Annual Report 2010

FABRE TP: its aims and developments up to 2010

The Sustainable Farm Animal Breeding and Reproduction Technology Platform (FABRE

TP) is an EC recognised technology platform (http://cordis.europa.eu/technology-

platforms/bio_en.html). European technology platforms (ETPs) are industry-led

stakeholder forums in areas of key importance to European competitiveness with the aim

of defining medium to long-term research and technological objectives and developing

roadmaps to achieve them.

A vibrant effective animal breeding industry is essential if Europe is to meet the future

challenges of animal agriculture in a rapidly changing ecological, economic and social

environment. This is a globally highly competitive, knowledge intensive sector. Because

European breeding organisations are major players in the global market, currently

Europe has a major influence on the genetic make-up of future animals and hence on the

whole of animal production. Animal production is important for European society with an

annual value of > €130 billion (~ 40% of European agricultural production) and > 15

million jobs. Livestock industry also supports the agrifood industry (2.6 million jobs and

an annual turnover of about € 600 billion).The added value of animal breeding in

economic gain (cumulative, permanent) is estimated to be €1,89 billion/year.

FABRE TP works as a contact point for Farm Animal Breeding and Reproduction in Europe

for organising annual updates on research and implementation and initiating European

efforts and activities.

FABRE TP is supported by 116 organisations across Europe to enhance the sustainability

of animal breeding and reproduction in (and outside) Europe. After its start as an

independent initiative in 2005, the development of a Strategic Research Agenda and

Implementation Plan was funded by the European Commission (FOOD-CT-2006-044228).

As from 2009, FABRE TP has been funded as a joint initiative of the European Forum of

Farm Animal Breeders, Institut National de la Recherche Agronomique, Biosciences

Knowledge Transfer Network, NOFIMA, and Wageningen University and Research Centre.

The Technology Platform is demand driven: it considers the need for animal food

(livestock revolution), and looks to overcome the consequences of climate change

through development and uptake of better approaches to animal breeding and

reproduction. From 2006-2008, FABRE TP has developed a Vision for the next 10-25

years, a Strategic Research Agenda and Implementation Plan. These were based on 13

expert groups reports in a) cattle, sheep and goats, horse, pig, poultry, aquaculture,

other animals (rabbit, fur, dog, honeybee), b) genetics, genomics, reproduction, c)

quality and safety, robustness health and welfare, and diversity/distinctiveness, and also

on discussions in 34 countries. A summary is available in 28 languages.

In 2010, the update of the 13 expert group reports has been taken up, and will be

finalised in 2011. Also, White Papers on Animal Breeding and Reproduction for Food

Security and Climate Change will be prepared to support the Joint Programming Initiative

Agriculture, Food Security and Climate Change (www.faccejpi.com) which is being set up

to streamline research efforts between 22 countries.

ORGANISATION

Figure 1 shows the organisation structure of FABRE TP.

Figure 1. Organisation chart of FABRE TP

Steering Group / Board of Directors

• Biosciences Knowledge Transfer Network (Huw Jones, Chris Warkup)

• European Forum of Farm Animal Breeders (Roland Aumüller, Ashie Norris, Ingela

Velander)

• Institut National de la Recherche Agronomique (Didier Boichard, Patrick Herpin)

• NOFIMA (Kari Kolstad, Anna Sonesson)

• Wageningen University and Research Centre (Johan van Arendonk, Roel

Veerkamp)

• European Association for Animal Production (Andrea Rosati; observer)

Contact:

- EFFAB office

Office: Postal address:

De Valk Benedendorpsweg 98,

Dreijenlaan 2 6862 WL Oosterbeek

Office 1060/1061 The Netherlands

6703 HA Wageningen

The Netherlands

Tel: +31 317 412 006

Fax: +31 317 453 888

Email: effab@effab.info

- Web site – www.fabretp.info

In 2010 the website has been restyled.

Executing

office

(EFFAB)

Management Team

Board of

Directors/Steering

Group

= chair +

supporting

members + EAAP

(observer)

European Commission, Technology

Platforms…

Country groups

Expert groups

LOBBY

• Development of Research Priorities

FABRE TP has developed and forwarded research priorities to the European Commission

(Annex 1). In the call for proposals for 2010, various of these suggestions have been

taken on board and lead to subjects to calls for proposals.

• Representation at various Forums

FABRE TP has been invited and participated via its stakeholders to various meetings,

workshops and forums organised by the European Commission, and the Belgian

Presidency of the European Union. A non inclusive list includes:

Various Knowledge Bio-Based Economy events, e.g. Belgian Presidency KBBE event

Brussels, EurAsiaBio (presentation) Moscow, KBBE Net meeting, ETP conference (booth),

meeting with Members of European Parliament,

Standing Committee Agricultural Research Foresight Exercise.

• Initiation and further building of Animal Task Force

FABRE TP has been instrumental in the further development of the Animal Task Force.

Aim of the Animal Task Force is a sustainable and competitive animal (including

aquaculture) sector at the forefront of technological development and other innovations.

It aims to achieve an enabling environment and the adoption of an integrated approach

across the value chain.

In 2010, a project proposal, Aster, was proposed to the European Commission but

unfortunately did not get funded.

The four Technology Platforms in the animal area (FABRE TP, Global Animal Health, EATiP

(aquaculture) and Eufetec (feed) have agreed to support the Animal Task Force. All

FABRE TP funding bodies have been very active in the maturation of the ATF: Anna

Sonesson and Kari Kolstad of Nofima, Chris Warkup and Huw Jones of BKTN, the EFFAB

secretariat and board, Patrick Herpin and John Williams of INRA, Paul Vriesekoop of WUR.

The group of initiating research organisations has been extended to 8 by the end of

2010: INRA, WUR, SAC, Bonn University, Teagasc, Aarhus University, MTT, Uppsala

University.

A legal structure will be developed. The FABRE TP secretariat (Marjolein Neuteboom)

supports the current chair Paul Vriesekoop. Each organization will fund ATF with €5000

annually. The power of votes has been divided equally between industry (ETPs) and

research.

