Validation of Candidate Markers Associated with Reproductive Performance in PRRSV Naturally-Infected Replacement Gilts in Southern Sonora Mexico

Porcine respiratory and reproductive syndrome virus (PRRSV) in replacement gilts is an infection that decreases reproductive performance in breeding females, and affects the economy of Mexican swine industry. The objective of this study was to validate the associative relationship among average number of piglets alive (NPA) at first and second farrowing with genotypes in PRRSV early-infected gilts. The experiment included seventy-five, 8 mo-old females with breed composition of ¾-Landrace x ¼-Yorkshire. All gilts were exposed to a wild strain of PRRSV once they arrived into the breeding area, and blood samples were collected two weeks later to confirm virus infection by real-time PCR (Tetracore Nextgen Real-Time PCR). Gilts observed in estrus received two natural services with fertility-tested boars. Females confirmed as pregnant were maintained in a gestation area, and moved to the farrowing area the day before parturition. Blood samples were collected on each individual and spotted onto FTA cards for genotyping using a 8,826 low-density SNP chip (Infinium BeadChip, Illumina, San Diego, CA). Previous analysis of these genomic data identified twelve SNP associated with average NPA (P < 0.001), using multi-locus mixed models which were performed in SNP Variation Suite 7 of Golden Helix, Inc. A mixed effects model was used to validate the associative relationship between these SNP and reproductive phenotypes; this model included SNP genotype and age of dam as fixed effects, and sire as a random effect. An allele substitution effect was also calculated using a regression model that included genotype term as a covariate. Mean values for average NPA were 10.61 ± 0.38. From the SNP previously identified, only ALGA0056378 (rs81422969) and MARC0036292 (rs81229798) were associated with average NPA (P < 0.01). Least square means among ALGA0056378 genotypes CC, CT, and TT were 11.93 ± 0.62, 9.45 ± 0.59, and 8.59 ± 2.51; and among MARC0036292 genotypes AA, AG and GG were 6.22 ± 2.40, 8.69 ± 0.71, and 11.47 ± 0.51, respectively. The most favorable alleles increased NPA by 1.71 ± 0.88 and 2.73 ± 0.67 for ALGA0056378 and MARC0036292, respectively. In conclusion, a phenotype to genotype association analyses validated two specific genetic markers that explain genetic variation in the average number of piglets alive from gilts early-infected with PRRSV. Therefore, we propose such SNP as candidates to focus our study on the genetic basis that underlies reproductive performance in gilts infected with a wild PRRS virus strain in southern Sonora.