# Additive and Dominance Genomic Analysis for Litter Size in Purebred and Crossbred Iberian Pigs
## 3 Results and Discussion  
The results based on TNB and NBA were similar, which was expected because these two traits have a high genetic correlation [13], and the raw correlation between them in the analyzed dataset was 0.94; therefore, we focused on the results with the TNB, and the results for NBA are presented as Supplementary Information (Tables S1-S3 and Figure S1). The REML estimates of the additive genotypic (co) variances are shown in Tables 2 and 3 in TNB and NBA. The additive genotypic variance was higher in the crossbred populations than it was in the purebred populations. This may be due to scale effects, as the phenotypic variation in also greater. In addition, the estimates of the genotypic covariances between purebreds (Entrepelado and Retinto) and the crossbred population were all high and positive, and they corresponded to additive genotypic correlations of 0.704 (\(0.259/\sqrt{0.248\times 0.546}\)) between Entrepelado and Crossbred pigs, 0.988 (\(0.388/\sqrt{0.546\times 0.282}\)) between Retinto and Crossbred pigs, and 0.756 (\(0.200/\sqrt{0.248\times 0.282}\)) between the two purebreds. These results indicated that the genotype x environmental interaction was small, and the additive genotypic correlations were similar to those obtained by [PERSON] et al. [8] in white pig populations. The REML estimates of the dominance genotypic (co)variances ranged from 0.170 (Retinto) to 0.265 (Crossbred) (Table 3). The estimates of the dominance genotypic covariances were all positive, and reflected genotypic dominance correlations >0.95. The analysis provided the REML estimates of \begin{table}
\begin{tabular}{c c c c} \hline \hline  & **Entrepelado** & **Crossbred** & **Retinto** \\ \hline Entrepelado & 0.248 \(\pm\) 0.161 & 0.259 \(\pm\) 0.178 & 0.200 \(\pm\) 0.135 \\ Crossbred & - & 0.546 \(\pm\) 0.268 & 0.388 \(\pm\) 0.170 \\ Retinto & - & - & 0.282 \(\pm\) 0.146 \\ \hline \hline \end{tabular}
\end{table} 
Table 2: REML estimates \(\pm\) standard error (SE) of the additive genotypic (co)variances for the total number born (TNB). \begin{table}
\begin{tabular}{c c c c} \hline \hline  & **Entrepelado** & **Crossbred** & **Retinto** \\ \hline Entrepelado & 0.177 \(\pm\) 0.165 & 0.212 \(\pm\) 0.171 & 0.166 \(\pm\) 0.152 \\ Crossbred & - & 0.262 \(\pm\) 0.210 & 0.202 \(\pm\) 0.179 \\ Retinto & - & - & 0.172 \(\pm\) 0.199 \\ \hline \hline \end{tabular}
\end{table} 
Table 3: REML estimates \(\pm\) standard error (SE) of the dominance genotypic (co)variances for the total number born (TNB). the low permanent and residual effects (Table 4). The residual variance (\(\sigma_{E}^{2}\)) is greater in the crossbred population than in purebreds, consistently with the greater phenotypic variation. In contrast, the estimate of the sow environmental variance (\(\sigma_{R}^{2}\)) was very low in the crossbred population. The additive and dominance genotypic (co) variances were used to calculate the additive and dominance genetic variances in the purebred populations based on expressions (1) to (5) (Table 3). The estimates of the additive genetic variances were 0.170 (Entrepelado) and 0.150 (Retinto), and the estimates of the dominance genetic variances were 0.074 (Entrepelado) and 0.056 (Retinto). The heritability estimates were calculated using Equation (10); they were 0.052 (Entrepelado) and 0.037 (Retinto), which were within the range or slightly lower than those of white pigs [13; 14; 15] and in the same [5] or other Iberian [16; 17] populations. The dominance ratios were obtained from Equation (11), and were 0.023 for Entrepelado and 0.014 for Retinto. They were smaller than the heritabilities, but their ratios with them were approximately 40%, which was higher than those reported for white pig populations [8; 18] for litter size and similar to the results of [PERSON] et al. [19] in other swine traits. We used Equations (6) and (7) to calculate the additive variances for crossbred performance in the purebred populations, which were 0.413 (Entrepelado) and 0.293 (Retinto).