In 2011, ATF will organize a stakeholder event in Brussels, and a workshop at EAAP.

Website: www.animaltaskforce.eu

• Bioeconomy Technology Platforms: BECOTEPS

In BECOTEPS* the Bioeconomy Technology Platforms have developed the draft White

Paper on Innovation 2020. In 2009 three stakeholder workshops were organized (food-

feed, non-food and sustainability, two of which were organized by FABRE TP) to map

what was important in the bioeconomy , in 2010 an event was organized for the

European Parliament to raise awareness on the bioeconomy. At the end of 2010, a

workshop was organized (by FABRE TP) for the European Commission, to discuss with

them the draft White Paper. The primary focus of this document was to elaborate

common themes and joint priorities across the widely diverse sectors relevant for the

European Bioeconomy, which will lead to improve competitiveness of European

bioeconomy.

* The Bio-Economy Technology Platforms join forces to address synergies and gaps

between their Strategic Research Agendas (BECOTEPS, 226526) is an EC funded project

under the 7th Framework Programme for RTD. It runs until April 2011.

• WCGALP

FABRE TP has presented itself with a booth at the World Congress of Genetics in

Livestock Production in Leipzig, August 2010.

ANNEX 1. RESEARCH PRIORITIES SENT TO EUROPEAN COMMISSION

The Director of Directorate E

Mrs. Dr. Maive Rute

Rue de la Loi 200, SDME

1049 Brussels

Oosterbeek, 11 October 2010

Dear Mrs. Rute,

It is a pleasure to send to you the a list of important research subjects for the 2012 and 2013 calls the

Sustainable Farm Animal Breeding and Reproduction Technology Platform (FABRE-TP) has identified

(enclosure 1). These projects at the European level are urgently needed, in addition to the private

and national efforts that we stimulate. As the contribution to innovation in our sector is crucial, we

have been identifying importance and possibilities of the projects for SME, midsize industry and

industry.

Farm Animal Breeding and Reproduction is a knowledge intensive and highly competitive sector at

the start of the food chain with many SMEs, a few midsized and large international players. European

research funding is crucial to ensure that the European animal breeding industry is able to respond to

the needs of the society and to remain competitive at the global level.

- Its impact on animal food production is enormous: activities influence nearly every animal

product.

- Global animal breeding is largely in European hands.

- Animal breeding is based on sustainability and aims for a strong European knowledge base

with important outreach to the diverse smaller research and industry players in Europe.

- Animal breeding balances intellectual property issues via the EFFAB Patent Watch and ICAR

Sentinel.

- Animal breeding has implemented Code of Good Practice Code-EFABAR based on

sustainability and transparency.

- Animal breeding has a major influence on the European landscape, biodiversity, animal

welfare, environmental footprint, food safety and food quality.

- The midsized companies play a crucial role in uptaking the high level knowledge developments

(e.g. genomics, IT related, reproduction), and the relatively open structure ensures further

implementation to SMEs.

FABRE TP views itself as an integral part of the food and feed Bioeconomy. During the last year we

have been strengthening the links at the national levels, with the animal field and with the

Bioeconomy ETPs.

- FABRE TP plays a proactive role in the Animal Task Force, which stimulates the

cooperation between the animal based related ETPs and with animal research and

business.

- FABRE TP is writing White Papers on Food Security and Climate Change. These will be ready by

mid 2011 and link animal breeding and reproduction to these items with global importance,

and to the Joint Programming Initiative on Agriculture, Food Security and Climate Change.

- FABRE TP is actively involved in the Bioeconomy efforts in BECOTEPS, in organizing the

workshops on the Food-Feed chain and Sustainability, development of the BECOTEPS White

Paper, and organisation of the EC-ETP meeting on the draft White Paper at 14 October.

We trust you will be willing to contribute to the competitiveness, diversity, quality and consumer

trust of animal products. We appreciate presenting our Technology Platform and its outreach and

activities to you. Please do not hesitate to contact us for a personal encounter or for more

information.

Yours sincerely,

On behalf of FABRE TP,

Anne-Marie Neeteson-van Nieuwenhoven

Enclosure 1 to letter EC

Research Subjects

a. Reproduction - Sustainable robust farm animal reproduction systems

b. Social Interactions - Pigs and poultry and aquaculture

c. Breeding Goals to Answer Climate Change and Food Security

d. Use of Genomic Information in Commercial Populations - Opportunities to improve robustness

e. Monogastrics Feed Efficiency - Efficiency of livestock digestive systems and reduction of the

ecological footprint through a combination of systems biology, 'omics' and nutrition

f. Utilization of Whole Genome Sequence Information (bio-informatics)

g. Development of an Animal Trait Ontology - Creating a common language in animal genomics and

tools to exploit information across species

h. Boar Taint

i. Genetic Improvement of Robustness and Disease Resistance in Aquaculture Breeding Programmes

j. Improve Genetic and Genomic Basis of Aquaculture Fish Species for Coping with New

Vegetable Feed Sources

k. Sustainable Low-input systems of Reproduction in Ruminants

l. Farm Animal Genetic Diversity Access and Benefit Sharing

m. Animal Genetic Diversity Laboratories

n. Innovation Implementation - Lifelong learning post qualification scheme

a. Reproduction - Sustainable robust farm animal reproduction systems

Context : In the 21st

century, Europe is facing the challenge of competing effectively with animal product

imports from low cost overseas economies, and providing consumers with affordable animal products

that meet modern European standards of safety and ethics. Achieving good reproductive performance is

an essential component of any efficient system of production. Fertility is an important determinant of

lifetime productive efficiency and survival, and also the health and welfare status of farm animals. Good

fertility is important also in reducing the effects of animal agriculture on the environment. In addition,

genomic selection is today implemented in Europe as a new and rapidly developing technology with the

potential to deliver unprecedented rates of genetic gain in cattle. However, with the possibilities for an

improved genetic gain there are also major concerns that unwanted effects, through correlated selection

responses, may develop as fast. There is therefore a need for genomic assisted evaluation, to be based on

characters important for animal health, longevity and welfare, and of methods for implementation of

genomic selection to safeguard a sustainable use of this new technology.

