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BMC genomics2015; 16; 764; doi: 10.1186/s12864-015-1977-3

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

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. Methods: 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. Results: 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. Conclusions: 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.
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Publication Date: 2015-10-09 PubMed ID: 26452642PubMed Central: PMC4600213DOI: 10.1186/s12864-015-1977-3Google Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research examines the effect of positive selection on reproduction traits in certain populations of horses. A series of sequencing tests revealed specific regions of the genome, known as runs of homozygosity (ROHs), which show low genetic diversity due to selective pressures. The study contributes to understanding the impact of both artificial and natural selection on horse populations and their reproduction performance.

Methodology

  • The study began with next generation sequencing performed on ten horses from six populations, representing both breed and non-breed types. This involved two Sorraia, one Dülmen Horse, one Arabian, one Saxon-Thuringian Heavy Warmblood, one Thoroughbred, and four Hanoverian horses.
  • Following quality control, reads were mapped to the reference genome EquCab2.70.
  • ROH detection was done using PLINK, version 1.07 for a trimmed dataset consisting of 11,325,777 SNPs (Single Nucleotide Polymorphisms) and a mean read depth of 12.
  • The definition of ROHs was stretches containing over 40kb and beyond 400kb with homozygous genotypes.
  • Functional classification was performed on the genes annotated within these ROHs using PANTHER gene list analysis. Any functional variants were tested for their distribution between breed and non-breed groups.

Results

  • An average number of 3492 ROHs were detected in windows of a minimum of 50 consecutive homozygous SNPs, while around 292 ROHs were found in windows of 500 consecutive homozygous SNPs.
  • Functional analysis of these ROHs showed a high frequency of genes affecting cellular, metabolic, developmental, immune system, and reproduction processes.
  • In non-breed horses, there was an enrichment of genes involved in reproduction, embryonic development, energy metabolism, muscle and cardiac development present in 198 ROHs in 50-SNP windows and seven ROHs in 500-SNP windows.
  • Breed horses revealed only three common ROHs in 50-SNP windows containing the fertility-related gene YES1.
  • In the Hanoverian horse population, 18 private ROHs were found in the region of genes potentially involved in neurologic control, signaling, glycogen balance, and reproduction.
  • Collective analysis of all ten horses demonstrated three ROHs in the region of KITLG, a ligand known for its role in melanogenesis, haematopoiesis, and gametogenesis.

Conclusions

  • This study provides comprehensive insight into the number and frequency of ROHs across various horse populations, shedding light on their possible influence on population diversity and selection pressures.
  • Comparisons between breed and non-breed horses suggest significant artificial as well as natural selection pressure on reproduction performance in all horse populations.

Cite This Article

APA
Metzger J, Karwath M, Tonda R, Beltran S, Águeda L, Gut M, Gut IG, Distl O. (2015). Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses. BMC Genomics, 16, 764. https://doi.org/10.1186/s12864-015-1977-3

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 16
Pages: 764

Researcher Affiliations

Metzger, Julia
  • Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559, Hannover, Germany. julia.metzger@tiho-hannover.de.
Karwath, Matthias
  • Lower Saxony State Office for the Environment, Agriculture and Geology, Unit 74, Animal Breeding and Hygiene, Schlossallee 1, 01468, Moritzburg, Germany. Matthias.Karwath@smul.sachsen.de.
Tonda, Raul
  • Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Torre I Baldiri Reixac, 4, 08028, Barcelona, Spain. rtonda@pcb.ub.cat.
Beltran, Sergi
  • Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Torre I Baldiri Reixac, 4, 08028, Barcelona, Spain. sbeltrana@pcb.ub.cat.
Águeda, Lídia
  • Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Torre I Baldiri Reixac, 4, 08028, Barcelona, Spain. lagueda@pcb.ub.cat.
Gut, Marta
  • Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Torre I Baldiri Reixac, 4, 08028, Barcelona, Spain. mgut@pcb.ub.cat.
Gut, Ivo Glynne
  • Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Torre I Baldiri Reixac, 4, 08028, Barcelona, Spain. igut@pcb.ub.es.
Distl, Ottmar
  • Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559, Hannover, Germany. ottmar.distl@tiho-hannover.de.

MeSH Terms

  • Animals
  • Breeding
  • Genomics
  • Genotype
  • High-Throughput Nucleotide Sequencing
  • Homozygote
  • Horses / genetics
  • Phenotype
  • Polymorphism, Single Nucleotide
  • Reproduction / genetics
  • Selection, Genetic

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