- Latest update: February 2024 -
Dries Hulst
On Friday March 1, at 16.00 Dries Hulst will defend his thesis entitled 'Dark Genes: On genetic variation hidden in the transmission of infectious diseases.'
Jani de Vos
On Monday 18 December, at 16.00 Jani de Vos will defend her thesis entitled 'Disentangling the epigenome during development of pig and chicken.'
Pauline Jehannet
On Wednesday 4 October 2023, at 16.00 Pauline Jehannet will defend her thesis entitled 'How to make good eel larvae?'
Benan Gulzari
On Monday 2 October 2023, at 16.00 Benan Gulzari will defend his thesis entitled 'Integrated breeding in aquaculture.'
Priadi Setyawan
On Monday 2 October 2023, at 13.30 Priadi Setyawan will defend his thesis entitled 'Optimized design of a breeding program for saline tolerant tilapia.'
Ina Hulsegge
On Wednesday 27 September 2023, at 16.00 Ina Hulsegge will defend her thesis entitled 'Genomics applied to conservation of genetic diversity in Dutch livestock.'
Xue Pan
On Wednesday 11 January 2023, at 13.30 Xue Pan will defend his thesis entitled 'Development of immune response against H9N2 avian influenza after vaccination.'
H9N2 avian influenza virus (AIV) is the most prevalent and harmful low pathogenic avian influenza virus (LPAIV) in the world, which not only seriously harms animal husbandry, but also poses a huge challenge to public health. Vaccination is the main and most effective strategy to control H9N2 AIV. However, most vaccination programs against H9N2 AIV have shown to be ineffective in poultry in practice. Therefore, my project was 1) to figure out what factors may interfere with the H9N2 vaccine efficacy to sufficiently reduce transmission of H9N2 AIV in poultry, 2) to come up with some new vaccines, such as H9N2 inactivated whole virus vaccine with new CpG ODN based adjuvant and turkey herpesvirus (H9) vector vaccine for improving the vaccines’ efficacy in poultry, and 3) to explore the mechanisms that influence the vaccine efficacy in poultry in the field.
Xiaofei Yu
On Tuesday 13 December 2022, at 11.00 Xiaofei Yu will defend his thesis entitled 'Genomic architecture of selection for adaptation to challenging environments in aquaculture.'
Aquaculture is a sustainable way to meet the increased human demand for animal food. However, sustainability is threatened by the increasing effects of climate change, such as salinity due to drought and flooding, acidification of seawater due to carbon dioxide uptake, and oxygen shortages caused by any combination of the above that could result in algal blooms. In my thesis, I focus on three major environmental factors: dissolved oxygen, salinity, and temperature, which primarily are determined in aquaculture. The aim of this thesis is to provide an insight into the genomic architecture of adaptation to challenging environments of aquaculture species under farming conditions and further accelerate the marker-assisted selection. First, I determined the candidate QTL associated with phenotypic variation during adaptation to hypoxia or normoxia. I also showed the major difference of over-represented pathways that could explain the genetic regulation of hypoxia on growth. To select fish with better hypoxia tolerance and growth under a hypoxic environment, I quantified the genetic correlations between indicator trait for hypoxia tolerance (critical swimming performance) in early life and growth in later life. Beyond applying genome-wide association studies, I determined the QTLs and genes contributing to salinity tolerance that resulted from the selection signature. Finally, with the observed temperature divergence in the Mediterranean region, I investigated the QTLs associated with growth-related traits and organ weight growing out in two distinct commercial product sites (Spain and Greece farms), while the over-represented processes and pathways underlying temperature specific environment were underlined. Overall, this thesis provides comprehensive genomic insights into how fish adapt to challenging environments, which will assist marker-assisted selection for improved resilience of aquaculture species under climate change.
Yun Yu
On Tuesday 11 October 2022, at 16.00 Yun Yu will defend his thesis entitled 'Genomics underlying a canine hereditary thyroid follicular cell carcinoma.'
