Publications by authors named "Nick V L Serão"

26 Publications

  • Page 1 of 1

Genomics of response to PRRSV in purebred and crossbred sows: antibody response and performance following natural infection versus vaccination.

J Anim Sci 2021 Mar 30. Epub 2021 Mar 30.

Department of Animal Science, Iowa State University, Ames - IA, USA.

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 approximately 54 days after the start of a PRRSV outbreak, and on 906 F1 (Landrace x Large White) gilts approximately 50 days 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.
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http://dx.doi.org/10.1093/jas/skab097DOI Listing
March 2021

Assessing the Statistical Training in Animal Science Graduate Programs in the US: Survey on Statistical Training.

J Anim Sci 2021 Mar 19. Epub 2021 Mar 19.

Department of Animal Science, Iowa State University, Ames, IA, United States of America.

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 US ASGS. A survey with 38 questions was shared across US 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 overall scores 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, indicate substantial correlations in ASGS answers between PRE and PK. The cluster analysis resulted in distinct groups of "Traditional" and "Non-Traditional" statistical topics. ASGS showed lower (P < 0.05) scores of PRE, PK, and CPSA in "Non-Traditional" compared with "Traditional" statistical methods. Several factors were associated (P < 0.05) with the overall scores of PRE, PK, and CSPA. In general, factors related to greater training and interest in statistics of ASGS were associated with greater overall scores, 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 US. 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.
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http://dx.doi.org/10.1093/jas/skab086DOI Listing
March 2021

Gut microbiome associations with outcome following co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) in pigs immunized with a PRRS modified live virus vaccine.

Vet Microbiol 2021 Mar 16;254:109018. Epub 2021 Feb 16.

Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, Kansas 66506, United States. Electronic address:

Porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) are two of the most significant pathogens affecting swine. Co-infections are common and result in respiratory disease and reduced weight gain in growing pigs. Although PRRS modified live virus (MLV) vaccines are widely used to decrease PRRS-associated losses, they are generally considered inadequate for disease control. The gut microbiome provides an alternative strategy to enhance vaccine efficacy and improve PRRS control. The objective of this study was to identify gut microbiome characteristics associated with improved outcome in pigs immunized with a PRRS MLV and co-challenged with PRRSV and PCV2b. Twenty-eight days after vaccination and prior to co-challenge, fecal samples were collected from an experimental population of 50 nursery pigs. At 42 days post-challenge, 20 pigs were retrospectively identified as having high or low growth outcomes during the post-challenge period. Gut microbiomes of the two outcome groups were compared using the Lawrence Livermore Microbial Detection Array (LLMDA) and 16S rDNA sequencing. High growth outcomes were associated with several gut microbiome characteristics, such as increased bacterial diversity, increased Bacteroides pectinophilus, decreased Mycoplasmataceae species diversity, higher Firmicutes:Bacteroidetes ratios, increased relative abundance of the phylum Spirochaetes, reduced relative abundance of the family Lachnospiraceae, and increased Lachnospiraceae species C6A11 and P6B14. Overall, this study identifies gut microbiomes associated with improved outcomes in PRRS vaccinated pigs following a polymicrobial respiratory challenge and provides evidence towards the gut microbiome playing a role in PRRS vaccine efficacy.
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http://dx.doi.org/10.1016/j.vetmic.2021.109018DOI Listing
March 2021

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

J Anim Sci Biotechnol 2021 Jan 12;12(1). Epub 2021 Jan 12.

Department of Animal Science, Iowa State University, Ames, IA, 50011, USA.

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 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 and VSC. 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.
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http://dx.doi.org/10.1186/s40104-020-00527-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7805112PMC
January 2021

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

Front Microbiol 2020 8;11:564160. Epub 2020 Dec 8.

Department of Animal Science, Iowa State University, Ames, IA, United States.

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 ( = 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 ( < 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.
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http://dx.doi.org/10.3389/fmicb.2020.564160DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7752866PMC
December 2020

Evaluation of Resistance to Fescue Toxicosis in Purebred Angus Cattle Utilizing Animal Performance and Cytokine Response.

Toxins (Basel) 2020 12 14;12(12). Epub 2020 Dec 14.

Department of Animal Science, North Carolina State University, Raleigh, NC 27695, USA.

