PhD "Identification of unique or deleterious genetic variation across Dutch cattle breeds using...

We are looking for a PhD candidate who is interested in biodiversity, in particular the conservation of farm animal genetic diversity. Are you interested in this topic and in analysing whole genome sequencing data within and across Dutch cattle breeds? Then we might have an opportunity for you at Wageningen University & Research to start your PhD research.

Livestock breeds contain unique genetic variation, that can be neutral, adaptive to local conditions, or harmful. The genomic regions containing this variation can be under selection or moving to fixation due to inbreeding.

Whole genome sequence data can be used to locate variants of interest, but sequence data is usually aligned against the public reference genome. Novel sequencing technology, long read sequencing, has made it possible to create breed specific reference genomes, to which other sequenced individuals of the same breed can be aligned to identify within breed variation. Also, those breed specific reference genomes can be combined in a Pan-Genome to identify variation across breeds.

Long reads and pan-genome are especially powerful to detect unique structural variation like copy number variants, which has proven very difficult with short-read sequencing. Moreover investigating the presence and frequency of harmful mutations in the genome of rare breeds (=the genetic load), within and across populations, can indicate the risk of loss of fitness of populations or individuals.

The aim of the project is to better understand the genomic differences within and between Dutch cattle breeds. The results of the PhD project will be relevant for the further development of the conservation program and gene bank for livestock breeds, managed by the Centre for Genetic Resources, the Netherlands (CGN).

You will be part of the Animal Breeding and Genomics group of Wageningen University and Research, and in this research project you will collaborate closely with the Centre for Genetic Resources, the Netherlands (CGN). The project is funded by the Dutch Ministry of Agriculture, Nature and Food Quality.