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Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses

Overview of attention for article published in BMC Genomics, October 2015
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Citations

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84 Dimensions

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112 Mendeley
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3 CiteULike
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Title
Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses
Published in
BMC Genomics, October 2015
DOI 10.1186/s12864-015-1977-3
Pubmed ID
Authors

Julia Metzger, Matthias Karwath, Raul Tonda, Sergi Beltran, Lídia Águeda, Marta Gut, Ivo Glynne Gut, Ottmar Distl

Abstract

Modern horses represent heterogeneous populations specifically selected for appearance and performance. Genomic regions under high selective pressure show characteristic runs of homozygosity (ROH) which represent a low genetic diversity. This study aims at detecting the number and functional distribution of ROHs in different horse populations using next generation sequencing data. Next generation sequencing was performed for two Sorraia, one Dülmen Horse, one Arabian, one Saxon-Thuringian Heavy Warmblood, one Thoroughbred and four Hanoverian. After quality control reads were mapped to the reference genome EquCab2.70. ROH detection was performed using PLINK, version 1.07 for a trimmed dataset with 11,325,777 SNPs and a mean read depth of 12. Stretches with homozygous genotypes of >40 kb as well as >400 kb were defined as ROHs. SNPs within consensus ROHs were tested for neutrality. Functional classification was done for genes annotated within ROHs using PANTHER gene list analysis and functional variants were tested for their distribution among breed or non-breed groups. ROH detection was performed using whole genome sequences of ten horses of six populations representing various breed types and non-breed horses. In total, an average number of 3492 ROHs were detected in windows of a minimum of 50 consecutive homozygous SNPs and an average number of 292 ROHs in windows of 500 consecutive homozygous SNPs. Functional analyses of private ROHs in each horse revealed a high frequency of genes affecting cellular, metabolic, developmental, immune system and reproduction processes. In non-breed horses, 198 ROHs in 50-SNP windows and seven ROHs in 500-SNP windows showed an enrichment of genes involved in reproduction, embryonic development, energy metabolism, muscle and cardiac development whereas all seven breed horses revealed only three common ROHs in 50-SNP windows harboring the fertility-related gene YES1. In the Hanoverian, a total of 18 private ROHs could be shown to be located in the region of genes potentially involved in neurologic control, signaling, glycogen balance and reproduction. Comparative analysis of homozygous stretches common in all ten horses displayed three ROHs which were all located in the region of KITLG, the ligand of KIT known to be involved in melanogenesis, haematopoiesis and gametogenesis. The results of this study give a comprehensive insight into the frequency and number of ROHs in various horses and their potential influence on population diversity and selection pressures. Comparisons of breed and non-breed horses suggest a significant artificial as well as natural selection pressure on reproduction performance in all types of horse populations.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 112 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 1 <1%
Colombia 1 <1%
Portugal 1 <1%
Unknown 109 97%

Demographic breakdown

Readers by professional status Count As %
Student > Master 20 18%
Researcher 19 17%
Student > Ph. D. Student 18 16%
Student > Bachelor 13 12%
Student > Doctoral Student 7 6%
Other 17 15%
Unknown 18 16%
Readers by discipline Count As %
Agricultural and Biological Sciences 45 40%
Biochemistry, Genetics and Molecular Biology 23 21%
Veterinary Science and Veterinary Medicine 9 8%
Medicine and Dentistry 4 4%
Computer Science 3 3%
Other 3 3%
Unknown 25 22%

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 18 February 2016.
All research outputs
#2,627,193
of 7,211,484 outputs
Outputs from BMC Genomics
#1,968
of 5,384 outputs
Outputs of similar age
#72,637
of 237,409 outputs
Outputs of similar age from BMC Genomics
#139
of 376 outputs
Altmetric has tracked 7,211,484 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 5,384 research outputs from this source. They receive a mean Attention Score of 4.0. This one has gotten more attention than average, scoring higher than 62% 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 237,409 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 68% of its contemporaries.
We're also able to compare this research output to 376 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 62% of its contemporaries.