This paper was prepared by Professor Julius van der Werf, the 2021 recipient of the Helen Newton-Turner Medal. Julius was awarded the medal for his outstanding contribution to genetic improvement of Australian livestock.

The present study highlighted the potential benefits of incorporating commercial data from Angus-based beef supply chain, which are independent of the Angus Australia reference population, into the existing reference population of Angus SteerSELECT genomic tool. The results help demonstrate to commercial beef producers the opportunity to apply genomic tools within commercial populations as part of routine management, since higher accuracies translate into an improved ability to predict performance, reducing the risk of steers not performing to expectation during feedlot regimes.

Commercial beef and sheep producers have adopted using condition score for management of cows and ewes to maximise productivity. Approximately ¾ of the genetic variation in adult body condition score (BCS) is independent of genetic variation in young weight and composition traits. Producers need to be careful with premiums paid for bulls and rams with superior yearling composition traits with the aim of changing adult BCS. The best way to achieve this is for seedstock breeders to record and report breeding values for cow and ewe BCS.

Cow breeding value for daughter fertility is a determinant of reproductive performance. Temporal trends in estimated breeding values for daughter fertility were described for Holstein and Jersey cows in Australian dairy herds. Breeding values deteriorated markedly in Holsteins in the Australian dairy industry, commencing before 1980. The decline is being reversed, but recovery of herd means in the study population has been slow. An important ongoing task for animal breeding is to monitor traits for genetic decline.

The availability of highly complete and contiguous genome assemblies in agricultural species will enable precise identification of genetic variations, from single nucleotide polymorphisms to large structural variants. Using Pore-C pipeline, the high-quality genome assembly for Bos indicus species and higher-order 3D chromatin structure are first provided in one assay, offering a precious resource for understanding gene regulation. The Pore-C approach will open a new era of 3D genome organisation studies across agriculture species.

Fertility is an economically important trait for both male and female cattle in northern Australian beef herds; however, little emphasis has been placed on selection for fertility. Understanding fertility traits and their relationship with each other and other production traits is essential for improving response to selection in breeding programs. This study demonstrated the genetic and phenotypic correlations between male and female fertility traits as well as fertility traits with body composition traits.

Combining data from multiple cattle breeds may help identify variants that affect important quantitative traits. However, when these variants occur with different allele frequencies in different breeds, the advantage of multi-breed analyses over within breed analyses can reduce. Our results demonstrated the potential benefits and limitations of multi-breed analyses.

The roan pattern in alpacas can cause contamination of coloured fibre, which is a loss to the industry. We investigated the genome of >40 alpacas and found a variant near a known pattern gene, KITLG, that is associated with the roan pattern. Variants in KITLG are known to cause roan in other species, so this discovery is the first step to being able to provide a DNA test that will help alpaca breeders manage their herds more productively.

Animals better adapted to cope with cold stress conditions should have higher survival rates, but the merit of these animals would not be visible under mild conditions. Accounting for the level of cold stress in the earliest days after birth allows for new ways to evaluate the genetic merit of survival or mortality traits. Cold-stress adaption is likely to have been an important part of the very favourable survival rate of the Elsenburg Merino H-Line.

Survival in dairy cows is an important welfare and economic trait that is affected by many factors. The reasons for culling a cow from the first to the second lactation are often different from the ones influencing survival of cows in later lactations. To incorporate this possible difference for genetic evaluations, we explored the benefits of partitioning the cow survival trait into ‘early survival’ and ‘late survival’. This could improve the accuracy and the stability of genetic predictions.

Alpaca fibre comes in a wide range of colours, and not all of the variation can be explained by known base-colour genotypes; therefore, this is a problem for the textile industry that requires bulk quantities of the same-colour fibre. We investigated the genomes of >60 alpacas to see whether genetic markers for pigment intensity could be found, and six regions of the genome were strongly associated with intensity of pigmentation, including a region that is known to affect pigment intensity in dogs. If specific markers are able to be found that affect alpaca pigment intensity, then breeders will be able to select more effectively for the colours desired by the textile industry.

The use of DNA markers through genomic selection to predict the performance of young animals has increased genetic gains in dairy cattle. We investigated the usefulness of Australian genomic breeding values for evaluating sires in New Zealand. This is quite helpful for assessing and selecting sires that have no daughters in New Zealand but have Australian genomic breeding values for the traits in the New Zealand national breeding objective.

Genotyping, to test an animal or herd genetic merit, has become a routine part of most livestock production systems. New genotyping methods offer the potential to significantly decrease the turnaround time of genotyping and also incorporate new genetic information into the analysis. In this study, we have demonstrated that one such genotyping method can be used to genotype cattle and detect bacterial bovine respiratory pathogens in 24 h at a cost similar to that of existing methods.

The accuracy of estimated breeding values is routinely provided to breeders as part of genetic evaluations in Australia. A new method to approximate accuracies using genomic information has been developed and is presented in this paper. The new model has been implemented in Australia’s routine sheep and beef genetic evaluation systems. This development ensures that the calculation of accuracies is sustainable with increasing numbers of animals with genotypes.

This study evaluated machine-learning (ML) algorithms for the prediction of calving difficulty in dairy herds on the basis of relevant herd–cow risk factors. ML algorithms were found to be successful in the prediction of calving difficulty. Data sampling and modification to reduce imbalances in the dataset can improve ML performance for the prediction of low-frequency traits such as calving difficulty. Overall, the ability to predict calving difficulty could help farmers make better farm management decisions, thereby improving dairy farm profitability and animal welfare.

Birth weight can be an important trait in beef cattle through its association with dystocia and increased likelihood of calf and cow mortality. Recording birth weight can be difficult, and coronet circumference measures were assessed but found unsuitable as a suitable predictor of birth weight. Therefore, despite being difficult to record, genetic improvement in birth weight still requires birth weight to be recorded.

Genetic improvement of feed efficiency to produce milk in dairy cattle would provide considerable economic benefits but measuring feed intake is difficult and expensive. Therefore, we used existing data to determine the best period of lactation to measure feed intake and then used advanced genomics to improve the accuracy of genomic breeding values for feed intake and efficiency. The results are an important step towards a more accurate and cost-effective approach to genetically improve dairy cow feed efficiency.

Corriedale sheep breeders select for pigmented nose skin and hooves, as it is believed to be linked with stronger hooves and resistance to internal parasites. This study found a significant association between nose skin pigmentation and a SNP located within the gene MITF. This discovery provides potential for employing DNA technology to select for increased nose pigmentation. Importantly, the identified SNP had no adverse effects on production traits.

The present study investigated implications of lambing ease for lamb survival outcomes, accounting for litter size, and examined associations with other traits recorded at or shortly after lambing in maternal sheep breeds. Individual lamb survival outcomes inferred from field data and dead at birth lambs are lowly heritable traits influenced by both direct and maternal effects. Expanding the current lambing ease analysis to include dead at birth records and lamb survival outcomes would provide more detailed options for breeders to develop breeding goals that will improve outcomes for both ewes and lambs.