In this context, fertility and development of optimized breeding and reproductive strategies is crucial to

limit the higher risk for increased inbreeding and reduced biodiversity that may be associated with

genomic selection.

Objectives : This multidisciplinary project focuses on developing strategies to improve reproductive

performance in farm animals in an ethical and sustainable manner. Advantage will be taken from this to

develop breeding strategies to implement multiple traits based genetic schemes that will answer the

demand for preservation of biodiversity.

Proposed Actions : Improved understanding of the underlying physiological basis of (sub)fertility using

“omics” approaches with relevant and novel animal models is necessary. Areas of relevance for

investigation include – but are not limited to – oestrus expression, oocyte competence and fertilization,

embryo developmental competence, uterine environment, maternal recognition of pregnancy, nutrient

partitioning and bioenergetic status. Deriving the capability to link new knowledge from “omic”

techniques to genetic selection programmes is encouraged. It is well established that nutrition plays an

important role in regulating reproductive efficiency in all animals. Development of nutrition and

management strategies that will reduce or eliminate the shortfall between nutrient intake and nutrient

output (milk, meat, eggs etc), thereby promoting improved reproductive performance, is desired.

Evaluation of semen characteristics and reproduction technologies to maximize fertility is required.

Modern IT based approaches to automate the management of reproduction replacing the use of

hormones for heat induction are sought. Practical solutions stemming from better understanding the

physiological mechanisms that regulate metabolism, ovarian function, uterine environment and

embryonic development, can be part of this multidisciplinary project together with a more basic approach

to understand the interactions involved in the control of fertility. This can be combined with the

development of optimized reproductive scenarios based or not on the use of currently available or arising

embryo based biotechnologies to define the best breeding strategies to implement sustainable genetic

schemes. This may involve technical-economical simulations in relation with the preservation of

biodiversity and exchanges with bodies representing/relaying social demand.

Justification: Sustainability encompasses a balance of economy, environment and society. The project run

under this topic aims at addressing this balance and will contribute to the objective of sustainable

production and management of farming in two ways.

It will provide new markers for fertility and new methods to improve fertility making the system of

production more efficient. Through the identification of optimized reproductive and breeding strategies,

this will allow the development of efficient and well balanced genetic schemes for many traits that fits

with EU policy in terms of welfare and preservation of biodiversity.

The development of these strategies will also reduce undesirable side effects in relation with the

maintenance of additional animals under inefficient production systems. The project will also address

questions in relation with climatic changes.

Contribution to EU policy objectives

Common agricultural policy

Preservation of biodiversity

EU research potential

Europe is one of the leaders in genomic selection and selecting for multiple traits, especially for

reproductive traits. This project will provide the stimulus to move to the next phase to maintain its lead

for the future.

EU added value

Although there is growing interest in several European countries in the subject of sustainable methods to

select for fertility and other functional traits current efforts are dispersed. This proposal would allow

many teams to join forces towards a shared objective. Given the complexity and the technical needs the

specialized and complementary expertise of different European laboratories is crucial and an EU funding

of a joint research program is thus justified.

Funding Scheme: Large collaborative project

Expected impact: Sustainable production and management of biological resources, production of

healthier, safer and higher quality food. Improved welfare of farm animals by selecting the most

appropriate type of animal for the production circumstances. Optimization of the management of

reproduction and it’s influences, and better understanding of the mechanisms in the animal that influence

reproduction characteristics. Use of reproductive strategies to optimize genetic schemes for the sake of

efficient, well balanced and sustainable selection for functional traits (health, longevity, welfare).

Fit for SME? Yes

b. Social Interactions - Pigs and poultry and aquaculture – housing – welfare – social interactions

Social interactions are present everywhere in the living world. In livestock, social interactions can harm

animal welfare and reduce productivity. In laying hens, for example, cannibalism causes mortality, while

aggression in pigs causes tail biting and reduces growth. To improve the welfare and productivity of

livestock populations, we need to understand better the genetics of social interactions. Farm animals are

increasingly kept in groups which increases the importance of understanding consequences of social

interactions.

Classical quantitative genetic theory does not take into account social interactions with regard to

response to artificial selection. As a consequence, we do not know how to design genetic selection

programmes that will improve traits affected by social interactions. Recently, it has been demonstrated

that social interactions can substantially increase heritable variance in trait values. However, the

statistical models are not yet adequate to take social interaction into account. Further development of

the theory, statistical models and understanding of social interaction is needed to ensure that social

interactions can be taken into account properly.

The goal of this project, is to better understand the inheritance of traits affected by social interactions in

commercial crossbred populations of poultry and pigs, and how this knowledge can be used to improve

selection strategies, and for aquabreeding the opportunities to design specific structures based on large

family sizes.

This project will build on theoretical knowledge of the inheritance of socially-affected traits and statistical

methods for estimating social genetic effects. Statistical methods will be extended to allow estimation of

breeding values of purebred animals for social performance of their crossbred offspring. Data analysis will

focus on quantifying the magnitude of social genetic effects for crossbred performance, and on estimating

the effects of group size and feeding level on social genetic effects. Moreover, theory will be developed to

predict how traits affected by social interactions will respond to artificial selection in commercial breeding

programmes for crossbred performance.

Funding scheme: Large collaborative project

Expected impact: Designing and operating animal breeding programmes requires a sound understanding

of the genetic mechanisms underlying variation among animals. The current genetic selection

methodologies are not yet equipped to include social interactions among individuals. Farm animals like

pigs and poultry and fishes, however, are (increasingly) kept in groups in which social interactions not only

reduce growth and productivity, but can also negatively affect welfare and vitality – this project provides

the tools to make better finetuned balanced sustainable animal breeding programmes. For optimal animal

production, understanding how to reduce harmful social interactions among individuals in order to

improve animal welfare and productivity is of critical importance. This project will yield both fundamental

scientific knowledge and methods and tools that can be implemented in commercial breeding

programmes. Using these new breeding strategies, breeding companies can improve traits affected by

social interactions among individuals, resulting in improved animal welfare and productivity.

