Within aquaculture industries, selection based on genomic information (genomic selection) has the profound potential to change genetic improvement programs and production systems. Genomic selection exploits the use of realized genomic relationships among individuals and information from genome-wide markers in close linkage disequilibrium with genes of biological and economic importance. We discuss the technical advances, practical requirements, and commercial applications that have made genomic selection feasible in a range of aquaculture industries, with a particular focus on molluscs (pearl oysters, Pinctada maxima) and marine shrimp (Litopenaeus vannamei and Penaeus monodon). The use of low-cost genome sequencing has enabled cost-effective genotyping on a large scale and is of particular value for species without a reference genome or access to commercial genotyping arrays. We highlight the pitfalls and offer the solutions to the genotyping by sequencing approach and the building of appropriate genetic resources to undertake genomic selection from first-hand experience. We describe the potential to capture large-scale commercial phenotypes based on image analysis and artificial intelligence through machine learning, as inputs for calculation of genomic breeding values. The application of genomic selection over traditional aquatic breeding programs offers significant advantages through being able to accurately predict complex polygenic traits including disease resistance; increasing rates of genetic gain; minimizing inbreeding; and negating potential limiting effects of genotype by environment interactions. Further practical advantages of genomic selection through the use of large-scale communal mating and rearing systems are highlighted, as well as presenting rate-limiting steps that impact on attaining maximum benefits from adopting genomic selection. Genomic selection is now at the tipping point where commercial applications can be readily adopted and offer significant short- and long-term solutions to sustainable and profitable aquaculture industries.

Background: We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. Results: The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. Conclusions: Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution.

The extent of linkage disequilibrium (LD) within a population determines the number of markers that will be required for successful association mapping and marker-assisted selection. Most studies on LD in cattle reported to date are based on microsatellite markers or small numbers of single nucleotide polymorphisms (SNPs) covering one or only a few chromosomes. This is the first comprehensive study on the extent of LD in cattle by analyzing data on 1,546 Holstein-Friesian bulls genotyped for 15,036 SNP markers covering all regions of all autosomes. Furthermore, most studies in cattle have used relatively small sample sizes and, consequently, may have had biased estimates of measures commonly used to describe LD. We examine minimum sample sizes required to estimate LD without bias and loss in accuracy. Finally, relatively little information is available on comparative LD structures including other mammalian species such as human and mouse, and we compare LD structure in cattle with public-domain data from both human and mouse.