A Bayesian Multivariate Gametic Model in a Reciprocal Cross with Genomic Information: An Example with Two Iberian Varieties

SIMPLE SUMMARY: INGA FOOD, S.A. initiated a crossbreeding program involving two Iberian pig varieties: Retinto and Entrepelado. The primary objective of this program is to produce an F1 hybrid sow that exhibits enhanced reproductive performance. In a previous investigation, variations in the reproductive performance of sows, specifically litter size, were observed among the reciprocal crosses. These variations indicate the presence of genomic imprinting effects. To assess the influence of genetic origin, we developed a multivariate gametic model to estimate the gametic correlations between paternal and maternal effects. Gametic correlations lower than one could potentially explain the performance differences observed across the reciprocal crosses. Despite having limited data, the study’s findings suggest that the gametic correlation estimate between paternal and maternal effects on litter size is lower in the Entrepelado population compared to the Retinto population. ABSTRACT: INGA FOOD, S.A. initiated a crossbreeding program between two Iberian pig varieties, Retinto (R) and Entrepelado (E), with the goal of producing a hybrid sow (F1). Several studies have been conducted to evaluate its productive performance, and these studies have revealed differences in litter size between the two reciprocal crosses, suggesting the presence of genomic imprinting effects. To further investigate these effects, this study introduces a multivariate gametic model designed to estimate gametic correlations between paternal and maternal effects originating from both genetic backgrounds involved in the reciprocal crosses. The dataset consisted of 1258 records (the total number born—TNB and the number born alive—NBA) from 203 crossbred dams for the Entrepelado (sire) × Retinto (dam) cross and 700 records from 125 crossbred dams for the Retinto (sire) × Entrepelado (dam) cross. All animals were genotyped using the GeneSeek(®) GPP Porcine 70 K HDchip (Illumina Inc., San Diego, CA, USA). The results indicated that the posterior distribution of the gametic correlation between paternal and maternal effects was distinctly different between the two populations. Specifically, in the Retinto population, the gametic correlation showed a positive skew with posterior probabilities of 0.78 for the TNB and 0.80 for the NBA. On the other hand, the Entrepelado population showed a posterior probability of a positive gametic correlation between paternal and maternal effects of approximately 0.50. The differences in the shape of the posterior distribution of the gametic correlations between paternal and maternal effects observed in the two varieties may account for the distinct performance outcomes observed in the reciprocal crosses.