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Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle

We herein study genetic recombination in three cattle populations from France, New Zealand, and the Netherlands. We identify 2,395,177 crossover (CO) events in 94,516 male gametes, and 579,996 CO events in 25,332 female gametes. The average number of COs was found to be larger in males (23.3) than i...

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Autores principales: Kadri, Naveen Kumar, Harland, Chad, Faux, Pierre, Cambisano, Nadine, Karim, Latifa, Coppieters, Wouter, Fritz, Sébastien, Mullaart, Erik, Baurain, Denis, Boichard, Didier, Spelman, Richard, Charlier, Carole, Georges, Michel, Druet, Tom
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5052053/
https://www.ncbi.nlm.nih.gov/pubmed/27516620
http://dx.doi.org/10.1101/gr.204214.116
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author Kadri, Naveen Kumar
Harland, Chad
Faux, Pierre
Cambisano, Nadine
Karim, Latifa
Coppieters, Wouter
Fritz, Sébastien
Mullaart, Erik
Baurain, Denis
Boichard, Didier
Spelman, Richard
Charlier, Carole
Georges, Michel
Druet, Tom
author_facet Kadri, Naveen Kumar
Harland, Chad
Faux, Pierre
Cambisano, Nadine
Karim, Latifa
Coppieters, Wouter
Fritz, Sébastien
Mullaart, Erik
Baurain, Denis
Boichard, Didier
Spelman, Richard
Charlier, Carole
Georges, Michel
Druet, Tom
author_sort Kadri, Naveen Kumar
collection PubMed
description We herein study genetic recombination in three cattle populations from France, New Zealand, and the Netherlands. We identify 2,395,177 crossover (CO) events in 94,516 male gametes, and 579,996 CO events in 25,332 female gametes. The average number of COs was found to be larger in males (23.3) than in females (21.4). The heritability of global recombination rate (GRR) was estimated at 0.13 in males and 0.08 in females, with a genetic correlation of 0.66 indicating that shared variants are influencing GRR in both sexes. A genome-wide association study identified seven quantitative trait loci (QTL) for GRR. Fine-mapping following sequence-based imputation in 14,401 animals pinpointed likely causative coding (5) and noncoding (1) variants in genes known to be involved in meiotic recombination (HFM1, MSH4, RNF212, MLH3, MSH5) for 5/7 QTL, and noncoding variants (3) in RNF212B for 1/7 QTL. This suggests that this RNF212 paralog might also be involved in recombination. Most of the identified mutations had significant effects in both sexes, with three of them each accounting for ∼10% of the genetic variance in males.
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spelling pubmed-50520532017-04-01 Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle Kadri, Naveen Kumar Harland, Chad Faux, Pierre Cambisano, Nadine Karim, Latifa Coppieters, Wouter Fritz, Sébastien Mullaart, Erik Baurain, Denis Boichard, Didier Spelman, Richard Charlier, Carole Georges, Michel Druet, Tom Genome Res Research We herein study genetic recombination in three cattle populations from France, New Zealand, and the Netherlands. We identify 2,395,177 crossover (CO) events in 94,516 male gametes, and 579,996 CO events in 25,332 female gametes. The average number of COs was found to be larger in males (23.3) than in females (21.4). The heritability of global recombination rate (GRR) was estimated at 0.13 in males and 0.08 in females, with a genetic correlation of 0.66 indicating that shared variants are influencing GRR in both sexes. A genome-wide association study identified seven quantitative trait loci (QTL) for GRR. Fine-mapping following sequence-based imputation in 14,401 animals pinpointed likely causative coding (5) and noncoding (1) variants in genes known to be involved in meiotic recombination (HFM1, MSH4, RNF212, MLH3, MSH5) for 5/7 QTL, and noncoding variants (3) in RNF212B for 1/7 QTL. This suggests that this RNF212 paralog might also be involved in recombination. Most of the identified mutations had significant effects in both sexes, with three of them each accounting for ∼10% of the genetic variance in males. Cold Spring Harbor Laboratory Press 2016-10 /pmc/articles/PMC5052053/ /pubmed/27516620 http://dx.doi.org/10.1101/gr.204214.116 Text en © 2016 Kadri 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 Research
Kadri, Naveen Kumar
Harland, Chad
Faux, Pierre
Cambisano, Nadine
Karim, Latifa
Coppieters, Wouter
Fritz, Sébastien
Mullaart, Erik
Baurain, Denis
Boichard, Didier
Spelman, Richard
Charlier, Carole
Georges, Michel
Druet, Tom
Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle
title Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle
title_full Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle
title_fullStr Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle
title_full_unstemmed Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle
title_short Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle
title_sort coding and noncoding variants in hfm1, mlh3, msh4, msh5, rnf212, and rnf212b affect recombination rate in cattle
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5052053/
https://www.ncbi.nlm.nih.gov/pubmed/27516620
http://dx.doi.org/10.1101/gr.204214.116
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