Fit for SME? Important to have significant contributions from industries, not specifically

SMEs, or umbrella organisations

c. Breeding Goals to answer Climate Change and Food Security

Animal breeding is a long term activity – it needs to be planned well ahead. The concept of sustainability

in animal breeding has been worked out in the beginning of this decade by cooperating groups of

breeders, scientists, welfare organisation, ethicists, sociologists and economists. Not one aspect makes

breeding sustainable, but the whole set – the balanced choices for the various markets. The set of

sustainability subjects for which animal breeding can make a difference consists of: food safety, welfare

and health, efficiency, environment, product quality and genetic diversity. They are all interlinked.

Similarly animal welfare is the result of the many different aspects that define it. Very importantly, as for

other aspects in breeding, there are minimum requirements – thresholds that every individual selected

animal has to meet.In this project national and international animal breeding organisations including - but

not limited to - ruminants, pig, poultry, aquaculture will come together to discuss breeding goals, based

on white papers on climate change and food security designed by the FABRE TP expert groups, and

including input from stakeholders and socio-economy/society. Workshops will be organised to outline

what is ongoing, what are the consequences, what are the opportunities to improve breeding to answer

the consequences of climate change and food security. From the results of the workshops, research and

industry scientists from breeding and reproduction in cooperation, will design for each species two

climate change and two food security scenarios, and one answering the challenges of both, and indicate

the necessary science, society and regulatory climate to achieve these. The scenarios will be discussed

with an audience of industry, science and balanced society input from environment,

sustainability/balance/welfare/ethics.

Funding scheme: Coordinated Action

Expected impact: Globally animal protein consumption will be increasing in the next 15-20 years due to

the demand driven livestock revolution where the consumption will increase in the developing economies

as it has been doing in the developed world during the last 50 years, especially in Asia, Africa and South

America, and so will animal production. Animal breeding must contribute to this huge increase by

providing genetics that can sustain this production increase with less input per kg of animal protein. The

expected climate change will increase the need for genetics that are fit for high production efficiency

under less favourable conditions than in Europe and North America.

To be able to answer the global consumer driven demand for animal products, and at the same time

health, welfare, safety, biodiversity and environmental needs, breeders need to continuously improve the

focus, functionality and broadness of their breeding programmes and have access to the best feed back

mechanisms. With climate change production areas and ways of production may change. Responsible

development of phenotypes, husbandry and stockmanship will be necessary to meet these global

developments in a sustainable i.e. environmentally and welfare friendly, healthy, and safe way. The

concept of welfare – the well being of the animal in its broad sense - as an intrinsic and important item for

breeding companies needs to be communicated clearly and in a transparent way.

Fit for SME? Yes, for SME association and midsized companies

d. Use of Genomic Information in Commercial Populations - Opportunities to improve robustness

In recent decades, genetic improvement of farm animals has contributed to meeting the needs of the

growing world population. Genetic improvement programmes exploit genetic variation among animals.

Improvements have been made in traits by selection based on estimated breeding values.

Over the past few years, we have seen spectacular advancements in molecular genetics. One recent

advancement is high-density single-nucleotide polymorphism (SNP) technology, which enables genotyping

of an individual at many thousands of SNPs at low cost in some of the major species. It is anticipated, that

in a couple of years, an entire individual genome will be sequenced for less than 1000 US$. These recent

advancements in the field of molecular genetics will enable revolutionary changes in genetic analysis of

populations and in genetic improvement programmes. We are at the threshold of an era in which these

advancements will require us to revise completely our assumptions about which traits can be addressed

by breeding, and what impact breeding may have on populations. Paradoxically, current quantitative

genetic models and tools to use molecular data lag behind the amount of data accumulated. In many farm

animal species, in particular fish and shellfish, pigs and poultry, that have very high fecundity and many

tiers, molecular information offers a unique opportunity to exploit data collected on animals that is no

longer constrained by the need for pedigree registration or reared in commercial conditions. With the

recent development of genomic tools for aquaculture species, pigs and poultry, now is the time to

investigate these opportunities.

The state of the art of animal breeding is based largely on quantitative genetics. Examples of the value of

molecular information for animal breeding has been demonstrated, in particular in the use of genome-

wide evaluation in dairy cattle and in monitoring population structure (Flint and Woolliams, 2008,

Goddard and Hayes, 2009). In the near future our assumptions of which traits can be addressed by

breeding, how breeding values are estimated, and what impact breeding may have needs to be

completely revised. In future breeding schemes, phenotypic and genetic information collected in a

population can be exploited without the need of pedigree information. This offers unique opportunities to

improve the robustness by exploiting information collected in the slaughter house or under field

conditions where pedigree information on animals is missing.

In more detail the objectives are:

1. to develop breeding schemes to improve robustness of animals;

2. to better use information collected in commercial unpedigreed or pedigreed populations.

Information collected on individuals at commercial farms, for example, can be used to predict

genomic-assisted breeding values of selection candidates in the nucleus, using genomic information

on nucleus and commercial animals. This ability circumvents the need for pedigree registration on

commercial farms and avoids loss in genetic response due to genotype by environment interaction

between nucleus and commercial farms;

3. to use information more efficiently on traits with low frequency, by exploiting the power offered by

the large size of commercial populations;

4. to develop genomic SNP chips adapted for genetic indexation about robustness.

The methods will form the basic tools to design innovative breeding programmes that exploit

within- and/or between-breed genetic variance, to generate maximum genetic improvement while

restricting loss of genetic variance. Consequences of different genomics-assisted breeding

strategies for aquaculture species, pigs and poultry will be evaluated using computer simulation

and analysis of (experimental) data.

