Genetic selection has brought substantial progress to farmers since the early 1970s. Selecting the best individuals has increased productivity and ensured animal fertility and health as well as reducing the use of resources and environmental impact. Especially in the last decade, Genomic Selection (GS) has sped up and has provided opportunities to extend the number of selected traits. But there are still limits to GS, when for instance several complex traits are targeted simultaneously and not individually, or the genetic selection causes problems when a certain, desired trait is bred for, but is linked to functional traits causing unwanted changes, such as declining fertility and high levels of mastitis. In addition, GS requires large training populations, which are hard to reach with local breeds, making these breeds a disadvantage from an economical perspective. The preservation of local breeds is therefore also at risk. Despite its tremendous advances in the last 10 years, GS still fails to take efficiently into account rare genetic variants and/or de novo-mutations. All these limitations cause not only biological, technical and economic issues, but also societal concerns regarding breeding objectives and biodiversity.

Genomic selection or genome editing?

Animal breeding makes use of the natural genetic variation among animals to yield permanent and cumulative improvements, and uses several technologies to increase genetic gains. However, embryo biotechnologies have been implemented in breeding programs and, more recently, genome editing has been suggested as a promising technology to speed up selection and design disease resistant alleles.

This raises both technical and ethical issues. Very few data is available regarding potential genome integrity, and in Europe, organisms produced from these technologies are considered genetically modified. This limits the societal acceptability of these technologies.

An ethical dimension: Room of acceptance

In order to address the societal issues and improve the public’s understanding of new animal breeding technologies, the RUMIGEN project operates with the term ‘room of acceptance’. ‘Room of acceptance’ is defined as a conceptual space of societal approaches, opinions, and attitudes towards breeding scenarios that are regarded acceptable now and potentially in a future of renewed societal and political dialogue.

The RUMIGEN project will develop a hypothetic ‘room of acceptance’ reflecting the limits between the acceptable and the non-acceptable in animal breeding and the involved technologies, as seen in previous research on societal discourse on these issues.

Such a ‘room of acceptance’ will be used to develop scenarios for potentially acceptable breeding approaches. There are clear advantages of exploring the ‘room of acceptance’ via scenarios. The basic purpose is to test whether entering into a renewed ‘social contract’ about certain techniques and approaches to application is at all possible, and if so, on which conditions and premises. This is possible to test by constructing scenarios that outline the particularities of new techniques and their implications for society, citizens, environment, and animals: What is the ‘societal readiness level’ in terms of acceptance of new technologies among European citizens? In which ways and in which areas of production would society be ready to accept new technologies?

Adding an ethical dimension to a classic GS breeding program project is a novel method to create an operational framework for future assessment of how society will react and (not) accept new technical agendas – in breeding and elsewhere.

Project goals

RUMIGEN will develop models combining genomics, epigenomics and biotechnologies to improve genomic selection, preserve genetic biodiversity, and avoid genetic load. Improved phenotype prediction will pave the way to new management indexes for precision farming.

The main goal of RUMIGEN is to produce robust and efficient cattle able to manage the trade-offs between production and adaptation to extreme climate conditions (heat stress, reduced feed qualities and quantities, and disease pressures). To preserve the genetic diversity, RUMIGEN will deliver improved sustainable breeding programs for both cosmopolitan and local cattle breeds in a diversity of environmental conditions. RUMIGEN will also deliver new management indexes for precision farming combining genomic, phenotypic and epigenetic information through a multi-actor approach, ensuring societal acceptance, feasibility and economic efficiency.

QGG’s role in the project

Researchers from QGG participate in several parts of the project with the center’s substantial expertise in large-scale data and genomic prediction models.

QGG will be involved in studies of the impact of trade-offs on productive lifespan, using large-scale data collected in commercial farms and meteorological records describing climatic conditions. QGG researchers will also study the phenotypic performances of Danish and Indian half-sisters born from Jersey bulls, which will help verify whether our conclusions are valuable in more extreme farming conditions.

QGG’s unique part will be in work package 6, where animals from Denmark and India will be examined in a Jersey epigenetic study. Since no epigenotyping tools are currently available in cattle, the aim will be to set up an epigenotyping platform that will be used to epigenotype several ejaculates from hundreds of marketed bulls housed in various environments (including related Jersey bulls raised in Denmark and India), as well as thousands of their daughters. By this approach, ejaculates having contrasting epigenetic profiles will be identified, and the impact of epigenome changes will be assessed both statistically by comparing progeny performance across contrasting ejaculates, and experimentally by in vitro embryo production.

Researchers from QGG will also take part in WP8, where the results from WP2 to 6 will be combined in order to develop new, sustainable and socially acceptable breeding programs and management practices. The new breeding methods will target both cosmopolitan and local cattle breeds. These tools will aim to mitigate trade-off between efficiency and resilience and to increase the adaptation to heat tolerance while balancing short- and long-term responses while maintaining genetic diversity. The new tools will better capture genetic variations due to genome-edited variants, rare alleles and de novo mutations, and they will help manage the genetic variability and limit the genetic drift for traits not included in the selection and the genetic load.

- ‘RUMIGEN is a large-scale study on the impact of epigenome on phenotype especially under environmental stress’, QGG work package responsible, senior researcher Goutam Sahana, explains, and continues: ‘QGG researchers will participate in both identifying the genomic regions under epigenetic control and validating their effects with real data from extreme environmental conditions. This will be generating new knowledge and simultaneously applying to practical breeding’.

Goutam Sahana especially stresses the importance of the project’s Room of acceptance dimension:

- ‘Another unique aspect of RUMIGEN is accessing societal acceptance of future breeding technologies. This has become paramount importance with growing public awareness, not only on how the food is produced but also the technologies’ future impact on public health and climate change’.

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In short:

Project title: RUMIGEN - Towards improvement of ruminant breeding through genomic and epigenomic approaches.

The RUMIGEN project has received a total grant of 7 million € from EU H2020. The 18 project partners across nine European countries have formed a consortium to lift the scope of the project with a total of nine work packages.

The project duration is five years, starting from June 2021.

More information:

Center Director, Professor Mogens Sandø Lund, Center for Quantitative Genetics and Genomics

Email: mogens.lund@qgg.au.dk  // Tel.: +45 2075 1222

Senior researcher Goutam Sahana, Center for Quantitative Genetics and Genomics

Email: goutam.sahana@qgg.au.dk // Tel.: +45 8715 7501