Angus compared to Nellore cattle (P≤0.05). A greater abundance of adipo/fibrogenic cells, evaluated by the PDGFRα content, was observed in skeletal muscle of Angus than Nellore cattle (P≤0.05). No differences in fibrogenesis were observed in skeletal muscle of Angus and Nellore cattle, which is in accordance with the lack of differences in intramuscular collagen content in beef from both breeds (P>0.05). These findings demonstrate that difference in intramuscular fat content is associated with a slightly enhanced adipogenesis in skeletal muscle of Angus compared to Nellore cattle, while no difference in fibrogenesis.

Not All SCID Pigs Are Created Equally: Two Independent Mutations in the Artemis Gene Cause SCID in Pigs

Mutations in >30 genes are known to result in impairment of the adaptive immune system, causing a group of disorders collectively known as SCID. SCID disorders are split into groups based on their presence and/or functionality of B, T, and NK cells. Piglets from a line of Yorkshire pigs at Iowa State University were shown to be affected by T(-)B(-)NK(+) SCID, representing, to our knowledge, the first example of naturally occurring SCID in pigs. In this study, we present evidence for two spontaneous mutations as the molecular basis for this SCID phenotype. Flow cytometry analysis of thymocytes showed an increased frequency of immature T cells in SCID pigs. Fibroblasts from these pigs were more sensitive to ionizing radiation than non-SCID piglets, eliminating the RAG1 and RAG2 genes. Genetic and molecular analyses showed that two mutations were present in the Artemis gene, which in the homozygous or compound heterozygous state cause the immunodeficient phenotype. Rescue of SCID fibroblast radiosensitivity by human Artemis protein demonstrated that the identified Artemis mutations are the direct cause of this cellular phenotype. The work presented in the present study reveals two mutations in the Artemis gene that cause T(-)B(-)NK(+) SCID in pigs. The SCID pig can be an important biomedical model, but these mutations would be undesirable in commercial pig populations. The identified mutations and associated genetic tests can be used to address both of these issues.

Identification of a putative quantitative trait nucleotide in guanylate binding protein 5 for host response to PRRS virus infection

Background

Previously, we identified a major quantitative trait locus (QTL) for host response to Porcine Respiratory and Reproductive Syndrome virus (PRRSV) infection in high linkage disequilibrium (LD) with SNP rs80800372 on Sus scrofa chromosome 4 (SSC4).

Results

Within this QTL, guanylate binding protein 5 (GBP5) was differentially expressed (DE) (p < 0.05) in blood from AA versus AB rs80800372 genotyped pigs at 7,11, and 14 days post PRRSV infection. All variants within the GBP5 transcript in LD with rs80800372 exhibited allele specific expression (ASE) in AB individuals (p < 0.0001). A transcript re-assembly revealed three alternatively spliced transcripts for GBP5. An intronic SNP in GBP5, rs340943904, introduces a splice acceptor site that inserts five nucleotides into the transcript. Individuals homozygous for the unfavorable AA genotype predominantly produced this transcript, with a shifted reading frame and early stop codon that truncates the 88 C-terminal amino acids of the protein. RNA-seq analysis confirmed this SNP was associated with differential splicing by QTL genotype (p < 0.0001) and this was validated by quantitative capillary electrophoresis (p < 0.0001). The wild-type transcript was expressed at a higher level in AB versus AA individuals, whereas the five-nucleotide insertion transcript was the dominant form in AA individuals. Splicing and ASE results are consistent with the observed dominant nature of the favorable QTL allele. The rs340943904 SNP was also 100 % concordant with rs80800372 in a validation population that possessed an alternate form of the favorable B QTL haplotype.

Conclusions

GBP5 is known to play a role in inflammasome assembly during immune response. However, the role of GBP5 host genetic variation in viral immunity is novel. These findings demonstrate that rs340943904 is a strong candidate causal mutation for the SSC4 QTL that controls variation in host response to PRRSV.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1635-9) contains supplementary material, which is available to authorized users.

Quantitative relationships between standardized total tract digestible phosphorus and total calcium intakes and their retention and excretion in growing pigs fed corn-soybean meal diets