Funding Scheme: Large collaborative project

Expected Impact: Robust animals are crucial to sustainable, welfare friendly and economically viable

animal production. Now, and more so in the future when climate change may change the environment of

many animals. Until now, breeding was based on pedigree information and quantitative genetics. This

included relatively few traits, costly gathered, and resulted in ever larger breeding goals – but still limited

by the gathering of data and the keeping of family information. This project will develop fundamentally

new breeding schemes, using information without the need to have full pedigree information, especially

from traits with low frequency – these are specifically health and welfare related traits, and other traits

improving the robustness of animals. Not only newly domesticated animals, fishes, poultry and pigs will

profit, when the tools become more mature, they will serve the many cattle, sheep, goat, horse and other

animal populations in countries where ancestor information is only limitedly available.

Fit for SME? Yes, also midsized companies

e. Monogastrics Feed Efficiency - Efficiency of livestock digestive systems and reduction of the

ecological footprint through a combination of systems biology, 'omics' and nutrition

Objective: A key element of Europe 2020 is the reduction of greenhouse gas emissions. There is an urgent

requirement to improve the efficiency of livestock production and reduce the environmental footprint of

the sector. This need is particularly acute as it occurs against a backdrop of increasing global demand for

animal products.

The gut is responsible for the efficient digestion and absorption of feed and nutrients, however this also

results in the production of greenhouse gases such as CH4, N2O & CO2. Both the microbial flora of the gut

and feeding regime exert a profound influence on digestive efficiency and greenhouse gas production.

Increased understanding of the biology of the monogastric gut will offer new approaches to improve feed

efficiency whilst simultaneously reducing greenhouse gas emission.

The availability of the genome sequences of key monogastric livestock species, combined with recent

advances in understanding of the interactions between bacterial species and the gut wall, make more

detailed studies possible of the interaction between the host and its gut flora. Metagenomics techniques

can be applied to the gut microbiome to study the diversity of microbial flora and the efficiency of

digestion. Understanding the factors that influence monogastric digestion is a first step in developing

improved production systems.

The project will bring together systems biology, metagenomics, microbiology of both host and microflora

and genetics to better understand the network of interactions between gut microflora, feed regime, and

the host genome. The project will determine how these interactions influence greenhouse gas

production, feed efficiency and product quality and safety.

The project will focus on Pigs and Poultry to identify key indicator traits with which to measure the

efficiency of digestion and greenhouse gas production, and to explore the genetic basis of these traits. It

should both complement and collaborate with related EC projects dealing with livestock gut function for

improved nutritional efficiency or environmental footprint.

The project should include the development of bioinformatic tools for use by scientists beyond the

beneficiaries in the project. The project should include industries, in particular SMEs, to enable close

interaction and fine tuning to ensure that the knowledge generated will be converted into tools and

technologies for use by industry and SMEs.

Funding scheme: Collaborative Project-IP, 6 Million Euros

Expected impact: The expected outcomes of this research are improved understanding of the variation in

the monogastric digestive system, new systems models and tools applicable to selective breeding and

nutrition for improved gut health and functionality, reduced greenhouse gas emission and improved

product quality. This is a multi-disciplinary project which will improve collaboration between different

disciplines of animal production and between academia and industry.

Fit for SME? Yes, various industries. It is viewed that the participation of relevant industrial partners, not

specifically SMEs, is essential to achieve the expected impact of the research to be undertaken.

Therefore, the topic is designed to encourage SME and industry (mainly midsized company) efforts

towards research and innovation representing the complete value added of the targeted sectors.

f. Utilization of Whole Genome Sequence Information (bio-informatics)

Within the next few years, the opportunity will develop to analyze both the whole animal phenotype

association and basic-biology phenotype association within the light of protein networks and biological

pathways: this will require, next to large computing power, the development of new analysis tools.

Life sciences and in particular genomics have seen a huge data explosion and ongoing developments (e.g.

new sequencing technology) show that data accumulation will further increase rather than stabilize.

Improvement of existing tools and the development of new tools to efficiently handle this data and to

enable the combined analyses of different data resources are clearly needed. Of particular importance to

farm animals is the efficient use of new sequencing technology in combination with the existing draft

genome sequences to create high quality sequence assemblies of these genomes. Also, the genetic

structures of farm and companion animal populations/breeds offer unique possibilities for the dissection

of complex genetic traits. This project will include the development of specialized tools specifically

designed to utilise the population structure and history of livestock populations. Requirements are, that

the infrastructure needs to be scalable as data volumes will continue to grow, there needs to be a close

relationship between the biologists and the computing scientists/informaticians, existing systems for

human or model organism should be used as a basis. The project must include an important and

integrated training part, involving the education of bio-informaticians, and the improvement of

bioinformatics skills of biologists. The emphasis should be to stimulate the use of the large amounts of

data. The project must aim to develop the most effective solution for the management and analysis of

data, in robust production quality systems (rather than on quick-fix provisional systems developed in

individual research laboratories), focusing on the need of the users, rather than on cutting edge

computing science.

Funding Scheme: Large collaborative project

Expected Impact: Life sciences and in particular genomics have seen a tremendous increase in data

generation both in terms of volume and complexity. Farm and companion animals provide a rich resource

of different well defined breeds, with a variety of highly interesting phenotypes. Cataloguing intra-species

variation is of tremendous importance in farm animals and a main research objective in many industry

funded research projects. The large scale use of high density SNP chips as well as the analysis of copy

number variation (CNV) is growing exponentially in farm animals. The association of intra-species with

functional variation is a key strength within Europe. These associations are what one needs to discover in

order to be able to exploit scientific knowledge to improve animal health, welfare and productivity.

To fully benefit from the growing amount of data generated for farm and other animals of veterinary

significance it is essential that the available infrastructure to specifically address the data needs within

these species are further improved, and that a strong bioinformatics research community targeting

research questions relevant to those species is being established. This will not only be essential to support

agricultural/veterinary research but it will also further extend our knowledge pertaining to human

biomedical research as accurate primary annotation information from farmed animals can be used to

‘reverse the flow’ of data to illuminate the human genome.

