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Genotype and Environment contributing to the sustainability of dairy cow production systems through the optimal integration of genomic selection and novel management protocols based on the development

Periodic Report Summary 2 - GPLUSE (Genotype and Environment contributing to the sustainability of dairy cow production systems through the optimal integration of genomic selection and novel management protocols based on the development)

Project Context and Objectives:
GplusE was funded under an FP7 call that focused on developing and exploiting genomic data and analytical tools, new phenotyping approaches and breeding strategies for sustainable animal production systems. GplusE aims to identify those genotypes that control biological variation of the important phenotypes of dairy cows, to appreciate how these are influenced by environmental and management factors, and thus to allow more informed and accurate use of Genomic Selection (GS). The specific phenotypes of interest are production (milk yield and milk quality), cow health and cow physiological status including fertility and environmental footprint. The combined approach will promote expansion of the EU dairy industry in a way which is profitable, environmentally sustainable and which improves cow health and welfare.
Both GS and management systems are dependent on accurate phenotype description based on easily accessible data and samples. The description of animal phenotypes in GplusE are based on traditional direct measures of performance, disease and fertility. In addition, conceptually proven biomarkers/indicators of rumen function and efficiency, of physiological and metabolic imbalances and of subclinical disease and fertility are being used. The preferred matrix in which to measure the biomarkers is milk, as it is more easily accessible than blood and allows low-cost, automated repeat sampling using recently developed ‘in-line’ sampling and analytical technologies. Accordingly, within this project, milk is being validated as an appropriate matrix for future industry-wide application through the use of a common dataset of traditional and novel phenotypes collected from a large population of primarily Holstein dairy cows under a variety of well characterized management systems. The data aims to provide a strong foundation through which to improve both GS and management systems. Additionally, a better understanding of the underlying biology will enable GS to be continually adapted to produce cows that perform well under differing environmental conditions. Increasing use of the phenotype data in dairy management will facilitate the earlier identification of disease and the adjustment of real-time feeding systems according to the physiological status of the individual cow. This will not only improve production efficiency and environmental sustainability but also will promote cow health and welfare, favouring a ‘win-win’ outcome.
To date the project is in month 36 out of 60 and deliverables have been largely met/completed.

Project Results:
Period 1 (M1-18) concentrated on developing and validating easily measured phenotypes (WP2, WP3), preparing for the genome-wide association study (GWAS; WP4), collecting samples for relating molecular phenotypes to genome haplotypes (WP5) and disseminating knowledge (WP9).

Period 2 (M19-36) focused on completion of WP3 animal studies, associated laboratory analyses and a substantial effort on data analyses to get clear outcomes from WP3 to inform WP4 and WP6. Activities in all other WPs are also in progress.

Data Harmonisation (WP2)
Within WP2, mapping of multiple data-streams (MIR, glycans, phenotypic, genotypic) and enabling of data transfer and exchange continued. The IGenoP database for pedigree information and associated genotype data has been established by ICBF.

Phenotypic Associations (WP3)
WP3 was completed with 240 cows enrolled from AU, FBN, AFBI, UCD, CRA-W and CREA, and used to evaluate new phenotypes. Metabolites, MIR and glycan analyses have been completed and tissue samples were provided for WP5. A substantial effort on data analyses has been completed and has informed deliverables 3.1 3.2 and 3.3 which are key to decisions to progress WP4 and WP6.

The GWAS study started in January 2016 (M24), with criteria for selection of the cow populations being defined, herds recruited and the animal studies are now ongoing. An amendment is awaiting decision from the EC to allow budget re-distribution for completion of genotyping and amended phenotyping in WP4.

Relationship between molecular phenotypes for key physiological traits (WP5)
Samples were collected for WP5 (from WP3) and transcriptomic / functional assays are underway for the detailed functional genomic studies. Data are now coming on stream to feed into WP8.

