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Fredriksen S, Neila-Ibáñez C, Hennig-Pauka I, Guan X, Dunkelberger J, de Oliveira IF, Ferrando ML, Correa-Fiz F, Aragon V, Boekhorst J, van Baarlen P, Wells JM. Streptococcus suis infection on European farms is associated with an altered tonsil microbiome and resistome. Microb Genom 2024; 10. [PMID: 39699589 DOI: 10.1099/mgen.0.001334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2024] Open
Abstract
Streptococcus suis is a Gram-positive opportunistic pathogen causing systemic disease in piglets around weaning age. The factors predisposing to disease are not known. We hypothesized that the tonsillar microbiota might influence disease risk via colonization resistance and/or co-infections. We conducted a cross-sectional case-control study within outbreak farms complemented by selective longitudinal sampling and comparison with control farms without disease occurrence. We found a small but significant difference in tonsil microbiota composition between case and control piglets (n=45+45). Variants of putative commensal taxa, including Rothia nasimurium, were reduced in abundance in case piglets compared to asymptomatic controls. Case piglets had higher relative abundances of Fusobacterium gastrosuis, Bacteroides heparinolyticus and uncultured Prevotella and Alloprevotella species. Piglets developing disease post-weaning had reduced alpha diversity pre-weaning. Despite case-control pairs receiving equal antimicrobial treatment, case piglets had a higher abundance of antimicrobial resistance genes conferring resistance to antimicrobial classes used to treat S. suis. This might be an adaption of disease-associated strains to frequent antimicrobial treatment.
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Little EA, Dunkelberger J, Hanson D, Eggert J, Gonda MG, MacNeil MD, Dee S. Comparison of differences in performance between pigs whose sires were identified using different selection strategies after experimental infection with PRRSV. Transl Anim Sci 2024; 8:txae128. [PMID: 39296530 PMCID: PMC11408270 DOI: 10.1093/tas/txae128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 08/22/2024] [Indexed: 09/21/2024] Open
Abstract
The objective of this study was to evaluate differences in the performance of offspring of boars selected with an index emphasizing resilience and boars selected based on a traditional index, emphasizing feed efficiency and carcass quality (traditional) index vs. a customized (resilience) index. The resilience index was identical to the traditional index, except that extra emphasis was placed on piglet vitality (increased by 66%), growth rate (decreased by 14%), and feed intake (increased substantially by 5,157%). Sows were mated to either boars selected based on the resilience index or boars selected on the traditional index. Weaned offspring were vaccinated for Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and experimentally infected with PRRSV RFLP 1-7-4 four weeks later. Offspring were allocated to pens (n ~ 27 pigs/pen; n = 27 pens/group) by sire-selection group for a total of 1,458 pigs in 54 pens. The weight of each pen was recorded on 0, 42, and 110 d postinfection (DPI) and used to calculate average daily gain (ADG), average daily feed intake (ADFI), and feed conversion ratio (FCR). Mortalities were recorded from 0 to 110 DPI and necropsies were routinely performed to characterize pathogens present within the barn. Pigs classified as full value (i.e., >104 kg and void of defects) were slaughtered and hot carcass weight (HCW), backfat, loin depth, and lean weight were obtained from the slaughter plant. Effects of progeny group on performance, carcass characteristics, and mortality rate were estimated with a mixed linear model. Differences between progeny groups in ADG (P > 0.27), HCW (P = 0.68), backfat (P = 0.13), or loin depth (P = 0.39), and mortality rate (P = 0.29) were not detected. From 0 to 42 DPI, offspring of boars selected based on the resilience index had higher ADFI (0.06 kg/d, P = 0.01) and higher FCR (0.12, P = 0.01). In summary, results from this study do not support selection of boars for increased feed intake, piglet viability, and robustness in order to prevent losses caused by PRRSV, but selection response was only measured after one generation of male selection. The impact of multiple generations of selection, or the development of an index including traits derived from data collected under disease-challenged conditions should be explored. The data collected for this study are a valuable resource to explore additional genetic selection strategies for enhanced resilience to a multifactorial PRRS challenge.