This project will result in increased transatlantic collaboration – the subject has been discussed and

proposed during the EC US discussion on bioinformatics.

g. Development of an Animal Trait Ontology - Creating a common language in animal genomics and

tools to exploit information across species

Genomics will enable farm animal breeding to select in a more sustainable and competitive way. To fully

exploit the potential of comparative genomics it will be essential to describe the biology, physiology and

specific traits in farm animals using a common structured universal language. A suitable Ontology

(comprising all necessary software tools, database infrastructure and content) is necessary to create a

common language and link knowledge at the gene and pathway level with the relevant traits in the

various animal breeding programmes. This will involve the use of (functional) genomics data from across

species, to optimise the design of new genomics projects and to improve the interpretation and use of the

results. In particular, exploiting the increasing amount of information across species, including human,

mouse and rat, and across fields, is a major challenge. The development of a trait ontology that can be

linked to and is in agreement with trait ontologies being developed in human and model organisms

therefore is essential.

Although the first steps towards a farm animal trait ontology have been taken within the EU funded

projects EADGENE and SABRE, in close connection with the global animal trait ontology exercise (INRA-

France, ISU-US), more input is needed within this area.

The project will further build on the work performed, in collaboration with the global animal trait

ontology network, in order to

i) further develop a tool for the collection of information on traits and relationships between traits that is

based on a common framework across species;

ii) develop a repository for the definitions of traits and relationships between traits;

iii) develop a repository for quantitative trait information;

iv) collect information on traits for core farm animal breeding species (cattle, pigs, poultry, salmonides,

...);

v) define and create the links between the ATO industry terms (traits used) and the terms used in

biological databases and ontologies;

vi) identify and fine-tune the available tools and those that are being developed by the research

community, in particular human, mouse and rat, to exploit the growing amount of information in

biological and genomic data bases for animal breeding projects;

vii) test the ATO and tools, and

viii) develop projects with SMEs to demonstrate the value to the breeding community and provide

feedback.

Training sessions for industries (SMEs and midcap) need to be an integral part of the project.

Funding scheme: Collaborative Project (small or medium-scale focused research project).

Expected impact: The overall objective is to strengthen the innovation capacity of European animal

breeding SMEs and midsized companies, and their ability to develop new technology based products and

markets by more efficiently exploiting research results across species and acquiring technological know-

how, bridging the gap between research and innovation. The expected outcomes of this research is a

common language on animal traits aiming at the improved uptake of results of genomics research across

species. This is a multi-disciplinary project which will improve collaboration between different disciplines

of animal production and between academia and industry, in particular SMEs. A strong participation of

industry and SMEs in the project itself will ensure that the knowledge generated will be converted into

tools and technologies for use by industry, including SMEs. The challenge for farm animal breeding SMEs

in Europe, often serving niche markets, is to be able to utilise information derived from genomic studies in

their breeding programme in a cost effective way, so that they can compete, survive, and develop a

sustainable programme. The trend is for larger organisations to leverage the genomics investments across

species and across larger segments of the market. It will be important for them to integrate genomics into

sustainable breeding programmes as soon as possible in order to stay in business and maintain/develop

reasonable market shares at reasonable cost and at the same time to preserve genetic diversity.

Fit for SMEs? Yes, SME umbrellas and Midsized companies

h. Boar Taint

Numerous methods to solve the problem of boar taint in non-castrated male slaughter pigs have been

elaborated such as castration with analgesia in combination with castration, castration with local

anesthesia, castration with inhalation anesthesia, vaccination to create immunity against hormones

(Improvac®), responsible for the testicular development and sexual function, sexing of semen to produce

exclusively female offspring, slaughter of whole boars in combination with identification of so called

“stinkers” at the slaughter line, what is performed either by humane professional sniffers or by

automated boar taint detection and last but not least the genetic selection against boar taint compounds.

The conclusion of these attempts is that research shall focus on the genetic selection without castration

and having no negative effects on reproduction parameters of boars or female reproduction traits. It is

expected that a genetic contribution is important. Recent advancements in genomic technology offer new

opportunities to address for instance the sequencing of the genome, which allows screening of billions of

nucleotides within entire genomes of pigs to identify specific SNPs (Single Nucleotide Polymorphisms)

which may affect boar taint. Several chromosomal regions associated with boar taint have already been

identified through research within the SABRE project. The strategy of identification of functional

mutations in combination with functional SNP panel will offer the opportunity to select practically and

effectively against boar taint. This project aims to identify genes and mutations which are related to boar

taint, to integrate genomic information in selection methods for commercial breeding programmes and to

provide genomic selection tools and strategies to Midsized companies and to SMEs for the integration in

pig breeding. The training and the transfer of knowledge for the effective use of the recommended

breeding strategies and tools will be provided.

Funding Scheme: Collaborative Project

Expected Impact: In most European countries the castration of male piglets is a common practice to

prevent boar taint . The practice is highly undesirable from the animal welfare point of view as well as pig

production perspectives, except except for the production of traditional specialities which require heavier

pigs and for which no alternatives, such as immunocastration, seem available at the moment.. Due to lack

of a practical and economic solution for the prevention of boar taint, which is smelled as an unpleasant

odour arising from pork of entire males. This project will take an active role in offering an effective,

economic and sustainable genetic solution to the problem.

