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Genomic population structure and prevalence of copy number variations in South African Nguni cattle

Overview of attention for article published in BMC Genomics, November 2015
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About this Attention Score

  • Above-average Attention Score compared to outputs of the same age (61st percentile)
  • Above-average Attention Score compared to outputs of the same age and source (52nd percentile)

Mentioned by

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4 tweeters
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1 Facebook page

Citations

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20 Dimensions

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31 Mendeley
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Title
Genomic population structure and prevalence of copy number variations in South African Nguni cattle
Published in
BMC Genomics, November 2015
DOI 10.1186/s12864-015-2122-z
Pubmed ID
Authors

Magretha Diane Wang, Kennedy Dzama, Charles A. Hefer, Farai C. Muchadeyi

Abstract

Copy number variations (CNVs) are modifications in DNA structure comprising of deletions, duplications, insertions and complex multi-site variants. Although CNVs are proven to be involved in a variety of phenotypic discrepancies, the full extent and consequence of CNVs is yet to be understood. To date, no such genomic characterization has been performed in indigenous South African Nguni cattle. Nguni cattle are recognized for their ability to sustain harsh environmental conditions while exhibiting enhanced resistance to disease and parasites and are thought to comprise of up to nine different ecotypes. Illumina BovineSNP50 Beadchip data was utilized to investigate genomic population structure and the prevalence of CNVs in 492 South African Nguni cattle. PLINK, ADMIXTURE, R, gPLINK and Haploview software was utilized for quality control, population structure and haplotype block determination. PennCNV hidden Markov model identified CNVs and genes contained within and 10 Mb downstream from reported CNVs. PANTHER and Ensembl databases were subsequently utilized for gene annotation analyses. Population structure analyses on Nguni cattle revealed 5 sub-populations with a possible sub-structure evident at K equal to 8. Four hundred and thirty three CNVs that formed 334 CNVRs ranging from 30 kb to 1 Mb in size are reported. Only 231 of the 492 animals demonstrated CNVRs. Two hundred and eighty nine genes were observed within CNVRs identified. Of these 149, 28, 44, 2 and 14 genes were unique to sub-populations A, B, C, D and E respectively. Gene ontology analyses demonstrated a number of pathways to be represented by respective genes, including immune response, response to abiotic stress and biological regulation processess. CNVs may explain part of the phenotypic diversity and the enhanced adaptation evident in Nguni cattle. Genes involved in a number of cellular components, biological processes and molecular functions are reported within CNVRs identified. The significance of such CNVRs and the possible effect thereof needs to be ascertained and may hold interesting insight into the functional and adaptive consequence of CNVs in cattle.

Twitter Demographics

The data shown below were collected from the profiles of 4 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 31 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Brazil 2 6%
South Africa 1 3%
Colombia 1 3%
Unknown 27 87%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 13 42%
Student > Master 8 26%
Unspecified 4 13%
Student > Doctoral Student 2 6%
Student > Bachelor 1 3%
Other 3 10%
Readers by discipline Count As %
Agricultural and Biological Sciences 16 52%
Unspecified 5 16%
Biochemistry, Genetics and Molecular Biology 4 13%
Veterinary Science and Veterinary Medicine 3 10%
Medicine and Dentistry 3 10%
Other 0 0%

Attention Score in Context

This research output has an Altmetric Attention Score of 3. 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 06 November 2015.
All research outputs
#2,337,082
of 6,535,212 outputs
Outputs from BMC Genomics
#2,172
of 5,136 outputs
Outputs of similar age
#77,581
of 209,386 outputs
Outputs of similar age from BMC Genomics
#177
of 393 outputs
Altmetric has tracked 6,535,212 research outputs across all sources so far. This one has received more attention than most of these and is in the 63rd percentile.
So far Altmetric has tracked 5,136 research outputs from this source. They receive a mean Attention Score of 3.9. This one has gotten more attention than average, scoring higher than 55% 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 209,386 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 61% of its contemporaries.
We're also able to compare this research output to 393 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 52% of its contemporaries.