Including genotypic information in genetic evaluations increases the accuracy of sheep breeding values.

The impact of inclusion of genome-wide genotypes into breeding value predictions for UK Texel sheep is addressed in this article. The main aim was to investigate the level of change in the accuracy values for EBVs when information from animal genotypes is incorporated into the genetic evaluations. New genetic parameters for a range of lamb growth, carcass composition and health traits are described and applied in the estimation of conventional breeding values (EBVs) for almost 822,000 animals as well as genomic breeding values (gEBVs) after adding 10,143 genotypes. Principal component analyses showed that there are no major distinct groups; hence, the population is mainly homogenous and genetically well-linked. Results suggested that the highest change in accuracy was observed for the animals that are not phenotyped but have good links to the reference population. This was seen especially for the lowly heritable health traits thereby proving that the use of genotypes in breeding values estimation may accelerate the genetic gain by producing more accurate values especially for young, un-phenotyped animals.

Salivary IgA: A biomarker for resistance to Teladorsagia circumcincta and a new estimated breeding value.

Teladorsagia circumcincta is the dominant nematode of sheep in cool, temperate climates. Faecal nematode egg counts (FEC) are widely used to identify the intensity of infection and as a measure of host resistance to nematodes. However due to density-dependent effects on worm fecundity the relationship between FEC and worm burden is not linear. In addition collecting FEC data is challenging on a practical level and there is a need for more reliable markers of resistance. There are two major known mechanisms of immunity to T. circumcincta: IgE against third stage larvae (L3) and IgA against fourth stage larvae (L4), which inhibits parasite growth. In this study salivary IgA responses were measured in over 5000 animals against L3 antigen by Enzyme Linked Immunosorbent Assay (ELISA). Antigen-specific IgA levels were negatively correlated with FEC (r=-0.26, SE = 0.02) and were heritable (h2 = 0.16, SE = 0.04) indicating that they can be used to identify resistant animals suitable for inclusion in selective breeding programs. Antigen-specific IgA responses were not negatively correlated with muscle depth. Our analyses indicate that selection for T. circumcincta L3 antigen-specific IgA is possible without impacting on the production traits for the Lleyn breed.

Forensic use of the genomic relationship matrix to validate and discover livestock pedigrees.

Correct pedigree is essential to produce accurate genetic evaluations of livestock populations. Pedigree validation has traditionally been undertaken using microsatellites and more recently, based on checks on opposing homozygotes using single nucleotide polymorphisms (SNPs). In this study, the genomic relationship matrix was examined to see whether it was a useful tool to forensically validate pedigree and discover unknown pedigree. Using 5,993 genotyped Limousin animals which were imputed to a core set of 38,907 SNPs, the genomic relationships between animals were assessed to validate the reported pedigree. Using already pedigree-verified animals, the genomic relationships between animals of different relationships were shown to be on average 0.58, 0.59, 0.32, 0.32, 0.19, and 0.14 between animals and their parents, full siblings, half siblings, grandparents, great grandparents, and great great grandparents, respectively. Threshold values were defined based on the minimum genomic relationship reported between already pedigree-verified animals; 0.46, 0.41, 0.17, 0.17, 0.07, and 0.05, respectively for animals and their parents, full siblings, half siblings, grandparents, great grandparents, and great great grandparents. Using the wider population and the above genomic relationship threshold values, potential pedigree conflicts were identified within each relationship type. Pedigree error rates of between 0.9% (animal and great great grandparent) and 4.0% (full siblings) were identified. A forensic genomic pedigree validation and discovery system was developed to enable pedigree to be verified for individual genotyped animals. This system verifies not just the parents, but also a wide number of other genotyped relatives and can therefore identify more potential errors in the pedigree than current conventional methods. A novel aspect to this algorithm is that it can also be used to discover closely related animals on the basis of their genomic relationships although they are not recorded as such in the pedigree. This functionality enables missing pedigree information to be discovered and corrected in the pedigree of livestock populations. The methods in this paper demonstrate that the genomic relationship matrix can be a useful tool in the validation and discovery of pedigree in livestock populations. However, the method does rely on being able to define threshold values appropriate to the specific livestock population, which will require sufficient number of animals to be genotyped and pedigree validated before it can be used.