Genetic Parameters and Effect of WUR Genotype on Piglet Response to Co-Infection with PRRS and PCV2b, with or without Vaccination for PRRS

Commercial crossbred nursery piglets were either vaccinated or not using a modified live porcine reproductive and respiratory syndrome (PRRS) virus vaccine and all pigs were co-infected with PRRS virus (PRRSV) and porcine circovirus type 2b (PCV2b) 28 days later. Genetic correlations indicate that traits associated with primary exposure to PRRSV infection (PRRS viral load (VL) of vaccinated pigs prior to co-infection and PRRS VL of non-vaccinated pigs post co-infection) are genetically the same trait. The WUR single nucleotide polymorphism on chromosome 4, previously associated with reduced PRRS VL under PRRSV-only infection, was associated with significantly reduced PRRS VL following vaccination and co-infection (for non-vaccinated pigs), but also with reduced PCV2b VL of vaccinated pigs. These results indicate a significant effect of WUR genotype on PRRS VL upon primary PRRS exposure, whether in a PRRSV-only or PRRS and PCV2b co-infected population, but also with PCV2b VL of vaccinated pigs under PRRS and PCV2b co- infection

Effect of WUR Genotype and PRRS Vaccination on Pigs Co-Infected with PRRS and PCV2b

Average daily gain (ADG) and viral load (VL) were evaluated for pigs co-infected with porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV) and porcine circovirus type 2b (PCV2b). Pigs were pre-selected for WUR genotype (a marker on chromosome 4 associated with weight gain and VL under PRRSV-challenge), half were vaccinated for PRRS, and half were not. Results indicate that vaccination for PRRS resulted in slower growth prior to co-infection and that the AB WUR genotype was associated with faster growth prior to co-infection, lower PRRS VL, and lower PCV2b VL in vaccinated pigs

Genetic Analysis of Reproductive Traits and Antibody Response in PRRS Infected Sows

The genetic components of reproductive performance and antibody response of 641 commercial sows were assessed in a commercial herd that faced a PRRS outbreak. Antibody response after the PRRS outbreak was highly heritable and had high genetic correlations with reproductive traits. Many genomic regions were associated with antibody response in this study. These results indicate that there is a significant genomic component associated with PRRS antibody response and its high genetic correlations with reproductive traits during PRRS suggest that this trait could be used as an indicator trait to reduce the impact of PRRS on reproductive performance

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

Abstract 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

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

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

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

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.This article is published in Sanglard, Leticia P., Yijian Huang, Kent A. Gray, Daniel CL Linhares, Jack Dekkers, Megan C. Niederwerder, Rohan L. Fernando, and Nick VL Serão. "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." Genetics Selection Evolution 53, no. 1 (2021): 1-17. DOI: 10.1186/s12711-021-00676-5. Copyright 2021 The Author(s). Attribution 4.0 International (CC BY 4.0). Posted with permission

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

Abstract 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

Enriched¹ Gene Ontology molecular functions from SNPs detected by the bivariate uni-SNP analysis.

1<p>P-value <0.0001.</p