The human population is growing, and as a result we need to produce more food whilst reducing the impact of farming on the environment. Selective breeding and genomic selection have had a transformational impact on livestock productivity, and now transgenic and genome-editing technologies offer exciting opportunities for the production of fitter, healthier and more-productive livestock. Here, we review recent progress in the application of genome editing to farmed animal species and discuss the potential impact on our ability to produce food.

Background: Fighting and controlling epidemic and endemic diseases represents a considerable cost to livestock production. Much research is dedicated to breeding disease resilient livestock, but this is not yet a common objective in practical breeding programs. In this paper, we investigate how future breeding programs may benefit from recent research on disease resilience. Main body: We define disease resilience in terms of its component traits resistance (R: the ability of a host animal to limit within-host pathogen load (PL)) and tolerance (T: the ability of an infected host to limit the damage caused by a given PL), and model the host's production performance as a reaction norm on PL, depending on R and T. Based on this, we derive equations for the economic values of resilience and its component traits. A case study on porcine respiratory and reproductive syndrome (PRRS) in pigs illustrates that the economic value of increasing production in infectious conditions through selection for R and T can be more than three times higher than by selection for production in disease-free conditions. Although this reaction norm model of resilience is helpful for quantifying its relationship to its component traits, its parameters are difficult and expensive to quantify. We consider the consequences of ignoring R and T in breeding programs that measure resilience as production in infectious conditions with unknown PL—particularly, the risk that the genetic correlation between R and T is unfavourable (antagonistic) and that a trade-off between them neutralizes the resilience improvement. We describe four approaches to avoid such antagonisms: (1) by producing sufficient PL records to estimate this correlation and check for antagonisms—if found, continue routine PL recording, and if not found, shift to cheaper proxies for PL; (2) by selection on quantitative trait loci (QTL) known to influence both R and T in favourable ways; (3) by rapidly modifying towards near-complete resistance or tolerance, (4) by re-defining resilience as the animal's capacity to resist (or recover from) the perturbation caused by an infection, measured as temporal deviations of production traits in within-host longitudinal data series. Conclusions: All four alternatives offer promising options for genetic improvement of disease resilience, and most rely on technological and methodological developments and innovation in automated data generation.

The genetic diversity and frequent emergence of novel genetic variants of porcine reproductive and respiratory syndrome virus type-2 (PRRSV) hinders control efforts, yet drivers of macro-evolutionary patterns of PRRSV remain poorly documented. Utilizing a comprehensive database of >20,000 orf5 sequences, our objective was to classify variants according to the phylogenetic structure of PRRSV co-circulating in the U.S., quantify evolutionary dynamics of sub-lineage emergence, and describe potential antigenic differences among sub-lineages. We subdivided the most prevalent lineage (Lineage 1, accounting for approximately 60% of available sequences) into eight sub-lineages. Bayesian coalescent SkyGrid models were used to estimate each sub-lineage’s effective population size over time. We show that a new sub-lineage emerged every 1 to 4 years and that the time between emergence and peak population size was 4.5 years on average (range: 2–8 years). A pattern of sequential dominance of different sub-lineages was identified, with a new dominant sub-lineage replacing its predecessor approximately every 3 years. Consensus amino acid sequences for each sub-lineage differed in key GP5 sites related to host immunity, suggesting that sub-lineage turnover may be linked to immune-mediated competition. This has important implications for understanding drivers of genetic diversity and emergence of new PRRSV variants in the U.S.

The antibiotic pipeline is running dry and infectious disease remains a major threat to public health. An efficient strategy to stay ahead of rapidly adapting pathogens should include approaches that replace, complement, or enhance the effect of both current and novel antimicrobial compounds. In recent years, a number of innovative approaches managing disease without the aid of traditional antibiotics and without eliminating the pathogens directly have emerged. These include disabling pathogen virulence-factors, increasing host tissue damage control, or altering the microbiota to provide colonisation resistance, immune resistance or disease tolerance against pathogens. We discuss the therapeutic potential of these approaches and examine their possible consequences for pathogen evolution. To guarantee a longer half-life of these alternatives to directly killing pathogens, and to gain a full understanding of their population-level consequences, we encourage future work to incorporate evolutionary perspectives into the development of these treatments.

The objectives of this study were to determine nitrogen loss at different stages of growth and during the entire growing period and to investigate the associations between nitrogen excretion and production traits in growing pigs. Data from 315 pigs of an F₂ population which originated from crossing Pietrain sires with a commercial dam line were used. Nitrogen retention was derived from protein retention as measured using the deuterium dilution technique during different stages of growth (60 to 90 kg, 90 to 120 kg, and 120 to 140 kg). Pigs were fed ad libitum with 2 pelleted diets containing 17% (60 to 90 kg) and 16.5% (90 to 120 and 120 to 140 kg) CP. Average daily nitrogen excretion (ADNE) within each stage of growth was calculated on the basis of the accumulated difference between average daily nitrogen intake (ADNI) and average daily nitrogen retention (ADNR). Least ADNE, nitrogen excretion per BW gain (NEWG) and total nitrogen excretion (TNE) were observed during growth from 60 to 90 kg. In contrast, the greatest ADNE, NEWG, and TNE were found during growth from 120 to 140 kg. Statistical analyses indicated that gender, housing type, the ryanodine receptor 1 (RYR1) gene, and batch influenced nitrogen excretion (P < 0.05), but the degree and direction of influences differed between growth stages. Gender differences showed that gilts excreted less nitrogen than barrows (P < 0.05), which was associated with decreased feed conversion ratio (FCR; feed:gain) and lipid:protein gain ratio. Single-housed pigs showed reduced nitrogen excretion compared with group-housed pigs (P < 0.05). In comparison to other genotypes, pigs carrying genotype NN (homozygous normal) at the RYR1 locus had the least nitrogen excretion (P < 0.05) at all stages of growth except from 60 to 90 kg. The residual correlations indicated that NEWG and TNE have large positive correlations with FCR (r = 0.99 and 0.91, respectively) and moderate negative correlations with ADG (r = −0.53 and −0.48, respectively), for the entire growing period. Improvement in FCR, increase in ADG and reduction in lipid:protein gain ratio by 1 phenotypic SD reduced TNE per pig by 709 g, 307 g, and 211 g, respectively, over the entire growing period. The results indicate that nitrogen excretion changes substantially during growth, and it can be reduced most effectively by improvement of feed efficiency and to a lesser extent through the improvement of BW gain or body composition or both. Copyright © 2012. American Society of Animal Science .