Title: Population genomics

Projekt manager: Prof. Dr. H. Simianer (UGÖ-TZ)

Project partners: TUM-PG, TUM-PZ, TUM-TZ, UGÖ-TZ, UHO-ZI

Objective:
High resolution analysis of the genomic diversity of maize, cattle, and chicken, as shaped by evolution, domestication and selection, as the fundament for genome-based breeding programmes.

Summary:
In this project we will adapt methods and tools of population genomics to be used under the specific conditions of selected agricultural populations. They will be applied to the genome sequence and high throughput genotyping data for maize, cattle and chicken, generated in the project. In genome-wide scans we will asses the linkage disequilibrium and haplotype structure as well as recombination hot spots, selection signatures and selective sweeps. The allelic diversity of divergently selected populations provides evidence with respect to functional regions which may react to selection pressure. Coalescent approaches and forward simulation are the basis for tests on neutrality which need to be specifically adapted to the special setup in agricultural populations. All methods will be integrated into an analytic pipeline which will be sustained beyond the end of the actual project. The results of this co-operative effort will improve the understanding of the genomic architecture of the studied species and populations. They will provide an independent confirmation of results of QTL-mapping and genomic breeding value estimation, which will be the basis for more efficient approaches towards genomic selection and prediction.

Sub-projects:
A4.1: Development of methods in population genomics
A4.2: Population genomics in maize
A4.3: Population genomics in chicken
A4.4: Population genomic analysis of individual genomic sequences to indentify causal DNA variation in cattle