Fit for SMEs? Yes, SME umbrellas and Midsized companies

i. Genetic Improvement of Robustness and Disease Resistance in Aquaculture Breeding Programmes

Background: Aquaculture is a food production system, which is in tight relation to the aquatic

environment, because aquaculture species are cold-blooded, and gill breathers. Furthermore, some are

planktonovorous (shellfish). However, aquaculture farms have unavoidable fluctuations in environmental

conditions (temperature, oxygen levels, social interactions from crowding, pathogens). Global climatic

change is expected to generate even more environmental variation at the farm level, while global

economic constraints will tend to reduce the use of top quality feedstuffs. Additionally, in most species,

fish are bred in one environment, but then sold all over Europe for ongrowing in a variety of

environmental conditions. Hence, individuals that have high fitness and thus are robust to increasingly

more variable environmental parameters at the levels of macro-environment (between farm

environments) and the micro-environment (the within-farm environment) are needed, and are crucial to

the successful development of aquaculture species. The aim of this project is to genetically improve

robustness and specific disease resistance in aquaculture species. Today, an increasing part of the

European aquaculture production is based on genetically improved stocks. However, traits related to

animal robustness are only rarely included. Robustness traits shall be defined on the basis of

physiological, neural and behavioural measures, some developed using different –omics methodologies,

e.g. response to sub-clinical infections and fluctuations in environmental stressors (temperature, oxygen

levels), susceptibility to cardio-vascular diseases and welfare related traits, including social interactions

traits. Predictors of disease resistance and robustness measurable on a large numbers of individuals and

at a fine scale, with emphasis on non-lethal measurements, shall be developed. The effects of the

robustness traits shall be estimated as well as the interaction between them, and with disease and

production traits. Genotype x environment interactions over time and space shall be estimated.

Breeding and genetics is a field that increasingly incorporates genomics tools in the genetic evaluation,

with the use of marker-based pedigrees and the opportunities to develop genomic selection with

emerging high-throughput genome sequencing data. These genomic methodologies will be further

developed in this project for the genetic improvement of robustness and specific disease resistance in

aquaculture species.

Funding scheme: Large collaborative project

Expected impact: Robustness and disease resistance traits are currently not included in European

aquaculture breeding programmes (except in some Atlantic salmon and cod breeding programmes), and

this project will contribute to change that. Increased disease resistance and robustness will reduce

chemical/medical treatments of diseased individuals, improve the overall welfare levels in aquaculture

populations, and finally increase the profitability of aquaculture. This project will produce generic tools for

genetic improvement of robustness and disease resistance that can be used for all aquaculture species.

Specific research is needed, since aquaculture cannot fully benefit from advances in robustness traits in

terrestrial livestock species, since aquaculture species have very specific features in biology and rearing

methodologies (cold-blooded species, high dependency on environmental oxygen levels, little control on

rearing environment parameters). At present, production of some European aquaculture species is

reduced due to climatic changes. Increased genetic robustness and disease resistance will also safeguard

the populations against the effects of climatic changes. However, increased aquaculture production is

necessary in order to reduce the amount of imported products to Europe and the dependency on capture

fishing for fish products consumed in Europe (Synthesis of the Consultation on the Reform of the

Common Fisheries Policy, April 2010).

Results that aid the development of prioritised areas for maintaining sustainability of European

aquaculture will be created. When focussing on a multi-species project, all geographical areas of EU can

be included, which justifies funding by EU. Moreover, as selected fingerlings and spat are widely traded

among EU countries, a European approach is needed to take into account the needs of both the breeding

and the ongrowing industry.

Fit for SMEs? Yes

j. Improve Genetic and Genomic Basis of Aquaculture Fish Species for coping with New Vegetable Feed

Sources

The aquaculture development of carnivorous fish species requires increased utilisation of still emerging

vegetable feed sources to limit impact of fisheries on wild fish stocks. However, vegetable oils can contain

specific toxins and bioactive compounds and vegetable protein can contain specific toxins and anti-

nutritional compounds that may affect feed efficiency, processing yields and fish health and welfare

during the whole life-cycle, as well as the quality of the product. This project will investigate the potential

of selective breeding of aquaculture species and genomic information applied to extended phenotypes in

various environments and rearing systems to develop breeding programmes that maximise the utilization

of vegetable ingredients, while maintaining high levels of product quality and fish health and welfare.

Funding scheme: Large collaborative project

Expected impact: Development of European aquaculture industry requires a decrease in its utilisation of

marine oil and protein that are obtained by exploitation of limited natural marine stocks in order to limit the

ecological footprint of aquaculture. Substitution by vegetable feed sources is currently being addressed only

by nutritional approaches. This project will further decrease the utilisation of marine oil and protein by

adapting fish to this major change, through the investigation of long term breeding strategies that aim at

minimizing the utilization of marine feed sources while maintaining high levels of feed efficiency, product

quality and health for fish and human consumers.

k. Sustainable Low-input Systems of Reproduction in Ruminants

Introduction: The challenge facing European animal production in the 21st

century is to compete

effectively with animal products from low cost overseas economies and provide consumers with

affordable animal products that meet modern European standards of safety and ethics. This requires an

alternative to the high input approach to animal production that will focus on production efficiency and

show regard for the environment, animal welfare and product safety. A high rate of reproduction is the

essential first step for efficient production in ruminants. Research will focus on strategies to reduce or

eliminate use of reproductive hormones, and to minimize the requirement for medications currently used

to manage the health and welfare issues associated with high input management systems. It will provide a

deeper understanding of the links between genetics and physiology with respect to reproductive

performance, animal welfare, and environmental impact. The project will build on these findings to

deliver efficient, low input, strategies for the management of reproduction in ruminant species that are

ethical and sustainable. Solutions that incorporate innovative non-invasive, precision technologies based

on modern IT based approaches to automate the management of reproduction and welfare will be

particularly welcome.

Objectives: Understand how genetics, environment, diet and socio-sexual behaviour affect reproduction

and how they interact with each other. Explore how this knowledge can be used to develop efficient, low

input methods to control fertility that are sustainable and ethical.

Innovative character and solution to problems: The reduction in the use of inputs, such as reproductive

hormones and antibiotics, will make the animals more dependent upon the environment (i.e.,

management, nutrition, welfare, etc). The effects of environmental factors on reproductive efficiency,

however, are only partly understood. Because these environmental effects are multi-factorial the

understanding of their interactions, overlooked because of the focus on hormones, is critical to develop

sustainable strategies for high rates of reproduction in controlled animal production systems.

Justification: This topic will contribute to the objective of sustainable production and management of

farming in two ways. It will reduce exogenous inputs (hormones and medications) and it will also

contribute to a reduction of labour costs through the innovative use of automated measurements.

