Large genomic deletions are potential candidate for loss-of-function, which could be lethal as homozygote. Such genetic mutations are responsible for a substantial yearly-economic loss in the dairy industry, and the mapping of such variants is essential for effective breeding planning and performance improvement. In this study, we have used a systematic approach for high-resolution structural variant mapping, genotyping, and validation from whole-genome sequence data in cattle, which is also of broader interest in livestock research. In the study, we identified about 8,500 large deletions; 82% of them are novel. These will be valuable information for the large scientific community working in gene mapping and genomic prediction in cattle. Our approach can identify the deletion breakpoints accurately; verified by both known deletions and new discovery. We have identified and confirmed a ~525 KB deletion on chromosome 23, causing stillbirth in cattle.

The highlights of the study

• deletion-genotype could recapitulate genetic structure of populations,
• there are some highly differentiated genic and intergenic deletions among the populations,
• deletions in essential genes could only be observed in heterozygotes, while for nonessential genes, live homozygote individuals could be observed,
• natural gene knockouts are enriched for immune-related and olfactory receptor genes,
• deletions are highly enriched for health and fertility related QTL, while highly depleted for production traits and
• the knowledge of deletion breakpoints facilitates understanding of deletion formation mechanism.

The article has been published in the international journal DNA Research with the title Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle

For more information, please contact

Md Mesbah Uddin

mesbah@mbg.au.dk

+4587157821

Goutam Sahana

goutam.sahana@mbg.au.dk

Fastnet: +4587157501