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Bhatia V, Stevens T, Derks MFL, Dunkelberger J, Knol EF, Ross JW, Dekkers JCM. Identification of the genetic basis of sow pelvic organ prolapse. Front Genet 2023; 14:1154713. [PMID: 37144137 PMCID: PMC10151575 DOI: 10.3389/fgene.2023.1154713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/23/2023] [Indexed: 05/06/2023] Open
Abstract
Introduction: Pelvic organ prolapse (POP) is one contributor to recent increases in sow mortality that have been observed in some populations and environments, leading to financial losses and welfare concerns. Methods: With inconsistent previous reports, the objective here was to investigate the role of genetics on susceptibility to POP, using data on 30,429 purebred sows, of which 14,186 were genotyped (25K), collected from 2012 to 2022 in two US multiplier farms with a high POP incidence of 7.1% among culled and dead sows and ranging from 2% to 4% of all sows present by parity. Given the low incidence of POP for parities 1 and >6, only data from parities 2 to 6 were retained for analyses. Genetic analyses were conducted both across parities, using cull data (culled for POP versus another reason), and by parity, using farrowing data. (culled for POP versus culled for another reason or not culled). Results and Discussion: Estimates of heritability from univariate logit models on the underlying scale were 0.35 ± 0.02 for the across-parity analysis and ranged from 0.41 ± 0.03 in parity 2 to 0.15 ± 0.07 in parity 6 for the by-parity analyses. Estimates of genetic correlations of POP between parities based on bivariate linear models indicated a similar genetic basis of POP across parities but less similar with increasing distance between parities. Genome wide association analyses revealed six 1 Mb windows that explained more than 1% of the genetic variance in the across-parity data. Most regions were confirmed in several by-parity analyses. Functional analyses of the identified genomic regions showed a potential role of several genes on chromosomes 1, 3, 7, 10, 12, and 14 in susceptibility to POP, including the Estrogen Receptor gene. Gene set enrichment analyses showed that genomic regions that explained more variation for POP were enriched for several terms from custom transcriptome and gene ontology libraries. Conclusion: The influence of genetics on susceptibility to POP in this population and environment was confirmed and several candidate genes and biological processes were identified that can be targeted to better understand and mitigate the incidence of POP.
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Stevens T, Dunkelberger J, Knol E. 508 Late-Breaking: Heritability and Validation of Sow Uterine Prolapse in the United States. J Anim Sci 2021. [DOI: 10.1093/jas/skab235.372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Uterine prolapse impacts animal welfare and reduces sow farm profitability. In general, the incidence of uterine prolapse is higher in the United States than in other countries. Some suspected causes of uterine prolapse include water quality, vitamin deficiency, mycotoxins, and genetics. The objectives of this study were to: 1.) estimate the heritability of uterine prolapse; and 2.) to validate estimated breeding values (EBVs) for uterine prolapse in an independent, related population. Prolapse records collected from purebred females at a commercial multiplier (n = 16,434) and nucleus farm (n = 4,096) were used for training and validation, respectively. Phenotypes were recorded as the presence/absence of uterine prolapse at the sow level. Heritability estimates were derived from the training dataset by fitting year-season of insemination and parity at removal of the sow as fixed effects and animal as a random effect. Using the same model, validation was performed by regressing corrected offspring performance on sire EBV in the validation dataset. A pedigree- and a genomics-based relationship matrix were used for parameter estimation and the validation analysis, respectively. Incidence of uterine prolapse was heritable at 0.15 ± 0.02 and 0.22 ± 0.02 when analyzed using a linear vs. threshold model, respectively. Regression of corrected offspring performance on sire EBV resulted in a slope parameter of 0.40 (95%-CI; 0.27 - 0.54, including the expected value of 0.5), indicating that sire EBV is predictive of uterine prolapse among his offspring. In conclusion, these results show that uterine prolapse is lowly-to-moderately heritable, and therefore, mainly due to environmental factors. Higher incidence of uterine prolapse within the United States vs. other geographic locations confirms the existence of a strong environmental component. Genetic selection can be used to address genetic factors, but identifying/mitigating environmental triggers remains critical to reducing the incidence of uterine prolapse within the U.S. swine industry.
