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

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...

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Detalles Bibliográficos
Autores principales: Beeson, Samantha K., Mickelson, James R., McCue, Molly E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6771410/
https://www.ncbi.nlm.nih.gov/pubmed/31434677
http://dx.doi.org/10.1101/gr.243311.118
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author Beeson, Samantha K.
Mickelson, James R.
McCue, Molly E.
author_facet Beeson, Samantha K.
Mickelson, James R.
McCue, Molly E.
author_sort Beeson, Samantha K.
collection PubMed
description 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 F(ST). 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 (P = 5.88 × 10(−27)) 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.
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spelling pubmed-67714102020-04-01 Exploration of fine-scale recombination rate variation in the domestic horse Beeson, Samantha K. Mickelson, James R. McCue, Molly E. Genome Res Resource 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 F(ST). 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 (P = 5.88 × 10(−27)) 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. Cold Spring Harbor Laboratory Press 2019-10 /pmc/articles/PMC6771410/ /pubmed/31434677 http://dx.doi.org/10.1101/gr.243311.118 Text en © 2019 Beeson et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
spellingShingle Resource
Beeson, Samantha K.
Mickelson, James R.
McCue, Molly E.
Exploration of fine-scale recombination rate variation in the domestic horse
title Exploration of fine-scale recombination rate variation in the domestic horse
title_full Exploration of fine-scale recombination rate variation in the domestic horse
title_fullStr Exploration of fine-scale recombination rate variation in the domestic horse
title_full_unstemmed Exploration of fine-scale recombination rate variation in the domestic horse
title_short Exploration of fine-scale recombination rate variation in the domestic horse
title_sort exploration of fine-scale recombination rate variation in the domestic horse
topic Resource
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6771410/
https://www.ncbi.nlm.nih.gov/pubmed/31434677
http://dx.doi.org/10.1101/gr.243311.118
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