Livestock Genomics

We characterize genomic variation within and across livestock populations using genome-wide DNA and RNA sequencing data. Using bioinformatics and statistical genomics approaches, we analyze whole-​genome sequencing data to assess sequence variability in individuals at nucleotide level. We are particularly interested in variants that affect phenotype and aim at developing tools to identify such variants in large cohorts of individuals with genotype and phenotype data. We mostly work in cattle but also have projects running in other domestic animal species including pigs, horses, goat, and sheep.

Ongoing projects

Mapping sequence variability within and across populations

We characterize the genomic variability in Swiss cattle and pig populations (Cattle: Brown Swiss, Original Braunvieh; Pigs: Premo, Swiss Large White) using whole-genome sequencing data. All newly generated sequencing data are deposited at public repositories to enable unrestricted access to ensure reproducibility and reusability. We contribute newly generated sequencing data to large international consortia such as the 1000 Bull Genomes Project and the Bovine Pan-genome Project.

Integrating genome and transcriptome data

We established a large cohort of animals with gene expression and genome variation data using RNA and DNA sequencing. These data enable us to pinpoint sequence variants that control variation in transcript abundance, alternative splicing, allelic imbalance, and other molecular phenotypes. We apply transcriptome-wide association testing to integrate variants affecting molecular phenotypes with results from genome-wide association studies to prioritize functional variants.

Recent publications

Nosková A, Bhati M, Kadri NK, Crysnanto D, Neuenschwander S, Hofer A, Pausch H. Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs. BMC Genomics, 2021;22:290. external page DOI: 10.1186/s12864-​021-07610-5

Lloret-Villas A, Bhati M, Kadri NK, Fries R, Pausch H. Investigating the impact of reference assembly choice on genomic analyses in a cattle breed. BMC Genomics, 2021;22:363. external page DOI: 10.1186/s12864-​021-07554-w

Bhati M, Kumar Kadri N, Crysnanto D, Pausch H. Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data. BMC Genomics, 2020;21:27. external page DOI: 10.1186/s12864-​020-6446-y

Bouwman AC, Daetwyler HD, Chamberlain AJ, Hurtado Ponce C, Sargolzaei M, Schenkel FS, Sahana G, Govignon-Gion A, Boitard S, Dolezal M, Pausch H, Brøndum R, Bowman PJ, Thomsen B, Guldbrantsen B, Lund MS, Servin B, Garrick DJ, Reecy J, Vilkki J, Bagnato A, Wang M, Hoff JL, Schnabel RD, Taylor J, Vinkhuyzen AAE, Panitz F, Bendixen C, Holm LE, Gredler B, Hozé C, Boussaha M, Sanchez M, Rocha D, Capitan A, Tribout T, Barbat A, Croiseau P, Drögemüller C, Jagannathan V, Vander Jagt C, Crowley JJ, Intergenomics Consortium, Bieber A, Purfield D, Berry DP, Emmerling R, Götz KU, Frischknecht M, Russ I, Sölkner J, Van Tassel CP, Fries R, Stothard P, Veerkamp RF, Boichard D, Goddard ME, Hayes BJ. Meta-analysis of genome wide association studies cattle stature identifies common genes that regulate body size in mammals. Nature Genetics, 2018;50(3):362-367. external page DOI: 10.1038/s41588-​018-0056-5