Fescue toxicosis is a multifaceted syndrome common in cattle grazing endophyte-infected tall fescue; however, varying symptomatic responses potentially imply genetic tolerance to the syndrome. It was hypothesized that a subpopulation of animals within a herd would develop tolerance to ergot alkaloid toxicity. Therefore, the goals of this study were to develop selection criteria to identify tolerant and susceptible animals within a herd based on animal performance, and then examine responsive phenotypic and cytokine profiles to fescue toxicosis. Angus cows grazed endophyte-infected tall fescue at two locations for 13 weeks starting in mid-April 2016. Forage measurements were collected to evaluate ergot alkaloid exposure during the study. A post hoc analysis of animal performance was utilized to designate cattle into either tolerant or susceptible groups, and weekly physiological measurements and blood samples were collected to evaluate responses to chronic exposure to endophyte-infected tall fescue. Findings from this study support the proposed fescue toxicosis selection method formulated herein, could accurately distinguish between tolerant and susceptible animals based on the performance parameters in cattle chronically exposed to ergot alkaloids, and provides evidence to warrant additional analysis to examine the impact of ergot alkaloids on immune responsiveness in cattle experiencing fescue toxicosis.
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http://dx.doi.org/10.3390/toxins12120796DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7764894PMC
December 2020

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

Transl Anim Sci 2020 Oct 1;4(4):txaa181. Epub 2020 Oct 1.

Department of Animal Science, North Carolina State University, Raleigh, NC.

Most tall fescue [ (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 ( = 0.15; interaction with location), change in body condition score (aBCSd; = 0.13), and adjWW ( = 0.06; interaction with location). For aBWd and adjWW, associations were found just within one location ( = 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 ( > 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.
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http://dx.doi.org/10.1093/tas/txaa181DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7724970PMC
October 2020

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

Front Genet 2020 23;11:593804. Epub 2020 Oct 23.

Department of Animal Science, Iowa State University, Ames, IA, United States.

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), (MH), porcine circovirus (PCV2), and (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 ) of Ab response to IAV with MH, PCV2, PRRSV, and APP (average Ab responses for all serotypes of APP) were positive (>0.29) at entry. APP 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.
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http://dx.doi.org/10.3389/fgene.2020.593804DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7646516PMC
October 2020

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

Front Genet 2020 11;11:1011. Epub 2020 Sep 11.

Department of Animal Science, Iowa State University, Ames, IA, United States.

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 () 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 ( = 0.06), and lower MUM P3 and NSB P3 ( = 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.
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http://dx.doi.org/10.3389/fgene.2020.01011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7516203PMC
September 2020

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

PLoS One 2020 23;15(7):e0229192. Epub 2020 Jul 23.

Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States of America.

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.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0229192PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7377488PMC
September 2020

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

BMC Genet 2020 03 12;21(1):28. Epub 2020 Mar 12.

Department of Animal Science, Iowa State University, IA50010, Ames, USA.

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.
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http://dx.doi.org/10.1186/s12863-020-0834-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7068987PMC
March 2020

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

Front Genet 2019 17;10:1197. Epub 2019 Dec 17.

Department of Animal Science, College of Agriculture and Life Sciences, Iowa State University, Ames, IA, United States.

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.
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http://dx.doi.org/10.3389/fgene.2019.01197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6934059PMC
December 2019

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

J Anim Breed Genet 2020 Jan 25;137(1):84-102. Epub 2019 Nov 25.

Department of Animal Science, Iowa State University, Ames, Iowa.

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.
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http://dx.doi.org/10.1111/jbg.12456DOI Listing
January 2020

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.

Anim Reprod Sci 2019 Jul 11;206:46-59. Epub 2019 May 11.

Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil. Electronic address:

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.
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http://dx.doi.org/10.1016/j.anireprosci.2019.05.006DOI Listing
July 2019

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

J Anim Sci Biotechnol 2019 1;10:22. Epub 2019 Mar 1.

1Department of Animal Science, Iowa State University, Ames, IA 50011 USA.

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 ( < 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.
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http://dx.doi.org/10.1186/s40104-019-0330-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6396479PMC
March 2019

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

J Anim Sci 2019 Mar;97(3):1101-1116

Department of Animal Science, Iowa State University, Ames, IA.

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.
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http://dx.doi.org/10.1093/jas/sky485DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6396237PMC
March 2019

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

J Anim Sci 2019 Jan;97(1):327-337

Department of Animal Science, Iowa State University, Ames, IA.

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.
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http://dx.doi.org/10.1093/jas/sky402DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6313144PMC
January 2019

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

BMC Genomics 2018 Sep 25;19(1):702. Epub 2018 Sep 25.

Department of Animal Science, Iowa State University, Ames, 50011, USA.

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.
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http://dx.doi.org/10.1186/s12864-018-5089-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6156876PMC
September 2018

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

Genet Sel Evol 2018 02 1;50(1). Epub 2018 Feb 1.

Department of Animal Science, Iowa State University, Ames, IA, USA.

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.
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http://dx.doi.org/10.1186/s12711-018-0371-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5801659PMC
February 2018

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

BMC Genomics 2017 Nov 13;18(1):865. Epub 2017 Nov 13.

