During his PhD studies, Houcheng Li investigated how genetic regulation shape complex traits in livestock under the cellular level. Landmark projects such as the Farm Animal Genotype-Tissue Expression (FarmGTEx) consortium have greatly enriched the functional and regulatory annotation of farm animal genomes. However, a key limitation of bulk data is that, by averaging molecular signals across heterogeneous cell populations, they obscure cell-type specific regulatory mechanisms and restrict the precise mapping of genetic variation to molecular functions within defined biological contexts.

In this project, single-cell sequencing was combined with computational cell-type deconvolution to map genetic regulatory variation at cellular resolution in cattle and pigs. By integrating millions of single cells with thousands of bulk transcriptomes, Houcheng Li identified tens of thousands of cell-type specific regulation variants and their specific contribution to economically important traits such as fertility, milk production and health, which remain hidden in traditional bulk-level analyses. The work also linked these cell-type molecular phenotypes to genomic regions under strong selection, helping to explain how genetic variants shape breed-specific traits through precise tissue- and cell-dependent pathways.

The PhD study was completed at the Center for Quantitative Genetics and Genomics (QGG), Faculty of Technical Science, Aarhus University.

This summary was prepared by the PhD student.

Time: Tuesday, 16 December 2025, at 1 p.m.
Place: AIAS Building 1630, Auditorium 201, Høegh-Guldbergsgade 6B, 8000 Aarhus.
Title of PhD thesis: Farm animal Cell Atlas (FarmCA): Exploiting regulatory variants and GWAS loci at single cellular level.
Contact information: Houcheng Li, e-mail: houcheng.li@qgg.au.dk, tel: +45 91886329
Members of the assessment committee:
Professor, Dominic Wright, Department of Physics, Chemistry and Biology, Lindköping University, Sweden.
Associate Professor, Yang Li, the Section of Genetic Medicine, The University of Chicago, USA.
Professor, Doug Speed (chair), Center of Quantitative Genetics and Genomics (QGG), Aarhus University, Denmark.
Main supervisor: Professor, Goutam Sahana, Center of Quantitative Genetics and Genomics (QGG), Aarhus University, Denmark.
Co-supervisor:
Tenure Track Assistant Professor, Lingzhao Fang, Center of Quantitative Genetics and Genomics (QGG), Aarhus University, Denmark.
Associate professor, Zexi Cai, Center of Quantitative Genetics and Genomics (QGG), Aarhus University, Denmark.
Language: The PhD dissertation will be defended in English

The defence is public.
The PhD thesis is available for reading at the Graduate School of Technical Sciences/GSTS, Ny Munkegade 120, building 1521, 8000 Aarhus C.