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Archaeological evidence indicates that pig domestication had begun by ~10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ~8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local Euro-pean wild boars, although it is also possible that European wild boars were domesticated independently without any genetic con-tribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.

Aim We focus on the biogeographical role of the Balkan Peninsula as a glacial refugium and source of northward post-glacial dispersal for many European taxa. Specifically, we analysed the genetic structure and variation of wild boar (Sus scrofa) samples primarily from Greece, a region that has repeatedly served as a glacial refugium within the Balkan Peninsula.

Location Continental Greece, the Aegean island of Samos and Bulgaria.

Methods We analysed wild boar samples from 18 localities. Samples from common domestic breeds were also examined to take into account interactions between wild and domesticated animals. Phylogenetic analyses were carried out on a 637-bp fragment of the mitochondrial DNA control region in 200 wild boar and 27 domestic pigs. The sequences were also compared with 791 Eurasian wild boar and domestic pig D-loop sequences obtained from GenBank.

Results Ninety-four haplotypes were identified in the European wild boar data set, of which 68 were found in the Balkan samples and assigned to two previously described clades: the E1 European and Near Eastern clades. All of the continental samples clustered in the E1 clade and the samples from Samos fell into the Near Eastern clade, consistent with the island’s proximity to Asia Minor. Intriguingly, 62 novel haplotypes were identified and are found exclusively in the Balkans. Only six haplotypes were shared between wild boar and domestic pigs.

Main conclusions Our data reveal numerous novel and geographically restricted haplotypes in wild boar populations, suggesting the presence of separate refugia in the Balkans. Our analyses support the hypothesis of a post-glacial wild boar expansion consistent with the leading edge model, north and west from modern day Greece, and suggest little maternal introgression of Near Eastern and domestic haplotypes into wild Balkan populations.

Historically, pig breeding programs have focused on a limited number of traits. Often growth rate, back fat and a measure of litter size at birth were the only traits considered. Genetic relationships with other unrecorded traits were ignored in this simple approach, although selection for these traits leads to correlated responses in feed efficiency, lean meat growth, carcase characteristics, meat quality, survival of piglets, disease resistance as well as characteristics of the sow such as mature weight, body composition and feed intake capacity. This long list of traits may seem daunting. However, ignoring (unfavourable) genetic associations between traits in pig breeding programs will lead to sub-optimal performance and ultimately impair health and welfare of pigs and sows (e.g. Rauw et al., 1998; Prunier et al., 2010).

Ten years ago, Jaco Eissen (Eissen, 2000) proposed selection for a higher feed intake during lactation as a strategy to overcome longevity and reproductive problems in sows, which were thought to be largely due to a widening gap between nutrients available from decreasing fat reserves at farrowing and nutrients required to meet increasing demands of litters. However, focus on a single trait is inadequate, given the complex associations between the physiological states of sows during transition from gestation to lactation and finally to mating following the weaning process. In addition, various physiological parameters of the sow may interact with the changing requirements of the litter during gestation and lactation.

Genetic and phenotypic relationships between sow weight and body composition, lactation feed intake, reproductive traits of sows and lean meat growth of growing pigs have been outlined in a number of papers presented at this workshop, as well as the previous workshop in 2008. In this paper we look at some common paradigms in regard to sow and piglet performance and try to place them in context with alternative management or selection choices that could be made.

Introduction Pedigree relationships to control inbreeding in optimum-contribution selection (POCS) realised a higher rate of true genetic gain (ΔG) than use of genomic relationships for optimum-contribution selection (GOCS) at the same rate of true inbreeding (ΔF) (Henryon et al., 2019). Recently, Gautason et al. (2022) found that GOCS realised just as much ΔG as POCS but at lower ΔF when they fixed the number of selected sires in their simulations of a breeding scheme for dairy cattle. The striking difference with the study of Gautason et al. (2022) is that they restricted ΔF in POCS and GOCS to the same rate but did so on different scales based either on pedigree or genomic information. However, if DF based on the same scale in POCS and GOCS is compared at the same ΔG, POCS realises less ΔF by allocating matings to more sires and dams from more full-sib families than GOCS. This suggests that POCS may not be as good as GOCS when the number of sires and dams allocated to matings is fixed. Based on this information, it was hypothesised that GOCS would realise less ΔF at the same ΔG than POCS when number of sires and dams allocated to matings is fixed.

Pig breeding programs focus on growth and carcase composition traits in the growing pig as well as higher reproductive performance of sows leading to considerable genetic gain in these traits. These changes in genetic potential have consequences for piglet survival and husbandry requirements of sows. For example, comparison of body composition and physiological state of piglets from boars born in 1977 versus 1998 showed that selection had resulted in lower maturity of piglets at birth Canario et al., 2007). Further, Ball et al. (2008) reviewed nutrient requirements of sows concluding that recommendations have not kept pace with the increases in animal performance.

Lactating sow performance is a balance between meeting the demands of the litter and nutrients available from sow feed intake and the mobilization of body reserves. Understanding the consequences of selection on these components of sow performance is a first step towards optimizing both breeding programs that consider a wider range of traits, and management practices that continue to meet the changing needs of sow and piglet genotypes. It was the aim of this study to evaluate the effect of differences in estimated breeding values (EBVs) for traits that have been used as selection criteria on litter size, piglet birth weight, litter survival and litter weight gain as well as sow feed intake and weight and backfat of lactating sows.

Introduction: Seasonal effects on fertility in gilts and sows are characterised by reduced reproductive performance during the summer and autumn period (Love et al., 1993). Both the number born alive (NBA) and farrowing rate (FR) are affected by seasonal infertility. Economic values (EV) for these traits depend on assumed production parameters, cost parameters (Amer et al., 2014) and mean performance in FR (Hermesch, 2021), which consequently are influenced by seasonal effects. Both NBA and FR were genetically different traits between seasons or environments based on temperature groupings (Lewis and Bunter, 2011; Bunz et al., 2019). Both may be considered as different traits in the most challenging season (summer) versus the other seasons. The hypothesis of this study was that by considering the economic implications of seasonal effects in sow breeding objectives (BO), the relative emphasis placed on traits changes.