HACCP and EVOP approaches to improve dairy management systems (WP6)
WP6 is well underway with key surveys completed. For HACCP strategies these took the form of Delphi type expert surveys; specific focus is on critical energy balance for dairy cows (identification of risks and associated critical control points).
The EVOP system has focused on concentrate allocation for dairy cows. The objective is to use an EVOP setup (challenge-evaluation-challenge-evaluation) to maximize individual cow marginal milk production to feed concentrate on a weekly basis.
Novel phenoytypes from WP3 will be used in WP6.

Future breeding programmes (WP7)
Background data for dairy production worldwide have been collected from sources such as FAO, Eurostat, DADIS, and WHFF. These include dairy cow populations, Holstein-Friesian populations, dairy holdings, fertiliser application (both organic and inorganic), CO2 and methane emissions and outputs.
An electronic survey on breeding strategies has been created and sent to breeding organisations in Ireland, UK, Belgium and Denmark.

Genome annotation (WP8)
Integration of genomic variation, epigenetics, expression data and phenotypic inferences into an improved bovine genomic annotation is in progress. Linking of bovine, human and other genomes through a synteny-based orthology inference pipeline has been completed. Data will feed in from WP4 and WP5 to allow annotation of various mammalian genomes.

Producing guidelines and disseminating knowledge (WP9)
Social Media: The GplusE website ( along with a twitter and facebook page are kept updated.
Dissemination: Logos, leaflets and posters describing the project were created and distributed to each partner along with templates for presentations and documents. Key dissemination events include presentations at EAAP 2015 (industry engagement session) and EAAP 2016 and ADSA 2016 (Scientific sessions) with further sessions planned for both industry and scientific sessions at EAAP 2017, ISAG 2017 and ADSA 2017. A very successful “Professional Certificate in Bioinformatics” course for 30 animal and veterinary scientists (PhD and post doctoral) was held in May / June 2016 in UCD. Another offering of this course in July 2017 is planned.

Potential Impact:
Expected final results and their potential
The end result of GplusE project will be a comprehensive, integrated identification of genomic –phenotypic associations relevant to dairy production across Europe.
This information will be translated into benefits for animal breeding and management that will considerably improve productivity, efficiency, animal health, welfare and fertility in an environmentally sustainable way. It will also increase biological understanding of the mechanisms by which genotype, environment and their interaction influence performance.

Genomic Selection
During the last five years there has been a revolution in dairy cattle breeding as genomic selection has largely supplanted progeny testing for the identification of elite sires. Both GS and effective management strategies rely on information derived from accurate data on the relevant phenotypes measured in individual animals.
The Encyclopaedia of DNA Elements (ENCODE) project showed that the expression of each coding gene within the human genome is controlled by multiple regulatory sites located both near and distant from it, and that gene regulation is much more complex than was previously recognised. The Holstein cow is the dominant dairy breed worldwide and offers an ideal animal model in which to determine the genetic components responsible for biological trait variation. WP5 will generate ENCODE-like data for the bovine as a public resource that can then be used to improve GS. Offering the wider scientific community access to the results will also be of significant potential benefit to work in other species including man.

Hazard Analysis and Critical Control Point (HACCP) and Evolutionary Operation of Processes (EVOP)
HACCP and EVOP models will be built and validated to improve management “on farm” based on both existing knowledge and newly integrated data identified in WP3.
HACCP has become recognised as a systematic and preventative approach to identify hazards and is the preferred tool to ensure that consumers are provided with safe food in EU. GplusE will develop and validate a decision making management model based on resulting data that can be applied at farm and cow level to improve dairy production on a day to day level.
EVOP has been applied in the manufacturing industry for continual improvement of production processes by making small incremental changes in production factors and procedures. With the existence of in line health indicators the EVOP method is suitable for dynamically optimising the feed ration of the individual cow as well as other key management related strategies.

Breeding Strategy
Using the unique data generated from the GplusE project, new breeding strategies for future breeding of more efficient, environmentally friendly and healthier cows will be proposed and evaluated.

The outcomes of GplusE will be disseminated globally through a combination of the scientific media and direct contact with cattle breeding companies.
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