Research – University of Copenhagen

GIFT > Research

Main research objectives

The GIFT project conducts quantitative genetics and animal breeding research on important attributes or traits related to Ovum Pick-Up (OPU) and in vitro production (IVP) of embryos. The project also contributes to profitability of OPU-IVP operations in the Brazilian and Danish cattle industry. Further, we use Vitrogen company data collected in 5-6 large experimental farms in the state of São Paulo. This is done to identify high genetic merit donor cows and recipient heifers with higher pregnancy rates via Genome-Wide Association Studies (GWAS) and Genomic Selection (GS) for OPU-IVP and pregnancy traits in several thousands of Brazilian cattle.

In Denmark, transcriptomics experiments using RNAseq profiles of OPU-IVP recipient cows will be conducted to identify differentially expressed genes and gene regulatory networks in maternal-conceptus tissues in recipient cows that do and do not maintain pregnancy.

Further, we compare conventional in vitro maturation (conIVM) versus Simulated Physiological Oocyte Maturation (SPOM) systems in both Bos taurus and Bos indicus breeds. This is done at the level of a) ultra-structural differences in the matured oocyte, b) gene expression in the blastocyst produced in vitro and c) pregnancy rates in recipient cows after transfer of embryos produced in vitro.

Finally, based on the results, we develop and deliver tools for genomic improvement of OPU-IVP and heifer pregnancy traits for practice by Brazilian and Danish companies.

The GIFT project consortium is organized in 6 major work packages. Work packages are coordinated in Denmark by Professor Haja Kadarmideen and in Brazil by Professor Marcelo FG Nogueira.

Work Package 1. GWAS and Systems Genetics of Fertilization and Pregnancy

Here we conduct GWAS on a group of Nellore donor females selected based on their oocyte production records maintained at Vitrogen. This work package also involves GWAS research on Nellore heifers with phenotypic records for heifer pregnancy. We use Illumina Bovine 777k HD SNP Bead Chip for genotyping. Functional and pathway information on lead candidate SNPs will be investigated via systems genetics methods.

Work Package 2. Quantitative Genetics and Genomic Selection (GS)

This work package involves genetic parameter estimation for OPU-IVP production records collected by Vitrogen on OPU sessions, oocyte production, quality, transport time (resistance), cleavage, embryo production, pregnancy rates, and other data in OPU-IVP traits from 5,000 cattle.

With genomic information on a subset of the cattle, we conduct genomic selection for OPU-IVP and heifer pregnancy.

Work Package 3. Conventional IVM versus Simulated Physiological Oocyte Maturation (SPOM)

Groups of cumulus-oocyte complexes (COCs) will be matured in conventional IVM and in SPOM systems for comparison. We assess the ultra-structural differences between conIVM and SPOM systems. Gene expression analysis will be performed in the microfluidic platform Fluidigm BioMark™ HD System to detect differential expression in COCs between two systems. Additional replicates will be performed to produce embryos for transfer to recipient Nellore cows. The health of delivered calf (weight, survival rate and pregnancy length in days) will be related to each treatment. The experiment will mainly be executed in Brazil.

Work Package 4. Donor cow and embryo characterization – for key IVM-IVP traits and transcriptomic profiles

Biological samples (blood and ovaries) will be collected at the slaughterhouse. Oocytes will be kept separate for each animal and will be in vitro matured (IVM), fertilized (IVF) and cultured (IVC) to the blastocyst stage. At the time of IVF, cumulus cells will be harvested for transcriptomic analyses. Semen from bulls with high genetic merit and low genetic merit for milk production traits will be used. The semen from these bulls will be both sexed and unsorted to create many experimental contrasts. The experiment will mainly be executed in Denmark.

Work Package 5: Recipient cow characterization – embryo and endometrial biopsies and transcriptomics

Endometrial biopsies will be collected when recipient animals have been synchronized for embryo transfer (ET). Pregnancy will be monitored and embryos and uterine biopsies will be collected from pregnant animals. From non-pregnant animals, exclusively endometrial biopsies will be collected. The endometrial tissue will be processed for transcriptomic (RNAseq) analyses and the embryos will be processed for detailed morphological evaluation as well as for transcriptomic analyses. The experiment will mainly be executed in Denmark.

Work Package 6: Bioinformatics & systems biology analyses of transcriptomic and genomic information

Bioinformatic and systems biology analyses will be conducted for

  1. establishing potential connections between cumulus cell transcriptomics and blood parameters in the donor cattle, and
  2. establishing potential connections between endometrial transcriptomics and its reflection on blood parameters in recipient cows in search for easily assessable biomarkers of recipient quality.

The bovine RNAseq gene expression data will be analyzed using statistical-bioinformatic approaches to identify a list of differentially expressed (DE) genes, differentially wired networks, co-expression and transcriptional regulatory networks and hub genes/biomarkers therein. The analyses will mainly be executed in Denmark.