GIGA-Medical Genomics

Harnessing genomic information for livestock improvement



Genomics as a new scientific discipline emerges at the end of the 1980s and the general use of technology has been remarkably fast. The world demand for animal- based food products is anticipated to increase by 70% by 2050. Meeting this demand in a way that has a minimal impact on the environment will require the implementation of advanced technologies, and methods to improve the genetic quality of livestock are expected to play a large part. Over the past 10 years, genomic selection (GS) has been introduced in several major livestock species and has more than doubled genetic progress in some. However, additional improvements are required. Genomic information of increasing complexity (including genomic, epigenomic, transcriptomic and microbiome data), combined with technological advances for its cost- effective collection and use, will make a major contribution.

In this Review, Michel Georges, Carole Charlier (GIGA-Medical Genomics) and Ben Hayes (University of Queensland, Brisbane, Australia) examine the status of genomic resources available in the major livestock species (that is, cattle, sheep, goat, pig, poultry and salmon) and how these are being used to accelerate the discovery and management of defect- causing genes, to improve the accuracy and extend the scope of GS, to orient genome editing strategies and to develop new applications that take advantage of the genomic information that is becoming widely available

Researchers take stock of the evolution of genomic resources and technological tools in recent years: whole genome sequencing, genotyping chips, bioinformatic methods, etc. The article also reviews new technologies available and evolution of genomic selection to dissect complex traits and on genome editing, which is currently a very popular subject but has fewer ethical barriers in its use for livestock compared to humans. The authors finally have a look at new applications. This is particularly the case of a technology developed within the GIGA that can detect in a herd of dairy cows which ones will develop mastitis (inflammation of the mammary gland). In fact, cows with subclinical mastitis (not yet developed) will have more cells present in their milk than other cows. Thanks to this application, it is enough to analyze the milk of the tank (of all the cows) and to see if the DNA of some cows is more represented than others. The results therefore enable the farmer to save money by being able to treat or discard the cows before they develop this inflammation.

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Understandably, attention to and investments in research and development faded somewhat as breeding organizations focused on the implementation and consolidation of GS. Now that these goals have been largely accomplished and GS has been widely adopted, its limitations as implemented today are recognized and better understood. Logically, there is, therefore, renewed interest and investment in the next round of innovation. Identified objectives include more effective forward and reverse genetic screens to identify genes with major effects, efforts to systematically identify and incorporate causative variants into improved models of GS, renewed attention to the CRISPR–Cas9-based editing of livestock genomes combined with GS and the development of novel uses of the growing body of genomic data. Thus, genomic information will be a critical component of the global response to the world’s pressing nutritional requirements.

Source

Harnessing genomic information for livestock improvement
Michel Georges, Carole Charlier & Ben Hayes
Nature Reviews Genetics (2018)

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