Intense human selection on domestic dogs over the past ~200 years created a variety of pure dog breeds, but also leads to breed-specific predispositions to many hereditary diseases/disorders. The incidence of thyroid tumor (TC) in the Dutch population of German Longhaired Pointer (GLP) dogs was extremely high over the past approximately 20 years, indicating a population predisposition to TC. To help the breeders to eradicate TCs from Dutch GLPs, I performed a series of analyses to decode TCs that occurred in those Dutch GLPs. Firstly, we determined the histology subtype of identified TCs and revealed that these TCs are a familial disease according to consanguinity of affected GLPs. I looked into the effect of inbreeding on the incidence of the familial TCs in these Dutch GLPs based on both pedigree and genotype data and revealed that inbreeding contributed to the high incidence of the familial TCs in these GLPs. Furthermore, I identified germline risk mutation for the familial TC using a combination of genome-wide association study and homozygosity mapping. The identified germline risk mutation is used in a genetic test that identifies GLPs at a high risk for the familial TC. To further understand molecular mechanism underlying the familial TC initiation and development, I profiled somatic mutation landscape of 7 familial TCs and identified a recurrent missense mutation that very likely drives the tumorigenesis. Furthermore, I genetically characterized GLP breed and identified specific selection signature that might contribute to hunting performance of GLPs. Lastly, I tested a novel approach to predict driver mutations using prior signaling pathway knowledge. Together I comprehensively decoded the familial TCs in the Dutch GLPs and developed a genetic test to identify dogs at a high risk for familial TCs.
Renzo Bonifazi
On Friday 16 September 2022, at 16.00 Renzo Bonifazi will defend his thesis entitled 'International genetic and genomic evaluations of beef cattle.'
In cattle, advancements in reproductive technologies, such as artificial insemination, allowed breeders to access the genetic material of superior bulls from foreign countries. However, animals’ estimated breeding values (EBV) computed from national evaluations are not directly comparable across countries due to differences in scales and genetic bases, trait and model definitions, and the possible presence of genotype-by-environment interactions. International evaluations account for such differences by jointly analysing all national data and modelling the same trait recorded in different countries as different correlated traits. The resulting international EBV (EBVint) facilitate the comparison of domestic and foreign sires and the worldwide trading of their genetic material. This thesis aims to improve and further develop methodologies for international beef cattle evaluations by addressing various challenges related to the estimation of across-country genetic correlations and their impact on the EBVint, the inclusion of national genomic information in international beef cattle evaluations using a single-step approach, and the inclusion of EVBint for elite sires back into national evaluation. Overall, by proposing new approaches and methodologies, this thesis contributes to the development of beef cattle international evaluations.
Samuel Mengistu
On Monday 29 August 2022, at 11.00 Samuel Mengistu will defend his thesis entitled 'Closing the yield gap: improving production efficiency under smallholder Nile tilapia farms through selective breeding.'
Currently, many smallholder Nile tilapia farms in developing countries still underperform in terms of feed efficiency, despite the use of genetically improved strains of Nile tilapia such as GIFT. Productivity differences among many smallholder Nile tilapia farms lead to a yield gap between the best performing and low performing farms. This thesis identifies the major field gap factors under smallholder Nile tilapia farming conditions where oxygen availability is limiting. Estimates of genotype by environment interaction between aerated and non-aerated ponds, heritabilities and genetic correlations for production and resilience traits were presented. The main finding is the production can be improved by including novel resilience traits in the breeding goal: Log transformed variance of deviations of body weight and critical swimming speed, which are assumed related to oxygen uptake efficiency of tolerance to low oxygen levels.
Henri van Kruistum
On Wednesday 6 April 2022, at 16.00 Henri van Kruistum will defend his thesis entitled 'The genomics of placenta evolution in livebearing fish'.
During vertebrate evolution, complex organs have evolved several times. The development of these organs is encoded in the genome. However, it is currently unclear how new complex organs, consisting of multiple interlocking parts, can evolve as a result of genomic change. In this thesis, I aim to find the genomic basis of one such newly evolved organ: the placenta in the livebearing fish family Poeciliidae. In this family, a placenta has evolved nine times independently, allowing for the investigation of multiple evolutionary origins of the same organ within a single group of species. First, I sequence and assemble the genomes of both placental and non-placental poeciliid species. Then, I compare the genomes of placental species with the genomes of non-placental species, aiming to find consistent genomic differences between the placental and non-placental species that can be associated with placenta evolution. I show that indeed, placental species show consistent mutations in both protein-coding and regulatory regions of the genome. Protein-coding mutations occur mainly around structural and metabolic genes, while regulatory changes occur mainly around developmental genes. I also show that, contrary to some predictions, gene duplications are not associated with placenta evolution in poeciliid fish. Together I provide a comprehensive overview of genome evolution in the fish family Poeciliidae, and provide new insights into the evolution of complex traits.
