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

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

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

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

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

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

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

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

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

Vaginal microbiota diverges in sows with low and high reproductive performance after porcine reproductive and respiratory syndrome vaccination

Previous studies have demonstrated evidence for a relationship between the vaginal microbiome and reproductive performance, suggesting the vaginal microbiota may serve as a tool to predict farrowing outcomes in commercial pigs. In this study, we compared the vaginal microbiome in sows with low and high farrowing performance and used it to classify animals with contrasting reproductive outcomes in commercial sows following immune challenge with porcine respiratory and reproductive syndrome (PRRS) vaccination. Eighteen microbes were differentially abundant (q-value < 0.05) between the Low and High farrowing performance groups. Among them, Campylobacter, Bacteroides, Porphyromonas, Lachnospiraceae unclassified, Prevotella, and Phascolarctobacterium were also selected in the discriminant and linear regression analyses, and could be used as potential biomarkers for reproductive outcomes. The correct classification rate in the two groups was 100%. In conclusion, this study demonstrates that vaginal microbiota collected after PRRS vaccination could be potentially used to classify sows into having low or high farrowing performance in commercial herds.