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Dong Q, Dunkelberger J, Lim KS, Lunney JK, Tuggle CK, Rowland RRR, Dekkers JCM. Associations of natural variation in the CD163 and other candidate genes on host response of nursery pigs to porcine reproductive and respiratory syndrome virus infection. J Anim Sci 2021; 99:6376573. [PMID: 34570877 PMCID: PMC8557627 DOI: 10.1093/jas/skab274] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/24/2021] [Indexed: 11/17/2022] Open
Abstract
Pigs with complete resistance to porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV) have been produced by genetically knocking out the CD163 gene that encodes a receptor of the PRRSV for entry into macrophages. The objectives of this study were to evaluate associations of naturally occurring single nucleotide polymorphisms (SNPs) in the CD163 gene and in three other candidate genes (CD169, RGS16, and TRAF1) with host response to PRRSV-only infection and to PRRS vaccination and PRRSV/porcine circovirus 2b (PCV2b) coinfection. SNPs in the CD163 gene were not included on SNP genotyping panels that were used for previous genome-wide association analyses of these data. An additional objective was to identify the potential genetic interaction of variants at these four candidate genes with a mutation in the GBP5 gene that was previously identified to be associated with host response to PRRSV infection. Finally, the association of SNPs with expression level of the nearby gene was tested. Several SNPs in the CD163, CD169, and RGS16 genes were significantly associated with host response under PRRSV-only and/or PRRSV/PCV2b coinfection. The effects of all SNPs that were significant in the PRRSV-only infection trials depend on genetic background. The effects of some SNPs in the CD163, CD169, and RGS16 genes depend on genotype at the putative causative mutation in the GBP5 gene, which indicates a potential biological interaction of these genes with GBP5. In addition, genome-wide association results for the PRRSV-only infection trials revealed that SNPs located in the CDK5RAP2 or MEGF9 genes, near the TRAF1 gene, had suggestive effects on PRRS viral load, which indicates that these SNPs might contribute to PRRSV neuropathogenesis. In conclusion, natural genetic variants in the CD163, CD169, and RGS16 genes are associated with resistance to PRRSV and/or PCV2b infection and appear to interact with the resistance quantitative trait locus in the GBP5 gene. The identified SNPs can be used to select for increased natural resistance to PRRSV and/or PRRSV-PCV2b coinfection.
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Manu H, Fletcher M, Fang K, Junior SRS, Dunkelberger J, Boler D, Eggert J, Baidoo SK. PSIII-10 The Effect of Sire Line on Grow-finish Performance, Carcass Characteristics, and Meat Pricing Variables for Commercial Crossbred Pigs. J Anim Sci 2021. [DOI: 10.1093/jas/skab054.286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
The objective of this study was to evaluate the effect of sire line on wean-to-finish performance, carcass characteristics, and meat pricing variables. Pigs used for this study were the progeny of a commercial Landrace x Large White female mated to one of the following sire lines: a purebred Duroc line (Line S1), or a synthetic (Line S2) or purebred Duroc line (Line S3) originating from a different genetic source. An equivalent number of pigs (n =144) were used per group, for 432 pigs placed on test. Average initial weights per line were 6.67 ± 0.24, 6.67 ± 0.24, and 6.60 ± 0.24 for lines S1, S2, and S3, respectively. At placement, 8 pigs were assigned to each pen (split sex) and blocked by line and initial BW, with 18 replicates per line. Data were analyzed at the pen level using the PROC MIXED procedure of SAS, where the effects of line, sex, and line*sex were fitted as fixed effects and replicate was fitted as a random effect. Overall, piglets from line S2 (0.403 vs 0.381; P ≤ 0.0004) and line S3 (0.402 vs 0.381; P ≤ 0.001) had improved GF compared with piglets from line S1. The ADFI was greater in piglets from line S1 relative to piglets from line S2 (2.264 vs 2.117 kg; P ≤ 0.0001) and line S3 (2.264 vs 2.159 kg; P ≤ 0.004). The ADG, HCW, dressing yield, and loin depth were not different among treatment (P > 1.00). Piglets from line S3 had greater percent lean (57.12 vs 56.29 %; P ≤ 0.0001) and better carcass grade premium ($7.07 vs 6.60; P ≤ 0.0291) relative to piglets from line S1. In conclusion, line S1 piglets had greatest ADFI, but line S2 pigs and line S3 piglets had better feed efficiency. Line S3 pigs were leaner and had better carcass grade premium.