An experiment was conducted to determine the quantitative relationships between standardized total tract digestible P (STTD P) and total Ca intakes with their retention and excretion by growing pigs fed corn-soybean meal diets. Forty-eight crossbred barrows (BW = 22.7 ± 2.9 kg) were allotted to 1 of 8 diets, housed individually in pens for 3 wk, and then moved to metabolism crates and allowed 4 d for adaptation and 5 d for collection of urine and fecal samples. Eight corn-soybean meal diets were formulated for similar NE, fat, and AA concentrations but to increase the STTD P from 0.16 to 0.62% using monocalcium phosphate. Dietary treatments were formulated for a constant Ca:STTD P ratio (2.2:1). The STTD P intake increased (P < 0.001) from 64 to 242% of the daily requirement (4.59 g/d of STTD P). Fecal and total excretion of P and Ca were linearly associated with mineral intake (P < 0.001). Constant urinary P excretion of 0.03 g/d P was observed, but at 4.96 g/d of STTD P intake, the urinary P excretion increased (P < 0.001). In contrast, Ca excretion in urine decreased (P < 0.001) with Ca intake, but constant excretion of 0.40 g/d Ca was reached at 17.97 g/d of Ca intake. The daily intakes of STTD P and Ca moderately explained the variation in urinary excretion of P (R2= 0.41) and Ca (R2= 0.64). The absorption and retention of P increased linearly (P< 0.001) with dietary P intake, whereas absorption and retention of Ca showed a quadratic response (P < 0.001). Absorption and retention of P and Ca were highly predictable from the STTD P and Ca intakes, with of 0.87 and 0.90, respectively. The femur mineral content (FMC) increased by 2.71 g with STTD P intake (P < 0.001) but reached a plateau (29.54 g of FMC) at 8.84 g/d of STTD P intake. The FMC was highly predictable from the STTD P intake (R2 = 0.89). The FMC affected the urinary P excretion ( P< 0.01), but moderately (R2= 0.19) explained the variation in urinary P. In conclusion, constant excretion of P in urine was observed but excretion increased linearly at STTD P intake levels above the requirement for maximum growth of growing pigs. The FMC increased with STTD P intake, but a plateau was reached at a STTD P intake level above the requirement. Dietary STTD P was used for growth and accumulated in bones until a plateau was reached and excess was excreted in urine. The predictability of P and Ca excretion in urine from the dietary STTD P and Ca intakes was moderate.

Relationships among dietary fiber components and the digestibility of energy, dietary fiber, and amino acids and energy content of nine corn coproducts fed to growing pigs

An experiment was conducted to determine a best fitting dietary fiber (DF) component to estimate the effect of DF concentration on the digestibility of energy, DF, and AA and energy value of 9 corn coproducts: corn bran (37.0% total nonstarch polysaccharides [NSP]); corn bran with solubles (17.1% NSP); cooked corn distillers dried grains with solubles (DDGS; 20.4% NSP); reduced oil DDGS (25.0% NSP); uncooked DDGS (22.0% NSP); high protein distillers dried grains (21.9% NSP); dehulled, degermed corn (1.1% NSP); corn germ meal (44.4% NSP); and corn gluten meal (4.9% NSP). A total of 20 growing pigs (initial BW: 25.9 ± 2.5 kg) were fitted with a T-cannula in the distal ileum and allotted to 10 dietary treatment groups in a 4-period incomplete block design with 8 observations per treatment. Treatments included a corn-soybean meal-based basal diet and 9 diets obtained by mixing 70% of the basal diet with 30% of the test ingredient. In tested ingredients, 11 DF components were determined: 1) ADF, 2) NDF, 3) total dietary fiber, 4) hemicellulose, 5) total NSP, 6) NSP arabinose, 7) NSP xylose, 8) NSP mannose, 9) NSP glucose, 10) NSP galactose, and 11) arabinoxylan. The apparent ileal digestibility (AID) and apparent total tract digestibility (ATTD) of GE, DM, and NDF and the AID of AA of ingredients were measured. A single best fitting DF component was assessed and ranked for each trait, showing that arabinoxylan concentration best explained variance in AID of GE (R(2) = 0.65; cubic, P < 0.01) and DM (R(2) = 0.67; cubic, P < 0.01). The NSP xylose residue best explained variance in ATTD of GE (R(2) = 0.80; cubic, P < 0.01), DM (R(2) = 0.78; cubic, P < 0.01), and NDF (R(2) = 0.63; cubic, P < 0.01); AID of Met (R(2) = 0.40; cubic, P = 0.02), Met + Cys (R(2) = 0.44; cubic, P = 0.04), and Trp (R(2) = 0.11; cubic, P = 0.04); and DE (R(2) = 0.66; linear, P = 0.02) and ME (R(2) = 0.71; cubic, P = 0.01) values. The AID of Lys was not predictable (P > 0.05) from the DF concentration. In conclusion, the arabinoxylan and NSP xylose residue were the DF components that best explained variation due to DF concentration and, with the exception of AID of Lys, can be used to predict the digestibility of energy and DF and the DE and ME values in corn coproducts.