Department of Animal Science, Iowa State University, Ames, IA, 50011, USA.

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 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 P = 5.6) and Post Co-X (-log P = 5.5). No SNPs were significantly associated with vaccination VL (-log P ≤ 4.7) or PRRS VL (-log 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.
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http://dx.doi.org/10.1186/s12864-017-4182-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5682865PMC
November 2017

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

Genet Sel Evol 2016 07 14;48(1):51. Epub 2016 Jul 14.

Department of Animal Science, Iowa State University, Ames, IA, 50011, USA.

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; QTLMHC 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 (SNPAll), SNPs in one (SNPMHC and SNP130) or both (SNPSSC7) QTL, or SNPs outside the QTL (SNPRest).

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 (SNPSSC7, with accuracies of 0.39 and 0.31 for outbreak and GA validation datasets, respectively. Average accuracies for SNPALL, SNPMHC, SNP130, and SNPRest 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.
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http://dx.doi.org/10.1186/s12711-016-0230-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4944421PMC
July 2016

Vaccination with a Porcine Reproductive and Respiratory Syndrome (PRRS) Modified Live Virus Vaccine Followed by Challenge with PRRS Virus and Porcine Circovirus Type 2 (PCV2) Protects against PRRS but Enhances PCV2 Replication and Pathogenesis Compared to Results for Nonvaccinated Cochallenged Controls.

Clin Vaccine Immunol 2015 Dec 7;22(12):1244-54. Epub 2015 Oct 7.

Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA.

Coinfections involving porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) contribute to a group of disease syndromes known as porcine circovirus-associated disease (PCVAD). Presumably, PRRSV infection enhances PCV2 replication as a result of modulation of host immunity. The purpose of this study was to evaluate PCV2 replication and pathogenesis in pigs vaccinated with a PRRS modified live virus (MLV) vaccine and subsequently challenged with a combination of PRRSV and PCV2. During the early postchallenge period, the number of pigs with PRRSV-associated clinical signs was decreased, and average daily gain (ADG) was increased, in the vaccinated group, demonstrating the protective effect of PRRS vaccination. However, during the later postchallenge period, more pigs in the vaccinated group showed increased PCV2 viremia, decreased ADG, increased PCVAD clinical signs, and increased mortality. In this disease model, the early benefits of PRRSV vaccination were outweighed by the later amplification of PCVAD.
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http://dx.doi.org/10.1128/CVI.00434-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4658591PMC
December 2015

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

PLoS One 2015 5;10(10):e0139943. Epub 2015 Oct 5.

Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil; Animal Biotechnology Laboratory-LABTEC, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.

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.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0139943PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4593631PMC
June 2016

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

J Immunol 2015 Oct 28;195(7):3171-9. Epub 2015 Aug 28.

Department of Animal Sciences, Iowa State University, Ames, IA 50011;

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.
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http://dx.doi.org/10.4049/jimmunol.1501132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5621739PMC
October 2015

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

BMC Genomics 2015 May 28;16:412. Epub 2015 May 28.

Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, 50011, USA.

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.
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http://dx.doi.org/10.1186/s12864-015-1635-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4446061PMC
May 2015

Bivariate genome-wide association analysis of the growth and intake components of feed efficiency.

PLoS One 2013 29;8(10):e78530. Epub 2013 Oct 29.

Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.

Single nucleotide polymorphisms (SNPs) associated with average daily gain (ADG) and dry matter intake (DMI), two major components of feed efficiency in cattle, were identified in a genome-wide association study (GWAS). Uni- and multi-SNP models were used to describe feed efficiency in a training data set and the results were confirmed in a validation data set. Results from the univariate and bivariate analyses of ADG and DMI, adjusted by the feedlot beef steer maintenance requirements, were compared. The bivariate uni-SNP analysis identified (P-value <0.0001) 11 SNPs, meanwhile the univariate analyses of ADG and DMI identified 8 and 9 SNPs, respectively. Among the six SNPs confirmed in the validation data set, five SNPs were mapped to KDELC2, PHOX2A, and TMEM40. Findings from the uni-SNP models were used to develop highly accurate predictive multi-SNP models in the training data set. Despite the substantially smaller size of the validation data set, the training multi-SNP models had slightly lower predictive ability when applied to the validation data set. Six Gene Ontology molecular functions related to ion transport activity were enriched (P-value <0.001) among the genes associated with the detected SNPs. The findings from this study demonstrate the complementary value of the uni- and multi-SNP models, and univariate and bivariate GWAS analyses. The identified SNPs can be used for genome-enabled improvement of feed efficiency in feedlot beef cattle, and can aid in the design of empirical studies to further confirm the associations.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0078530PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3812149PMC
August 2014