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Manu H, Fletcher M, Fang K, Junior SRS, Dunkelberger J, Boler D, Eggert J, Baidoo SK. PSIII-9 The Effect of Sire Line on Reproductive Performance During Lactation. J Anim Sci 2021. [DOI: 10.1093/jas/skab054.285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
The objective of this study was to estimate the effect of sire line on sow and piglet performance during lactation. Commercial Landrace x Large White females (n = 60) were bred to one of the following sire lines: a purebred Duroc line (Line S1), a synthetic (Line S2), or purebred Duroc (Line S3) from a different genetic source. Matings were balanced by line and parity. Females were fed a common gestation and lactation diet during these respective phases. Sow and piglet data were analyzed as a completely randomized design using the GLM procedure of SAS. Results show that, during lactation, females bred to line S3 lost significantly (P = 0.01) more BW (-16.93 ± 3.56 kg) than females bred to line S2 (-2.00 ± 3.50 kg). However, no evidence of a difference (P = 0.18) in BW loss was detected between females bred to line S3 (-16.93 ± 3.56 kg) vs. Line S1 (-7.90 ± 3.56 kg). Further, sows bred to line S3 weaned significantly (P = 0.03) more piglets (12.0 ± 0.28) than females bred to line S2 (10.9 ± 0.27), but not (P = 0.1) compared to females bred to line S1 (11.7 ± 0.27). No significant effect of line (P > 0.05) or parity (P > 0.05) on total number of piglet’s born, number born alive, number of stillborn piglets, or preweaning mortality was detected. The number of mummified fetus tended to be lower in line S2 (0.17 vs 0.66; P = 0.079) and line S3 (0.12 vs 0.66; P = 0.051) sows compared with line S1 sows, respectively. In conclusion, sire line did not have a significant effect on total number born, number born alive, number stillborn, or preweaning mortality. However, females bred to line S3 lost significantly more BW during lact but weaned significantly more piglets than females bred to line S2.
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Neveau M, Sanglard LP, Dekkers JC, Little E, Dee SA, Hanson DB, Mathur P, Knol E, Eggert J, Dunkelberger J, Serão NV. 15 Host genetics of antibody response to PRRS vaccination and infection in growing pigs. J Anim Sci 2020. [DOI: 10.1093/jas/skaa278.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Antibody response to Porcine Reproductive and Respiratory Syndrome (PRRS) vaccination and infection has been shown to be highly heritable in gilts and sows. This trait, measured as sample-to-positive (S/P) ratio, has been proposed as a selection tool for improved reproductive performance in sows. However, this novel trait has not yet been explored in growing pigs. Therefore, the objective of this study was to estimate genetic parameters for S/P in PRRS-challenged nursery pigs. A total of 854 PRRS-naïve crossbred barrows and gilts (51.9±4.8 d and 17.8±4.6 kg) were randomly allocated to 54 pens in two rooms and vaccinated with a modified live virus PRRS vaccine. Twenty-eight days later (d0), all animals were experimentally inoculated with a highly virulent strain of PRRS virus. Body weight (BW), S/P, and clinical signs of disease were recorded at this time and again at d13. Average daily gain (ADG) was calculated and used in combination with clinical signs to create two distinct groups, robust (R) and susceptible (S), with ~230 animals each. At d42, S/P was measured only in these classified animals. Genetic parameters and effect of classification were estimated for S/P for each collection day. Heritability estimates for S/P were 0.07±0.06, 0.52±0.09, and 0.43±0.28, for d0, d13, and d42, respectively. Genetic correlation estimates were high between collection days, ranging from 0.91±0.31 (d0 and d42) to 0.98±0.03 (d13 and d42). There was an effect of classification for S/P only at d13 (P=0.024), with R showing greater S/P (1.7±0.03) than S (1.64±0.03). These results indicate that, in PRRS-challenged growing pigs, S/P is highly heritable at later collection days, and differences in S/P exist between robust and susceptible animals.
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