Young-Lim Lee
On Tuesday 26 April 2022, at 13.30 Young-Lim lee will defend her thesis entitled 'Structural variants in the bovine genome'.
Cattle genomes contain various types of variant sites, which together are referred to as genetic variants. Recent advancements in genomics made it possible to capture small and abundant types of genetic variants, such as single nucleotide polymorphisms. However, there are larger, complex and less traceable variants, "structural variants", which come in various sizes and shapes.
This thesis investigated structural variants in the bovine genome using state-of-the-art computational methods and data. Two chapters were dedicated to detecting structural variants present in the bovine genomes, unravelling nearly ~ 5,000 variants per cow. This thesis further deeply characterized a structural variant which is associated with clinical mastitis. Finally, the emergence of de novo structural variants was investigated in a large cattle cohort, underlining that de novo structural variants arise more frequently in cows produced from in vitro fertilization. These findings together highlight the importance of investigating structural variants which have thus far been considered challenging.
Ibrahim Jibrila
On Wednesday 25 May 2022, at 16.00 Ibrahim Jibrila will defend his thesis entitled 'Impact of preselection in genomic evaluations'.
Recent development of genomic evaluation models has resulted in faster genetic improvement of animals, compared to when only pedigree-based genetic evaluation models were used. In large-scale animal breeding programs, selection of parents of the next generation takes place in multiple stages, and the initial stages of this selection are called preselection.
Preselection reduces the cost of running animal breeding programs, and takes place when animals are young. When the animals grow older, they are re-evaluated in subsequent evaluations to select the final set of parents of the next generation.
This thesis used both simulated and real datasets to investigate the impact of preselection on accuracy and unbiasedness of subsequent genomic evaluation of preselected animals. This thesis shows that preselection, regardless of its type and intensity, hardly affects the accuracy and unbiasedness with which genomic models evaluate preselected animals. This means that large-scale animal breeding programs can continue to save costs through preselection, without worrying about the quality of their subsequent genomic evaluations.
Fasil Kebede
On Monday 29 August 2022, at 13.30 Fasil Getachew Kebede will defend his thesis entitled 'Adaptive phenotypic and genetic variation in chickens: a landscape genomics approach'.
Smallholder chicken production systems in tropical countries contribute significantly to the livelihoods of millions of farmers. Current levels of productivity fall short of meeting growing demands for meat and eggs. Knowledge on adaptive phenotypic and genetic variation among livestock populations contributes to the design of sustainable breeding and development programmes leading to enhancements in productivity. This thesis integrated phenotypic, genomic, and environmental information to address two research questions: 1) What are the environmental drivers of local adaptation in indigenous chickens? and 2) How do improved chicken populations that are introduced into smallholder systems respond phenotypically to environmental variations? Environmental predictors that are associated with habitat suitability of chickens were identified. These predictors were then fitted into distribution models to define species-specific-agroecologies and improve GxE predictions. Multi-environment performance analysis (MEPA) frameworks are applicable to select breeds with optimal performance and wider adaptation (yield stability). Candidate loci and genomic regions render environmental adaptation to Ethiopian chickens.
Samuel Mengistu
On Monday 29 August 2022, at 11.00 Samuel Bekele Mengistu will defend his thesis entitled 'Closing the yield gap: Improving production efficiency under smallholder Nile tilapia farms through selective breeding'.
Currently, many smallholder Nile tilapia farms in developing countries still underperform in terms of feed efficiency, despite the use of genetically improved strains of Nile tilapia such as GIFT. Productivity differences among many smallholder Nile tilapia farms lead to a yield gap between the best performing and low performing farms. This thesis identifies the major field gap factors under smallholder Nile tilapia farming conditions where oxygen availability is limiting. Estimates of genotype by environment interaction between aerated and non-aerated ponds, heritabilities and genetic correlations for production and resilience traits were presented. The main finding is the production can be improved by including novel resilience traits in the breeding goal: Log transformed variance of deviations of body weight and critical swimming speed, which are assumed related to oxygen uptake efficiency of tolerance to low oxygen levels.
