Through sequence data, an enormous wealth of detailed DNA information becomes available for animal breeders. One important part of this project focuses on detection of structural variation, including karyotype abnormalities and copy number variants (CNVs), and development of pipelines for these purposes. Another part of the project is concerned with imputation and genome-wide association studies (GWAS) of whole genome sequence data in livestock, for instance through collaboration with the 1000 Bull Genomes project.
Published results in this project are:
Lee, Y.-L., M. Bosse, E. Mullaart, M. A. M. Groenen, R. F. Veerkamp, and A. C. Bouwman. 2020. Functional and population genetic features of copy number variations in two dairy cattle populations. BMC Genom. 21:89. https://doi.org/10.1186/s12864-020-6496-1
Bouwman, et al. 2018. Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals. Nat. Genet. 50:362. https://doi.org/10.1038/s41588-018-0056-5
Bouwman, A. C., M. van Son, B. Harlizius, and B. Zumbach. 2018. Imputation accuracy of whole-genome sequence in pigs. Page 424 in Proceedings of the 11th World Congress on Genetics Applied to Livestock Production. http://www.wcgalp.org/system/files/proceedings/2018/imputation-accuracy-whole-genome-sequence-pigs.pdf
Bouwman, A. C., B. J. Hayes, and M. P. L. Calus. 2017. Estimated allele substitution effects underlying genomic evaluation models depend on the scaling of allele counts. Genet. Sel. Evol. 49:79. https://doi.org/10.1186/s12711-017-0355-9