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

Overview of attention for article published in BMC Genomics, July 2015
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  • Good Attention Score compared to outputs of the same age and source (70th percentile)

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Title
Runs of homozygosity and distribution of functional variants in the cattle genome
Published in
BMC Genomics, July 2015
DOI 10.1186/s12864-015-1715-x
Pubmed ID
Authors

Qianqian Zhang, Bernt Guldbrandtsen, Mirte Bosse, Mogens S Lund, Goutam Sahana

Abstract

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. 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. 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.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 150 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Switzerland 1 <1%
Unknown 149 99%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 30 20%
Researcher 24 16%
Student > Master 20 13%
Student > Bachelor 11 7%
Other 9 6%
Other 21 14%
Unknown 35 23%
Readers by discipline Count As %
Agricultural and Biological Sciences 70 47%
Biochemistry, Genetics and Molecular Biology 22 15%
Veterinary Science and Veterinary Medicine 8 5%
Medicine and Dentistry 4 3%
Unspecified 1 <1%
Other 2 1%
Unknown 43 29%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 5. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 01 January 2023.
All research outputs
#6,250,406
of 23,462,326 outputs
Outputs from BMC Genomics
#2,581
of 10,777 outputs
Outputs of similar age
#70,619
of 265,359 outputs
Outputs of similar age from BMC Genomics
#74
of 266 outputs
Altmetric has tracked 23,462,326 research outputs across all sources so far. This one has received more attention than most of these and is in the 73rd percentile.
So far Altmetric has tracked 10,777 research outputs from this source. They receive a mean Attention Score of 4.7. This one has done well, scoring higher than 75% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 265,359 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 73% of its contemporaries.
We're also able to compare this research output to 266 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 70% of its contemporaries.