Breech strike is costing the wool industry A$170 per year. This study found no difference in the microbial profile on the skin between sheep resistant and susceptible to breech strike. This indicates that factors inherent to individual sheep makes them resistant or susceptible to breech flystrike.

In recent years, industry and government interest has increased in using genetic selection to mitigate greenhouse gasses, primarily methane, in dairy cattle. However, acquiring methane data on a large number of cows to estimate genomic prediction equations is challenging, as methane is expensive and laborious to measure. We developed an alternative strategy to reduce the environmental impact of cattle by developing a greenhouse gas subindex, using previously derived coefficients, to weight traits currently estimated in national genetic services based on environmental impact.

Genomic information can be used for traceability of meat products. The present study explored the required number of genetic markers to generate unique marker profiles for each animal in the dataset. Ultra-small panels of genetic markers can provide an efficient method for the large-scale task of industry-wide paddock to plate traceability.

Nitrogen leakage due to urinary nitrogen excretion by dairy cattle is an environmental concern. In contrast to urinary nitrogen excretion, the amount of urea in blood and milk is easier to measure and may be used as an alternative to select for cows that excrete less nitrogen. Our results showed that urea traits measured in Australia are moderately genetically correlated with those in New Zealand.

Lactating cow survival or productive life is an important trait because it affects profitability and environmental footprint of dairy farming. As productive life can be measured only after culling of cows, it can be improved through selecting bulls whose daughters stay in the herds longer. For bulls that have a limited number of daughters, exploiting the traits associated with reasons for culling of cows in the evaluation model could increase the accuracy of genetic predictions for survival.

Improving meat quality and feed efficiency, which is related to input costs and environmental concerns, are important breeding objectives for many beef breeding herds. Different definitions of feed efficiency were estimated and compared with meat quality traits on over 4000 Angus animals. The study confirmed the challenges with selecting for both feed efficiency and meat quality traits as they are generally antagonist at the genetic level, and investigation in alternative approaches for beef cattle selection is warranted.

Relationships between dentition and maturity, production and reproduction in young Merino sheep are not well described at this point in time. Merino progeny that were heavier, with higher fat and muscle measurements, matured earlier. Female progeny were more likely to be pregnant if they were classed as hoggets earlier in life. Dentition was a useful indicator of maturity and Merino sires showed significant variation in progeny dentition.

The present research used DNA data to estimate how heritable fertility traits are. We also investigated the correlations between male and female fertility. The results established that some fertility traits are heritable and can therefore be passed from one generation to the next. The implication is that selective breeding in one sex may improve fertility in the other sex as well. These correlated traits are an opportunity to improve cattle production

Genomic-based technologies are allowing commercial beef producers to predict the genetic merit of individual animals of unknown pedigree with increased ease and accuracy. We report here that the genomic product, Angus SteerSELECT, can predict differences in carcass weight, marbling score, ossification score and carcass value in both short-fed (100 days) and long-fed (270 days) Australian Angus steers. Genomic selection tools that can predict differences in performance of feedlot cattle have the potential to significantly increase profitability for the beef supply chain.

Immune competence phenotypes are moderately heritable and accurate genomic estimated breeding values can be generated for immune competence to allow for selection of cattle with an improved ability to mount an immune response. Our analyses suggest that ImmuneDEX will provide a tool to underpin long-term genetic strategies aimed at improving the immune competence of animals in production systems which in turn is expected to reduce the incidence of disease and our reliance on antibiotics to treat disease.

A genome-wide association study for breech flystrike resistance and its indicator traits using 1535 high-density genotypes did not find major genes of significant effect segregating in the Merino Breeding for Breech Flystrike Resistance Resource flocks in New South Wales and Western Australia. This supports evidence that the trait is controlled by a large number of genes of small effects, so that genomic-selection approaches will add to existing quantitative tools to enhance genetic progress in this hard-to-measure trait.

Two breeding indexes were updated and one index was removed from publication following a study that calculated new economic values for dairy traits for the Australian dairy industry. In contrast to previous index reviews, index options were tested using three breed populations. Developing a better understanding of the differences among breeds had a positive impact on engagement with the study and resulted in a modification of the balanced performance index for the Jersey breed.

Breeding sheep for improved production traits can be achieved more rapidly if we know their parentage. Parentage of lambs is expensive and laborious to measure, so we used proximity sensors to count the interactions between ewes and lambs to determine their parentage. The sensors provided a rapid result that was 97% accurate compared with DNA.

Genotype imputation is a statistical method to obtain a large quantity of DNA-based information at a low cost. Our proposed method improves the accuracy of imputed genotypes, which is of crucial importance for their utility. The presented method is straightforward and can be implemented at no extra cost to aid in genetic improvement of beef cattle.

Mortality of new-born lambs is well known to have important implications for both animal production and welfare, but the genetic improvement of survival traits is considered challenging. The derived heritability of survival traits was low, but favourable genetic trends were observed in the H-line following long-term selection for reproductive performance. From these results, it is recommended that survival traits be actively recorded and included into selection indices.

The design and use of breeding programs is of great importance to improve productivity, fitness and adaptation while controlling negative effects such as inbreeding or health and welfare problems. In this paper, we present a case study of stochastic simulation via the Modular Breeding Program Simulator (MoBPS) by using the Göttingen Minipigs breeding program as an example. Overall, stochastic simulations are a powerful tool for scientists and breeders to answer relevant research questions and optimise the practical design of modern breeding programs.