Background
Recent developments in sequencing technology have facilitated widespread investigations
of genomic variants, including continuous stretches of homozygous genomic regions.
For cattle, a large proportion of these runs of homozygosity (ROH) are likely the
result of inbreeding due to the accumulation of elite alleles from long-term selective
breeding programs. In the present study, ROH were characterized in four cattle breeds
with whole genome sequence data and the distribution of predicted functional variants
was detected in ROH regions and across different ROH length classes
Results
On average, 19.5 % of the genome was located in ROH across four cattle breeds. There
were an average of 715.5 ROH per genome with an average size of ~750 kbp, ranging
from 10 (minimum size considered) to 49,290 kbp. There was a significant correlation
between shared short ROH regions and regions putatively under selection (p < 0.001). By investigating the relationship between ROH and the predicted deleterious
and non-deleterious variants, we gained insight into the distribution of functional
variation in inbred (ROH) regions. Predicted deleterious variants were more enriched
in ROH regions than predicted non-deleterious variants, which is consistent with observations
in the human genome. We also found that increased enrichment of deleterious variants
was significantly higher in short (<100 kbp) and medium (0.1 to 3 Mbp) ROH regions
compared with long (>3 Mbp) ROH regions (P < 0.001), which is different than what has been observed in the human genome.
Conclusions
This study illustrates the distribution of ROH and functional variants within ROH
in cattle populations. These patterns are different from those in the human genome
but consistent with the natural history of cattle populations, which is confirmed
by the significant correlation between shared short ROH regions and regions putatively
under selection. These findings contribute to understanding the effects of inbreeding
and probably selection in shaping the distribution of functional variants in the cattle
genome.
