Chromosomes and fertility from progenitors to embryos: Investigating chromosomal abnormalities and development morphokinetics

Pig and cattle are the main two large livestock species in the farming industry. Due to the increasing demand for meat products, new techniques have been developed to improve their breeding, from embryology protocols to genetics analysis. Usually, in the farming industry, artificial insemination is one of the most popular procedures to generate new individuals. Reciprocal translocations (RT) are one the most common chromosomal abnormalities found in pigs, decreasing their fertility potential. To make sure no RT enters the breeding line, boars are screened using karyotype or FISH. However, these techniques have a limited resolution of detection. In this thesis, we developed a new method, based on long-read ONT sequencing to provide genome-wide data to screen for chromosomal abnormalities. However, chromosome abnormalities can also appear during embryogenesis, halting embryo development or implantation failure and miscarriages. With SNP-based Preimplantation Genetic Testing for Aneuploidies (PGT-A) algorithms, we can now investigate chromosomal errors as well as assess their level of mosaicism. In this thesis, we presented new approaches to apply them in livestock and investigated the prevalence and origin of each chromosomal defect in two species, pigs and cattle. Moreover, we established a new method to assess embryo morphokinetics in 3D volume through Optical Coherence Tomography (OCT) in a time-lapse manner. This has allowed us to visualise for the first-time oocyte and embryo development. All the new methodologies developed herein can be widely applicable to livestock species, and we suggest a new screening approach that will speed up the current breeding strategies and minimize the cost of animal rearing.