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Several factors, including breed, lead to divergent performance of pigs for production and reproduction traits in different environments. A recent genomics study showed that Modern European (ME) pig breeds contribute to the ancestry of smallholder pigs in the Hoima and Kamuli districts, Uganda. These pigs were also involved in a longitudinal study with several traits recorded, including 540 body weights (WT) of 374 growing pigs, 195 records of total number of piglets born alive (TBA) of 157 sows, and 110 total number weaned (TNW) records of 94 sows. Linear mixed-effects models were used to test for the significance of environmental effects, including housing system, geographic location, and the season when the events occurred as well as animal-specific effects like age, sex, parity, and farrow-to-weaning interval. Stepwise model reduction starting from models with all main effects and pairwise interactions was applied. The final models were then expanded to include proportions of Modern European (ME) ancestry for the subset of animals genotyped, following genomic ancestry analysis based on a Porcine 50K SNP Chip. ME ancestry proportions ranged from 0.02 to 0.50 and were categorized into three classes (low/medium/high ME) based on 33.3% quantiles. The effects of ME classes on WT and TBA were not significant. ME showed a significant effect on TNW. Sows with a high proportion of ME weaned 2.4 piglets more than the low group, the medium ME group being intermediate. This study used genomic data to investigate the effects of genetic ancestry on the performance of smallholder pigs in Uganda. The proportion of Modern European ancestry did not exceed 0.50, therefore not allowing for the comparison of local versus pure “exotic” types of pigs. For the range of ancestries observed, which is the relevant one for current smallholder systems in Uganda, differences were small for the body weight of growing pigs and the number of piglets born alive, while higher proportions of ME ancestry resulted in significantly more piglets weaned. The availability of genotypes of a higher number of growing pigs would have been beneficial for drawing conclusions on the effect of ME ancestry on the growth rates of smallholder pigs in Uganda.

IntroductionLitter size in pigs has increased steadily since 1990. Because of unfavorable genetic correlations with piglet mortality, breeding goals should include survival traits next to litter size. Unbalanced breeding programs that neglect this requirement have produced increased mortality levels, attracting negative public attention. Balanced breeding does not have this disadvantage, but the general public is largely unaware of this.MethodsWe present long-term time trends as realized in commercial breeding. The data includes (i) phenotypes of litter size, piglet birth weight, and piglet mortality, as used in routine breeding value estimation; and (ii) the genomic Best Linear Unbiased Prediction (gBLUP) estimated breeding values thus obtained. Piglet mortality (2001–2022) and birth weight (2009–2022) phenotypes were related to litter size by recording year. Estimated breeding values (EBVs) for the mortality traits were regressed on those for litter size by birth year (2012–2022).ResultsAverage litter size is very weakly correlated to the mortality (R2 ≤ 0.06) and birth weight (0.07 ≤ R2 ≤ 0.26) traits, and those correlations are unfavorable (antagonistic) within each year. However, all traits analyzed here show favorable simultaneous phenotypic and genetic trends over time: the antagonisms are neutralized by balanced breeding. Above the annual mean litter size level, farrowing and lactation mortality rates increased with increasing litter size in every year (unfavorable), but the annual intercepts and the slopes decreased from 2001 to 2022 (favorable). Average litter birth weight decreased with litter size in every year (unfavorable), but the annual intercepts increased and the slopes decreased from 2009 to 2022 (favorable). The within-litter birth weight variation coefficient increased with litter size in every year (unfavorable), but the annual intercepts decreased from 2009 to 2022 (favorable). The proportion of low birth weights (i.e.,

Pig herds in Africa comprise genotypes ranging from local ecotypes to commercial breeds. Many animals are composites of these two types and the best levels of crossbreeding for particular production systems are largely unknown. These pigs are managed without structured breeding programs and inbreeding is potentially limiting. The objective of this study was to quantify ancestry contributions and inbreeding levels in a population of smallholder pigs in Uganda. The study was set in the districts of Hoima and Kamuli in Uganda and involved 422 pigs. Pig hair samples were taken from adult and growing pigs in the framework of a longitudinal study investigating productivity and profitability of smallholder pig production. The samples were genotyped using the porcine GeneSeek Genomic Profiler (GGP) 50K SNP Chip. The SNP data was analyzed to infer breed ancestry and autozygosity of the Uganda pigs. The results showed that exotic breeds (modern European and old British) contributed an average of 22.8% with a range of 2–50% while “local” blood contributed 69.2% (36.9–95.2%) to the ancestry of the pigs. Runs of homozygosity (ROH) greater than 2 megabase (Mb) quantified the average genomic inbreeding coefficient of the pigs as 0.043. The scarcity of long ROH indicated low recent inbreeding. We conclude that the genomic background of the pig population in the study is a mix of old British and modern pig ancestries. Best levels of admixture for smallholder pigs are yet to be determined, by linking genotypes and phenotypic records.

This study examined the effects of porcine reproductive and respiratory syndrome virus (PRRSV) infection on (1) pregnant and (2) growing Landrace and crossbred (Large White × Pietrain) pigs. First, recently pregnant gilts were spilt into a control and a challenged group, which was inoculated with the PRRSV, and phenotypic effects were recorded. In the Landrace breed, infected gilts had a significantly reduced number of fetuses (8.9 versus 11.8), but there were insufficient data to make the same comparison in crossbred gilts. The Landrace had a smaller suppression of weight gain during pregnancy than the crossbred line [56% (0.66 to 0.29 kg/day) versus 85% (0.45 to 0.07 kg/day) reduction], suggesting greater tolerance of the PRRSV infection. Second, impacts on growing pigs were examined with the same deliberate challenge methodology. Some pigs appeared not to become infected from the initial inoculation, but were possibly subsequently infected by cohorts. However, there were indications of Landrace line resistance in terms of an increased time to seroconvert, with weight gain patterns also suggesting Landrace tolerance. In summary, this study demonstrated that breeds differ consistently in phenotypic impacts of PRRSV infection. [ABSTRACT FROM AUTHOR]