G. A. A. Albers

Breed utilization, genetic improvement, and industry consolidation are predicted to have major impacts on the genetic composition of commercial chickens. Consequently, the question arises as to whether sufficient genetic diversity remains within industry stocks to address future needs. With the chicken genome sequence and more than 2.8 million single-nucleotide polymorphisms (SNPs), it is now possible to address biodiversity using a previously unattainable metric: missing alleles. To achieve this assessment, 2551 informative SNPs were genotyped on 2580 individuals, including 1440 commercial birds. The proportion of alleles lacking in commercial populations was assessed by (1) estimating the global SNP allele frequency distribution from a hypothetical ancestral population as a reference, then determining the portion of the distribution lost, and then (2) determining the relationship between allele loss and the inbreeding coefficient. The results indicate that 50% or more of the genetic diversity in ancestral breeds is absent in commercial pure lines. The missing genetic diversity resulted from the limited number of incorporated breeds. As such, hypothetically combining stocks within a company could recover only preexisting within-breed variability, but not more rare ancestral alleles. We establish that SNP weights act as sentinels of biodiversity and provide an objective assessment of the strains that are most valuable for preserving genetic diversity. This is the first experimental analysis investigating the extant genetic diversity of virtually an entire agricultural commodity. The methods presented are the first to characterize biodiversity in terms of allelic diversity and to objectively link rate of allele loss with the inbreeding coefficient.

Social interactions between individuals living in a group can have both positive and negative effects on welfare, productivity, and health of these individuals. Negative effects of social interactions in livestock are easier to observe than positive effects. For example, laying hens may develop feather pecking, which can cause mortality due to cannibalism, and pigs may develop tail biting or excessive aggression. Several studies have shown that social interactions affect the genetic variation in a trait. Genetic improvement of socially-affected traits, however, has proven to be difficult until relatively recently. The use of classical selection methods, like individual selection, may result in selection responses opposite to expected, because these methods neglect the effect of an individual on its group mates (social genetic effects). It has become clear that improvement of socially-affected traits requires selection methods that take into account not only the direct effect of an individual on its own phenotype but also the social genetic effects, also known as indirect genetic effects, of an individual on the phenotypes of its group mates. Here, we review the theoretical and empirical work on social genetic effects, with a focus on livestock. First, we present the theory of social genetic effects. Subsequently, we evaluate the evidence for social genetic effects in livestock and other species, by reviewing estimates of genetic parameters for direct and social genetic effects. Then we describe the results of different selection experiments. Finally, we discuss issues concerning the implementation of social genetic effects in livestock breeding programs. This review demonstrates that selection for socially-affected traits, using methods that target both the direct and social genetic effects, is a promising, but sometimes difficult to use in practice, tool to simultaneously improve production and welfare in livestock.

The purpose of the present cross-sectional study was to evaluate the health status of organic broiler chickens and the contamination rate with Salmonella and Campylobacter in organic broiler production in Belgium. The broilers were screened for antibodies against routinely monitored poultry diseases at 1 day old and at slaughter. Fecal examination for the presence of worm eggs was done at slaughter. Bacteriological examination for the detection of Salmonella and Campylobacter was performed at day 1, week 2, week 4, week 7, week 10, and slaughter. Conventional broilers of the same poultry integration and reared in the same geographic area were also screened and served as reference. Serologic data indicated lower antibody titers against infectious bronchitis and Newcastle disease in organic flocks. No significant differences could be found in prevalence of Salmonella between organic and conventional broilers at slaughter. In contrast, Campylobacter infections at slaughter were significantly higher in organic flocks. Organic flocks most probably become infected with Campylobacter between week 7 and week 10. Worm eggs were found in neither the organic flocks nor the conventional flocks. In conclusion, there are indications that the respiratory health status is better in organic broilers but that organic flocks are more often infected with Campylobacter than are conventional flocks.

This chapter focuses on the developments in poultry breeding, which includes the egg-type and meat-type chickens.