PhD Graduates

We are proud to announce the graduations and upcoming defences of Animal Breeding & Genomics PhD candidates.

- Latest update: October 2020 -

Chiara Bortoluzzi

On Wednesday 14 October at 16:00, Chiara Bortoluzzi defended her thesis entitled ‘Using whole-genome sequencing data for demographic and functional evaluations of small managed populations’.

Read Chiara's thesis on


Genetic diversity forms the basis for selection to act upon a population: without diversity, evolution cannot occur and species cannot adapt to changing environments. In livestock populations, the rapid decline in genetic diversity calls for immediate and effective conservation measures to prevent future breeds to go extinct. However, parameters related to, for instance, genetic diversity and inbreeding should be estimated upfront in order to successfully intervene.

The aim of this thesis was to explore the use of whole-genome sequencing data to characterize, from a demographic and functional perspective, livestock diversity to guide conservation efforts. Local chicken breeds were the main breeds of interest. Results showed, among others, that (1) recent inbreeding and genetic drift are important threats in small populations, (2) the genetic basis of some of the phenotypic variation exhibited by local breeds has a complex evolutionary history, and that (3) genetic diversity can and should be measured at multiple levels to best manage populations and genetic resources.

Tessa Brinker

On Friday 13 November at 11:00, Tessa Brinker will defend her thesis entitled ‘Genetics and genomics of direct and social genetic effects on survival time and plumage condition in laying hens’.

Read Tessa's thesis on


Several traits in livestock are not only affected by genes of the individual itself, but also by genes of its group mates. This is due to social interactions between individuals.

In this thesis, the genetic background of two traits that depend on social interactions in laying hens was studied; plumage condition and survival time. For these traits the contribution of direct and social genetic effects to the total heritable variation were estimated, which showed that up to 94% of the heritable variation in plumage condition and up to 61% of the heritable variation in survival time can be attributed to social genetic effects.

The availability of genomic information provides new opportunities for estimating genetic parameters and allows identifying chromosomal regions underlying direct and social genetic effects. Results point to an interesting candidate gene which requires further study. This thesis makes a substantial contribution to our knowledge regarding social genetic effects in laying hens.

Jan van der Lee

On Friday 13 November at 16:00, Jan van der Lee will defend his thesis entitled ‘Understanding dairy commercialization - Evolving market linkages, transition, and resilience of dairy farming in the East African highlands’.


The objective of this thesis is to gain insights into factors affecting commercialization of dairy farming under land scarcity. The main research question was: in what ways do market quality and spatial factors affect commercialization of dairy farming systems under land scarcity in two countries in the East African highlands?

Three empirical chapters and a systematic literature review result in the following conclusions: spatial factors are critical drivers of commercialization of dairy farming, with proximity to local input and output markets and being located in a dairy cluster enhancing commercialization; concurrent and co-dependent upgrading in farming, market, and context domains enhances market quality; farmers’ market quality and feasibility space are also enhanced by the plurality and performance of input and service provision; and risks and risk perceptions around market quality play important roles in decisions of upgrading, especially around system jumps. Dairy commercialization will need to consider these effects to be sustained over time. 

Langqing Liu

On Wednesday 17 February 2021 at 16:00, Langqing Liu will defend his thesis entitled ‘A looking glass for pig evolution: comparative and speciation genomics of Suidae’.


Developments in sequencing technology have revolutionized our understanding of evolutionary biology and have led to the concept evolutionary genomics. Continuous efforts to sequence additional species have generated a comprehensive dataset for biologists to study the evolution of the diversity of life, to explore underlying biological mechanisms and to aid conservation efforts. In this thesis, Suidae (the family of pigs) was demonstrated to be a uniquely enriched system for investigating patterns and processes at the intersection of speciation and adaptation.

The evolutionary history of Suidae was described and a complex model of speciation with hybridization was examined. The critically endangered pygmy hog was used as model in the population study to reconstruct demographic trajectory and evaluate its genetic consequences. A de novo genome assembly of Sus cebifrons was used to characterize the evolution of genome architecture underlying the rapid speciation and adaptation of Sus. The importance of a fine-structured reference genome was also highlighted for the interpretation of selective signatures.

Zhou Wu

On Tuesday 23 February 2021 at 16:00, Zhou Wu will defend her PhD thesis entitled ‘Small chicken, big story: detection of the genetic background of dwarfism in chicken using genomic analysis’.


Dwarfism is an important trait in agriculture applied in animal breeding. Dwarfism is a condition characterized by restricted growth. Several forms of dwarfism in chicken have been described, for their distinct types and different extent of size reduction. Nowadays, dwarf chickens (bantam) have become an important component of the Dutch chicken population, which encompasses a recent history of human-mediated crossbreeding. However, the genetic basis underlying these dwarf phenotypes is not well understood.

The aim of this thesis was to study the genetic basis of dwarf phenotypes in chickens. To identify dwarf causative genes, the study focussed on two types of dwarfism in chickens, the autosomal dwarfism (adw) and the bantam. Results include novel candidate genes (e.g. TMEM263 and HMGA2) responsible for dwarf phenotypes. Results furthermore show how human-mediated crossbreeding may influence the genomic landscape of Dutch chicken population in a complex manner.