Genomics provides an opportunity to increase the efficiency of livestock production through faster gain in breeding value, exploitation of dominance and epistasis, minimisation of inbreeding and optimisation of management for individual animals. This increase in efficiency is needed for livestock agriculture to compete for researchers such as land, labour, grain, fertiliser and water in the future.

Poor signals along supply chains lead to suboptimal targeting of product outcomes and reduced production efficiency. Genetic and genomic information can be used to help form groups of animals and make management decisions that improve focus and profitability in the supply chain. This may be of notable use for some key traits affecting carcass quality and possibly disease resistance, but otherwise, given sufficiently low costs, genomic information will contribute through increased accuracy of management optimisation tools.

The development of DNA-based tools for use in the selection of livestock for economically relevant traits is advancing. An impediment to success in providing DNA predictions for traits that are not routinely collected by industry is the very large number of phenotypes required to develop tools with significant predictive power. Global collaborations aimed at combining information from existing datasets across populations are an attractive solution to cost-effectively develop more potent DNA-based selection tools.

Genomics offers the opportunity to significantly increase rates of genetic gain in beef cattle breeding by increasing accuracy of selection in young bulls. The immediate challenge is to increase the accuracy of genomic predictions primarily by having greater numbers of animals available with genotypes and phenotypes. Further challenges exist to effectively combine genomic information with traditional sources, and structural changes are needed in the breeding sector for the benefits of genomic selection to be realised by the Australian beef industry.

Genomic selection is the prediction of genetic merit using a large number of genetic markers. Here we review the implications of this technology on the design of dairy cattle breeding schemes. Rather than waiting until a bull has daughters with phenotypic records, a process that typically takes 5–6 years, young bulls with breeding values estimated using their genetic markers, that have no progeny, can be selected and used as sires of the next generation.

This paper presents how genomic selection is implemented and has rapidly developed in French dairy cattle since 2009. The approach is a generalised marker-assisted selection and relies on the preselection of several hundred genomic regions found to be important for the quality of the prediction. Young bulls evaluated on the basis of their genome are going to replace traditional progeny-tested bulls.

Feeding the world’s growing population with qualitative food is the core aim of agricultural production. The production of eggs in mainly developing countries will gain more significance as demands for the same soar. To safeguard the production of a high number of eggs, it is essential to conduct early selection of the most promising male within full sib families in poultry breeding. Genome-wide selection is presently in the initial stages but it is expected to increase significantly with the further development of single nucleotide polymorphism chips with greater capacity. This paper discusses the pros and cons and provides an elaborate insight into this subject.

Genomic information has the potential to change the way Australian beef cattle and sheep are selected. Both industries have made considerable progress in developing the resources required to underpin this genomic selection, including large populations of animals with DNA genotypes matched to performance for many economically important traits. Information from these populations is now being used to increase the accuracy of selecting animals in industry herds and flocks, with the potential of substantially increasing genetic gains.

Tropically adapted breeds of cattle have so far not been well characterised at the level of DNA variation. We sequenced the genomes of a Brahman, an Africander and a Tuli bull, using next generation sequencing. We discovered a total of 6.35 million single nucleotide polymorphisms in the three animals, as well as evidence of genetic selection and long stretches of homozygosity.

The age at which cattle achieve puberty affects the efficiency of beef production. As this trait is in part genetically determined, it is a worthwhile target for genetic selection. To assist with selective breeding, we performed a genome-wide association study and discovered genes associated with age at puberty on chromosomes 14 and X. Knowledge of genes with associations to cattle puberty contributes to our understanding of this important developmental process and will result in breeding a more reproductively efficient beef herd.

Marek’s disease, a T-cell lymphoma caused by an infectious herpesvirus, is one of the most serious diseases for the poultry industry. We implemented a novel strategy that identifies potentially all the individual genes that respond to virus infection. This provides the genetic basis for Marek’s disease resistance, which can be used to select birds that are healthy and have improved agronomic traits.

The SheepGENOMICS program was designed to deliver DNA markers for commercial breeding programs. A resource flock of almost 5000 ewes joined over 2 years to 21 industry sires was established, and progeny were extensively phenotyped and genotyped with DNA markers. Here, we describe the experimental design and sample collection procedures, and provide a summary of the basic measurements taken.

Ireland has implemented genomic selection in its dairy breeding program. A unique collaboration enabled genomic predictions to be developed and used widely to deliver a major increase in the rate of genetic gain. The Irish cattle breeding infrastructure needs to be modified to ensure the benefits of genomic selection for dairy and beef can be fully captured and risks associated with potential undesirable correlated responses are quickly identified and ameliorated.

In this paper we review some of the opportunities that dairy farmers have to use genetic marker technology to improve the profitability of their businesses. These include: optimal sire selection; improving difficult or expensive to measure traits; choosing the best heifers to become replacements; parentage verification; and avoiding genetic defects.

DNA technologies have the potential to generate information of value to beef cattle producers, meat processors and consumers. This information may be used to breed better cattle, optimise the management of cattle as they move from pasture to plate, and improve the quality of beef available to consumers. This field of genomics is likely to play an increasingly important role in beef cattle production, especially given the rapidly declining cost of genotyping and determining the DNA sequence of an animal.