Genetic analysis of reproductive traits and antibody response in a PRRS outbreak herd

Porcine reproductive and respiratory syndrome (PRRS) is the most economically significant disease impacting pig production in North America, Europe, and Asia, causing reproductive losses such as increased rates of stillbirth and mummified piglets. The objective of this study was to explore the genetic basis of host response to the PRRS virus (PRRSV) in a commercial multiplier sow herd before and after a PRRS outbreak, using antibody response and reproductive traits. Reproductive data comprising number born alive (NBA), number alive at 24 h (NA24), number stillborn (NSB), number born mummified (NBM), proportion born dead (PBD), number born dead (NBD), number weaned (NW), and number of mortalities through weaning (MW) of 5,227 litters from 1,967 purebred Landrace sows were used along with a pedigree comprising 2,995 pigs. The PRRS outbreak date was estimated from rolling averages of farrowing traits and was used to split the data into a pre-PRRS phase and a PRRS phase. All 641 sows in the herd during the outbreak were blood sampled 46 d after the estimated outbreak date and were tested for anti-PRRSV IgG using ELISA (sample-to-positive [S/P] ratio). Genetic parameters of traits were estimated separately for the pre-PRRS and PRRS phase data sets. Sows were genotyped using the PorcineSNP60 BeadChip, and genome-wide association studies (GWAS) were performed using method Bayes B. Heritability estimates for reproductive traits ranged from 0.01 (NBM) to 0.12 (NSB) and from 0.01 (MW) to 0.12 (NBD) for the pre-PRRS and PRRS phases, respectively. S/P ratio had heritability (0.45) and strong genetic correlations with most traits, ranging from -0.72 (NBM) to 0.73 (NBA). In the pre-PRRS phase, regions associated with NSB and PBD explained 1.6% and 3% of the genetic variance, respectively. In the PRRS phase, regions associated with NBD, NSB, and S/P ratio explained 0.8%, 11%, and 50.6% of the genetic variance, respectively. For S/P ratio, 2 regions on SSC 7 (SSC7) separated by 100 Mb explained 40% of the genetic variation, including a region encompassing the major histocompatibility complex, which explained 25% of the genetic variance. These results indicate a significant genomic component associated with PRRSV antibody response and NSB in this data set. Also, the high heritability and genetic correlation estimates for S/P ratio during the PRRS phase suggest that S/P ratio could be used as an indicator of the impact of PRRS on reproductive traits.

Effects of pregnancy and feeding level on carcass and meat quality traits of Nellore cows

Carcass and meat quality traits of 16 pregnant and 5 non-pregnant cows fed at 1.2 times maintenance and 16 pregnant and 6 non-pregnant fed ad libitum were evaluated. Pregnancy did not affect final body weight (FBW; P=0.0923), cold carcass yield (CCY; P=0.0513), longissimus muscle area (LMA; P=0.8260), rib fat thickness (RFT; P=0.1873) and shear force (WBSF; P=0.9707). A lower FBW (P=0.0028), LMA (P=0.0048) and RFT (P=0.0001) were observed in feed restricted cows. However, no differences were found for CCY (P=0.7243) and WBSF (P=0.0759) among feeding level groups. These data suggests that carcass and meat quality traits are not affected by pregnancy status in Nellore cows. Moreover, although cows experiencing feed restriction did have reduced deposition of subcutaneous fat and lean tissue, there were no major impacts on meat quality traits.

Candidate gene expression and intramuscular fat content in pigs

Seventy-two pigs of three genetic groups (Brazilian indigenous breed Piau, Commercial line and Crossbred) of both sexes were slaughtered at four live weights (30, 60, 90 and 120 kg). Intramuscular fat (IMF) content in Longissimus dorsi muscle of each animal was extracted and correlated with candidate gene mRNA expression (ATN1, EEF1A2, FABP3, LDLR, MGP, OBSCN, PDHB, TRDN and RYR1). Within slaughter weight of 120 kg, Piau and Crossbred pigs showed higher IMF content (p < 0.05) than commercial animals, with 2.48, 2.08 and 1.00% respectively. Barrows presented higher values of IMF (p < 0.05) than gilts (1.54 and 1.30% respectively). Gene expression of EEF1A2, FABP3, LDLR, OBSCN, PDHB, TRDN and RYR1 were correlated with IMF (p < 0.05) using the whole dataset. For Piau data only, expression of FABP3, LDLR, MGP, OBSCN, PDHB, TRDN and RYR1 showed correlation with IMF (p < 0.05). Genes that have important roles in lipid transportation inside the cell (FABP3) and tissues (LDLR) showed correlation with IMF of, respectively, 0.68 and 0.63 using the whole data set, and 0.90 and 0.91 using data from Piau animals. The highly positive correlation of the LDLR and FAPB3 expression with IMF content may confirm that these genes are important for fat deposition in the porcine L. dorsi muscle.