# Additive and Dominance Genomic Analysis for Litter Size in Purebred and Crossbred Iberian Pigs
## 3 Results and Discussion
Therefore, the additive genetic variance in the crossbred population was the average of the two (0.353), which was higher than the additive genetic variances in the purebred populations, which were similar to the results of [PERSON] et al. [8] with regard to litter size, and to the results of [PERSON] et al. [19] for other pig traits. Nevertheless, [PERSON] et al. [20] found the opposite in a cross between Landrace and Yorkshire breeds (0.86 and 0.54 in purebreds and 0.28 in crossbreds). In the present study, the dominance genetic variance in the crossbred population (0.079) was calculated based on the Equation (8), which was similar to the dominance genetic variance in the purebreds; however, its ratio with the additive genetic variances was lower (22%). Given those variance components, the heritability and dominance ratio estimates in the crossbred population were 0.072 and 0.016, respectively. In addition, the additive genetic correlations between purebred and crossbred performances in the Entrepelado and Retinto populations were calculated based on expressions (12) to (15), which were 0.663 in Entrepelado and 0.881 in Retinto populations. Those correlations were within the range of the estimates summarized by [PERSON] and [PERSON] [7], and suggest that the efficiency of the selection for increased crossbred performance by selecting for purebred performance will be more effective in Retinto than in Entrepelado pigs. We used Equations (16) and (17) to calculate the additive and dominance genotypic effects associated with each of the 34,316 SNP markers, which were used in Equations (18)-(21) to calculate the proportion of the additive genetic variance that was explained by segments of 30 consecutive SNPs (Figure 1). The distribution of the additive variance explained by segments of 20 and 40 SNP markers were similar, and are presented as supplementary information (Figures S2 and S3). \begin{table}
\begin{tabular}{c c c c} \hline \hline
**Variances 1** & **Entrepelado** & **Crossbred** & **Retinto** \\ \hline \(\sigma_{E}^{2}\) & 0.191 \(\pm\) 0.105 & 0.009 \(\pm\) 0.029 & 0.268 \(\pm\) 0.120 \\ \(\sigma_{E}^{2}\) & 2.810 \(\pm\) 0.099 & 4.467 \(\pm\) 0.155 & 3.534 \(\pm\) 0.128 \\ \hline \hline \end{tabular} \({}^{1}\)\(\sigma_{S}^{2}\): Sow permanent environmental variance; \(\sigma_{E}^{2}\): residual variance.  
\end{table} 
Table 4: REML estimates \(\pm\) standard error (SE) of the permanent environmental and residual variances for the total number born (TNB) in the Entrepelado, Crossbred and Retinto populations. The figure presents the distribution of the additive variance along the autosomal chromosomes in the Entrepelado and Retinto populations, and for the purebred and crossbred performance. Four genomic regions can be highlighted; each explained >2% of the additive genetic variance in at least one of the populations. The SNPs at the center of each of the genomic regions that explained the highest amount of additive genetic variance, and the genes in the Sus_Scrofa 11.1. genomic map that were within 1 Mb downstream or upstream, are presented in Table 5.  
Figure 1: Distribution of the percentage of the additive genetic variance explained by genomic segments of 30 SNPs within the autosomal genome of purebred and crossbred performance for the total number born (TNB) in the Entrepelado and Retinto varieties. Black: chromosomes 1, 9 and 17; red: chromosomes 2, 10 and 18; green: chromosomes 3 and 11; deep blue: chromosomes 4 and 12; blue: chromosomes 5 and 13; purple: chromosomes 6 and 14; yellow: chromosomes 7 and 15; grey: chromosomes 8 and 16. Among those genes, several can be proposed as candidate genes to explain the additive genetic variation. The genomic region surrounding bp 7,597,405 in SSC6 included BCO1 (\(\beta\)-_Carotene Oxygenase 1_), which encodes an enzyme that catalyzes the breakdown of provitamin A and provides retinoids for embryogenesis [21; 22]. Furthermore, the GCSH (_Glycine Cleavage System H_) protein plays an important role in embryonic viability [23].