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

Abstract

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.

Keywords: GWAS; Genomics; PRRS; QTL; S/P ratio; outbreak; reproduction; swine.

FIGURE 1

Manhattan plot for sample-to-positive (S/P) ratio during the porcine reproductive and respiratory syndrome (PRRS) outbreak in Duroc and Landrace sows. Each point represents a 1-Mb SNP window (x-axis) plotted against the percentage of total genetic variance accounted for by markers (TGVM; y-axis). (A,B) Results for Duroc and Landrace sows, respectively.

FIGURE 2

Linkage disequilibrium (LD) plots of the genotype data for the 3-Mb SNP window that harbors the major histocompatibility complex (MHC) on Sus Scrofa chromosome 7 (SSC 7: 24–25 Mb) associated with sample-to-positive (S/P) ratio. (A,B) Results for Duroc and Landrace sows, respectively. LD is expressed as r². The darker diamonds indicate greater LD. These plots indicate lower LD in Landrace sows than Duroc sows within this region.

FIGURE 3

Genomic prediction accuracies of sample-to-positive (S/P) ratio across different SNP sets. (A,B) Genomic prediction accuracies for the within-breed and between-breed genomic prediction, respectively. SNP_All represents the set of SNPs using all 29,799 SNPs across the genome, while SNP_MHC accounts for only SNPs in the QTL that harbors the major histocompatibility complex (MHC) region. For SNP_Rest, all SNPs across the genome were used excluding those in the MHC region and a 2-Mb window surrounding the QTL in the MHC region to avoid having any SNPs in linkage disequilibrium with this QTL. The error bars in panel (A) represent the standard deviations across the 5-fold used to calculate genomic prediction accuracies.

FIGURE 4

Simulated response to selection for increased number of piglets born alive (NBA) in Landrace sows after 10 generations based on (indirect) or not (direct) antibody response to porcine reproductive and respiratory syndrome virus infection, measured as sample-to-positive (S/P) ratio. The y- and x-axis represent the response to selection in genetic standard deviations and generations, respectively. Direct and indirect response to selection are represented by solid and dashed lines, respectively, assuming 5% selection intensity, using the genetic parameters obtained in this study.