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Runs of homozygosity and distribution of functional variants in the cattle genome.

Zhang Q, Guldbrandtsen B, Bosse M, Lund MS, Sahana G - BMC Genomics (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, DK-8830, Denmark. Qianqian.zhang@mbg.au.dk.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus

ROH general statistics. a Average genome-wide nucleotide diversity (polymorphic sites per 10,000 bp); b Average nucleotide diversity outside ROH (polymorphic sites per 10,000 bp); c Average ROH size (bp); d Average genome-wide ROH totals
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Fig1: ROH general statistics. a Average genome-wide nucleotide diversity (polymorphic sites per 10,000 bp); b Average nucleotide diversity outside ROH (polymorphic sites per 10,000 bp); c Average ROH size (bp); d Average genome-wide ROH totals

Mentions: 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 (old-RED), and New Danish Red Dairy cattle (new-RED) (Fig. 1 and Additional file 1: Figure S1). The average genomic ROH content was 19.5 % across the four cattle breeds, with HOL, JER, New-RED, and Old-RED having 18.67 %, 24.23 %, 11.84 %, and 23.26 %, respectively. The average number of ROH per genome was 715.5 ± 21.0, with an average size of 750,564.2 bp, ranging from 10 kbp (the minimum size considered) to 49,290 kbp (Additional file 10: Table S1). The mean ROH size varied significantly between HOL, JER, Old-RED, and New-RED (P < 0.001) with the exception of JER and Old-RED (Fig. 1c). The mean number of ROH was significantly different between HOL, JER, Old-RED, and New-RED cattle (P < 0.001) with the exception of HOL and Old-RED (Fig. 1d).Fig. 1


Runs of homozygosity and distribution of functional variants in the cattle genome.

Zhang Q, Guldbrandtsen B, Bosse M, Lund MS, Sahana G - BMC Genomics (2015)

ROH general statistics. a Average genome-wide nucleotide diversity (polymorphic sites per 10,000 bp); b Average nucleotide diversity outside ROH (polymorphic sites per 10,000 bp); c Average ROH size (bp); d Average genome-wide ROH totals
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4508970&req=5

Fig1: ROH general statistics. a Average genome-wide nucleotide diversity (polymorphic sites per 10,000 bp); b Average nucleotide diversity outside ROH (polymorphic sites per 10,000 bp); c Average ROH size (bp); d Average genome-wide ROH totals
Mentions: 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 (old-RED), and New Danish Red Dairy cattle (new-RED) (Fig. 1 and Additional file 1: Figure S1). The average genomic ROH content was 19.5 % across the four cattle breeds, with HOL, JER, New-RED, and Old-RED having 18.67 %, 24.23 %, 11.84 %, and 23.26 %, respectively. The average number of ROH per genome was 715.5 ± 21.0, with an average size of 750,564.2 bp, ranging from 10 kbp (the minimum size considered) to 49,290 kbp (Additional file 10: Table S1). The mean ROH size varied significantly between HOL, JER, Old-RED, and New-RED (P < 0.001) with the exception of JER and Old-RED (Fig. 1c). The mean number of ROH was significantly different between HOL, JER, Old-RED, and New-RED cattle (P < 0.001) with the exception of HOL and Old-RED (Fig. 1d).Fig. 1

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, DK-8830, Denmark. Qianqian.zhang@mbg.au.dk.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus