Abstract
BackgroundRecent 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.ResultsOn 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.ConclusionsThis 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1715-x) contains supplementary material, which is available to authorized users.
Highlights
Recent developments in sequencing technology have facilitated widespread investigations of genomic variants, including continuous stretches of homozygous genomic regions
The rate of inbreeding in cattle populations has increased in recent years [6, 9, 10], and there is a strong correlation between inbreeding levels and reduced fitness [11]
General statistics Runs of homozygosity (ROH) in the autosomes of 104 resequenced individuals were determined from four Danish dairy cattle breeds: Holstein (HOL), Jersey (JER), old Red Danish Dairy cattle, and New Danish Red Dairy cattle (Fig. 1 and Additional file 1: Figure S1)
Summary
Recent developments in sequencing technology have facilitated widespread investigations of genomic variants, including continuous stretches of homozygous genomic regions. 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. The rate of inbreeding in cattle populations has increased in recent years [6, 9, 10], and there is a strong correlation between inbreeding levels and reduced fitness [11]. Runs of homozygosity (ROH) are contiguous homozygous stretches in an individual genome due to transmission of identical haplotypes from parents to
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