Elucidation of underlying factors influencing fertility in modern, efficient livestock production through novel epigenomics and metabolomics

The Norwegian breeding companies Geno and Norsvin have through decades conducted systematic breeding of their respective species, focusing on important properties such as growth, meat- and milk production as well as health and fertility. All breeding organizations are now experiencing a paradigm shift due to extended use of genetic information for their selection of breeding animals, enhancing the genetic gain and reducing the generation interval. The main idea of the proposed project is to develop new generic knowledge on factors influencing fertility and sustainable health in modern intensive cattle and swine production. The project aims to expand the knowledge base for sustainable animal breeding and health by introducing new state of the art technology and to strengthen national competence in animal reproduction science. Key questions to be answered is whether use of artificial insemination influence the low-heritable trait fertility, and whether environmental changes and production stress influence fertility and hide genetic disposition. Novel epigenetic and metabolite analyses in combination with semen quality analyses will be applied on samples from selected animals based on existing data on fertility and productivity in breeding programs. Advanced bioinformatics will be performed to reveal possible phenotype correlation to genomics data. Semen quality in bulls of different ages has been studied, both before and after cryopreservation of the semen. The results show that young bulls have semen that tolerates cryopreservation less than what they have only a few months later. Epigenetic analyses show that there is a difference in DNA methylation in semen from the same bulls at different ages, and that these can be related to different genes and pathways of importance for reproductive capacity. Fertility data for relevant bulls have been analysed and compared with other data. Fertility was not affected by age, but there was a significantly higher discarding of semen doses from the youngest group, which is of great importance for production efficiency. Various advanced sperm analyses have been performed on a large semen material from bulls with documented high and low fertility. In this context, a novel methodology has been developed for the analysis of metabolites in frozen semen. This methodology has been applied to all samples from this material. Semen from selected bulls have also been tested in IVF. There were differences between several functional sperm parameters in semen from bulls with different fertility, and also in the case of intracellular metabolites, and metabolomics may prove to be a useful tool for identifying biomarkers for fertility. Further, methodology for application on boar semen has been tested. Metabolomics analysis of sperm and seminal plasma from boars were developed and successfully applied for a selection of samples. The samples were prepared from both undiluted and diluted fresh semen by centrifugation (sperm pellet and supernatant). The analysis included amino acids, amines, markers of oxidative stress (glutathione), fatty acids, cholesterol and high resolution non-targeted analysis. As could be expected, the detected levels were lower in the diluted samples, but the diluter did not cause interference in the analysis. The results are promising as they indicate that diluted samples are suitable for metabolomics analysis - thus enabling large cohort studies to investigate novel biomarkers. Epigenetics from boar semen with varying degrees of DNA breaks (DFI) was examined. Different parameters for measuring DNA integrity were compared and assessed if being correlated with epigenetic DNA methylation. We found that DFI was poorly correlated with the other DNA integrity parameters, which may be an indication that several parameters illuminate different aspects of DNA integrity in general. Furthermore, we found that sperm with varying degrees of DFI had different levels of DNA methylation, suggesting that sperm with higher DFI have several deficiencies in metabolic pathways involved in embryonic development. The project has been a collaboration between Inland University of Applied Sciences, SINTEF, and Geno and Norsvin.

Forskning som bidrar til økt kunnskap om fruktbarhet og avl er ønsket av industripartnerne for økt verdiskapning. Resultatene oppnådd i prosjektet har generert kunnskap om sædproduksjonskapasitet og fruktbarhetsparametere hos okser og råner og gitt ny innsikt hos så vel industripartnerne som hos de involverte forskningsinstitusjonene. Det er blant annet etablert ny metodikk for undersøkelse av frossen sæd som kan bidra til å si noe om befruktningsevnen. Konkret har prosjektet resultert i et PhD-prosjekt med fokus på tematikken etter ønske fra Geno. I PhD-prosjektet vil kunnskap og metodikk etablert i dette prosjektet benyttes. Videre har Høgskolen i Innlandet fått godkjent PhD-programmet i Anvendt økologi og bioteknologi i løpet av prosjektperioden. Den nevnte stipendiaten er tatt opp ved dette programmet, i tillegg til to andre, hvorav en nærings-PhD samt ytterligere en planlagt nærings-PhD innenfor tematikk tilknyttet fruktbarhet og avl på ulike arter.

The main idea of the proposed project is to develop new generic knowledge and technology by identifying epigenetic and metabolomic signatures associated with improved and sustainable health and fertility in cattle and swine. Breeding organisations experience a paradigm shift applying genomic selection enhancing the genetic gain and reducing the generation interval. A key question to be answered is whether the potential epigenetic influences of artificial insemination may confound the use of next generation sequencing data as the sole basis for sustainable genomic selection of low heritable traits like fertility, and whether the environmental changes and production stress animals have to adapt to in modern husbandry to some extent hide genetic disposition or generates specific phenotypes. The Norwegian breeding companies Geno and Norsvin have through decades conducted systematic breeding of their respective species, including significant amounts of information on fertility. By selecting contrast groups of male sires concerning phenotypic fertility based on advanced semen quality analyses and existing datasets on field fertility, novel epigenetics and metabolomics will be applied on samples from those individuals. Advanced bioinformatics and statistical analysis will be performed to reveal possible correlation to genomic sequencing data, applicable in breeding programs. Geno and Norsvin are in the international forefront due to a long-term commitment to systematic knowledge building in breeding and reproduction science, and their provision of unique quality data is a prerequisite for the project. The project aims to expand the knowledge base for sustainable animal breeding and health by introducing new state of the art technology and to strengthen national competence in animal reproduction science. The fellowships included in the project are strategic and in compliance with industry-oriented researcher training and long-term national competence development.