Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle
- Naveen Kumar Kadri1,
- Chad Harland1,2,
- Pierre Faux1,
- Nadine Cambisano1,3,
- Latifa Karim1,3,
- Wouter Coppieters1,3,
- Sébastien Fritz4,5,
- Erik Mullaart6,
- Denis Baurain7,
- Didier Boichard5,
- Richard Spelman2,
- Carole Charlier1,
- Michel Georges1 and
- Tom Druet1
- 1Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000 Liège, Belgium;
- 2Livestock Improvement Corporation, Newstead, 3240 Hamilton, New Zealand;
- 3Genomics Platform, GIGA, University of Liège (B34), 4000 Liège, Belgium;
- 4Allice, 75012 Paris, France;
- 5GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France;
- 6CRV BV, 6800 AL Arnhem, the Netherlands;
- 7InBioS-Eukaryotic Phylogenomics, Department of Life Sciences and PhytoSYSTEMS, University of Liège (B22), 4000 Liège, Belgium
- Corresponding author: Tom.Druet{at}ulg.ac.be
Abstract
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.204214.116.
- Received January 11, 2016.
- Accepted August 10, 2016.
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/.