Contribution to EU policy objectives

Common agricultural policy

Organic farming action plan

Elimination of food-borne risks (hormone residues)

EU research potential

Europe has provided the lead in hormone-assisted reproduction and this project will provide the stimulus

to move to the next phase to maintain its lead for the future.

EU added value

Although there is growing interest in several European countries in the subject of sustainable methods to

manipulate fertility, current efforts are dispersed. This proposal would allow many teams to join forces

towards a shared objective. Given the complexity of the environmental effects on reproduction and the

specialized and complimentary expertise of different European laboratories, EU funding of a joint

research programme is justified.

Funding scheme: Large collaborative project

Expected impact: Sustainable production and management of biological resources, production of

healthier, safer and higher quality food taking into account animal reproductive performance, animal

welfare, and environmental impacts.

l. Farm Animal Genetic Diversity Access and Benefit Sharing

This project will make an inventarisation of the (inter)national Farm Animal Genetic Resources (AnGR) and

knowledge sharing efforts in animal breeding and genetics, develop a focal point for Farm AnGR research

efforts linking the international cattle, pig, poultry and aquaculture breeding organizations, FAO, and the

focal point(s) of research scientists. The focal point will aim to finetune and link national and

international animal genetic research efforts, with the expertise and knowledge of animal cattle, pig,

poultry and aquaculture breeding organizations. The advantage for small breeding organizations will be

increased access and involvement in this type of effort, offering the possibility of international networking

and setting up quality genetic resource schemes, the advantage for larger breeding organizations is

streamlining of the various AnGR requests and avoidance of overlap.

Funding Scheme: Coordination Project

Expected Impact: Inventarisation of knowledge and expertise transfer from larger and specialized

research and businesses to those in rare breeds and small countries. Most effective use of the available

resources (research money, expertise, knowledge), avoid overlap, and ensure that breeding organizations

can be addressed effectively. Under the United Nations Access and Benefit Sharing Committee of the

Convention of Biological Diversity an international regime on access and benefit sharing is being

negotiated, and the plant and animal genetic resources may be dealt with by FAO. The FAO Commission

on Genetic Resources has the mandate for genetic resources on food and agriculture. In animal breeding

the capital that can be used is in the experience and knowledge of the internationally organised breeding

organizations in cattle, pig, poultry and aquaculture, and the networks of scientists European Focal Point

(of animal genetic resources), and European and international organizations.

m. Animal Genetic Diversity Laboratories

The project will, in order to optimise methods for the maintenance of farm animal diversity and for the

exploitation of useful genetic variation in breeding programmes, within and across breeds, anticipate the

latest development in high-throughput genomic technologies (i.e. dense SNP chips, CNV (copy number

variation) assays and re-sequencing). To improve measurement of biodiversity the project will develop

new tools to capture more accurate information on neutral and functional variation in livestock genomes.

It will improve methods for prioritisation for conservation that take account of these new genomic

measurement tools and simultaneously exploit phenotypic, farming-system, socio-economic and

geographic information, and develop more cost-effective strategies for bio-banking that can be integrated

into a portfolio of practical strategies for optimised in vivo, ex situ and in vitro conservation. For improved

exploitation of biodiversity new methods for professional breeding organisations will be made, to

optimise long-term balanced multi-trait selection at the same time as maintaining biodiversity. In

addition, new approaches to improve the efficiency of composite and cross breeding programmes will be

developed, with wide application across species. Training and knowledge dissemination will be part of the

project.

Funding Scheme: Collaborative Project

Expected Impact: Coordination among molecular biology laboratories will speed up data production and

analysis, reduce cost and promote synergies and coordinated development of technologies, hence

keeping European scientists at the forefront of research in AnGR. Integration of data, databases and

pipelines of data analysis will enhance the efficiency and effectiveness of research, hence promoting

expansion of scientific knowledge and its application in the field of animal genetic resource management.

Coordination among gene banks will initiate the process of creating an integrated European gene and

biological material bank network for long-term conservation of animal genetic resources that is fully

accessible to research and for conservation purposes.

n. Innovation Implementation - Lifelong learning post qualification scheme

The project will facilitate the existing educational/post qualification needs in the knowledge intensive

field of sustainable animal breeding and reproduction. The need for a complete, integrated, easy-to-

access European system where lifelong learning opportunities can be easily explored and utilized by end

users (scientists, professionals, technicians, etc) has been clearly identified. The Post Quality Framework

needs to be designed to fulfil these needs by building on existing educational offers, and by exploiting

successful outputs of projects and initiatives in the field. It will include a review on the current lifelong

learning offer and demand in the field of sustainable animal breeding & reproduction at EU level, the

development of a framework combining the existing education/training offer in the EU, thus creating a

virtual educational ‘one-stop shop’ for people in the sector, and the development of a Post Qualification

System including guidelines, standards and quality indicators. Dissemination will be an intrinsic element,

implemented through various activities: publications, presentations, the project website, targeted

meetings. Linguistic variability will be considered as far as possible in the project. A concrete business plan

will be followed throughout the project, while continuous monitoring and evaluation (internal and

external) shall guarantee the quality of the Framework. Indication must be made how the animal breeding

pilot can be worked out for animal science. Animal breeding and reproduction are a very knowledge

intensive area and knowledge is very much developed internationally – more and more people will need

to update themselves, international careers become more common, breeding organisations employ

people from all continents – a recognised lifelong learning standard is much needed.

Funding Scheme: Coordination Project

Expected impact: An international qualification framework for lifelong learning, based on existing and

upcoming targeted education is a prerequisite for the international availability and quality of animal

breeding specialists. This is necessary to ensure good researchers and practitioners in this quickly evolving

field. The Framework will provide increased opportunities for individual animal breeding scientists and

professionals via the accredited knowledge and professional skills, and provide education providers with

advanced networking, transparency and international recognition, whilst organisations in the sector will

benefit from building on their internal knowledge and capacities. The network will add value to the

knowledge base of the EU animal breeding sector and will thus enhance its competitiveness.

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