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Home / Equine Research Bank / Genome Res / Exploration of fine-scale recombination rate variation in th...
Genome research2019; 29(10); 1744-1752; doi: 10.1101/gr.243311.118

Exploration of fine-scale recombination rate variation in the domestic horse.

Abstract: Total genetic map length and local recombination landscapes typically vary within and across populations. As a first step to understanding the recombination landscape in the domestic horse, we calculated population recombination rates and identified likely recombination hotspots using approximately 1.8 million SNP genotypes for 485 horses from 32 distinct breeds. The resulting breed-averaged recombination map spans 2.36 Gb and accounts for 2939.07 cM. Recombination hotspots occur once per 23.8 Mb on average and account for ∼9% of the physical map length. Regions with elevated recombination rates in the entire cohort were enriched for genes in pathways involving interaction with the environment: immune system processes (specifically, MHC class I and class II genes), responses to stimuli, and serotonin receptor pathways. We found significant correlations between differences in local recombination rates and population differentiation quantified by Analysis of breed-specific maps revealed thousands of hotspot regions unique to particular breeds, as well as unique "coldspots," regions where a particular breed showed below-average recombination, whereas all other breeds had evidence of a hotspot. Finally, we identified relative enrichment ( = 5.88 × 10) for the in silico-predicted recognition motif for equine PR/SET domain 9 (PRDM9) in recombination hotspots. These results indicate that selective pressures and PRDM9 function contribute to variation in recombination rates across the domestic horse genome.
© 2019 Beeson et al.; Published by Cold Spring Harbor Laboratory Press.
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Publication Date: 2019-08-21 PubMed ID: 31434677PubMed Central: PMC6771410DOI: 10.1101/gr.243311.118Google Scholar: Lookup
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  • Journal Article
  • Research Support
  • N.I.H.
  • Extramural
  • Research Support
  • Non-U.S. Gov't
  • Research Support
  • U.S. Gov't
  • Non-P.H.S.

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 article explores the diversity in recombination rates observed within the domestic horse population, utilizing genetic data from different horse breeds to identify recombination hotspots and their relation to certain genetic pathways.

Understanding the Recombination Landscape

  • The research began by investigating the recombination rate within the domestic horse population. This was done by examining the Single Nucleotide Polymorphisms (SNPs), a DNA sequence variation occurring commonly within a population, from 485 horses across 32 distinct breeds. In total, approximately 1.8 million SNP genotypes were used for this part of the research.
  • They were able to create an averaged recombination map, which spans 2.36 Gb (gigabases) and accounts for 2939.07 cM (centimorgans). This map represents the frequency and likelihood of recombination events in the horse’s genome.

Recombination Hotspots and Coldspots

  • Findings indicated that recombination hotspots occur once per 23.8 megabases (Mb) on average, making up around 9% of the physical map length. These hotspots are areas in the DNA where recombination occurs at a higher rate.
  • Complementing hotspots, “coldspots” were also identified. These are regions where specific horse breed showed below-average recombination, whereas all other breeds had evidence of a hotspot.

Enrichment in Specific Genetic Pathways

  • Areas with higher recombination rates correlated with enrichment of genes in certain pathways. These included immune system processes (notably MHC class I and class II genes), responses to stimuli, and serotonin receptor pathways, all concerned with the organism’s interaction with its environment.

The Role of PRDM9

  • The researchers identified an in silico-predicted recognition motif for equine PR/SET domain 9 (PRDM9), a protein that plays a major role in determining the locations of recombination hotspots, in these recombination hotspots.
  • This result suggests that selective pressures and PRDM9 function contribute to the variation in recombination rates across the horse genome.

Cite This Article

APA
Beeson SK, Mickelson JR, McCue ME. (2019). Exploration of fine-scale recombination rate variation in the domestic horse. Genome Res, 29(10), 1744-1752. https://doi.org/10.1101/gr.243311.118

Publication

Genome research
ISSN: 1549-5469
NlmUniqueID: 9518021
Country: United States
Language: English
Volume: 29
Issue: 10
Pages: 1744-1752

Researcher Affiliations

Beeson, Samantha K
  • Veterinary Population Medicine Department, University of Minnesota, St. Paul, Minnesota 55108, USA.
Mickelson, James R
  • Veterinary and Biomedical Sciences Department, University of Minnesota, St. Paul, Minnesota 55108, USA.
McCue, Molly E
  • Veterinary Population Medicine Department, University of Minnesota, St. Paul, Minnesota 55108, USA.

MeSH Terms

  • Animals
  • Breeding
  • Chromosome Mapping
  • Evolution, Molecular
  • Genome / genetics
  • Horses / genetics
  • Humans
  • Meiosis / genetics
  • Polymorphism, Single Nucleotide / genetics
  • Recombination, Genetic / genetics

Grant Funding

  • F30 OD023369 / NIH HHS
  • T32 AR007612 / NIAMS NIH HHS

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