title: Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle.
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.
authors: Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000 Liège, Belgium.
authors: Naveen Kumar
authors: NK
authors: Kadri
authors: Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000 Liège, Belgium; Livestock Improvement Corporation, Newstead, 3240 Hamilton, New Zealand.
authors: Chad
authors: C
authors: Harland
authors: Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000 Liège, Belgium.
authors: Pierre
authors: P
authors: Faux
authors: Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000 Liège, Belgium; Genomics Platform, GIGA, University of Liège (B34), 4000 Liège, Belgium.
authors: Nadine
authors: N
authors: Cambisano
authors: Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000 Liège, Belgium; Genomics Platform, GIGA, University of Liège (B34), 4000 Liège, Belgium.
authors: Latifa
authors: L
authors: Karim
authors: Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000 Liège, Belgium; Genomics Platform, GIGA, University of Liège (B34), 4000 Liège, Belgium.
authors: Wouter
authors: W
authors: Coppieters
authors: Allice, 75012 Paris, France; GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
authors: Sébastien
authors: S
authors: Fritz
authors: CRV BV, 6800 AL Arnhem, the Netherlands.
authors: Erik
authors: E
authors: Mullaart
authors: InBioS-Eukaryotic Phylogenomics, Department of Life Sciences and PhytoSYSTEMS, University of Liège (B22), 4000 Liège, Belgium.
authors: Denis
authors: D
authors: Baurain
authors: GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
authors: Didier
authors: D
authors: Boichard
authors: Livestock Improvement Corporation, Newstead, 3240 Hamilton, New Zealand.
authors: Richard
authors: R
authors: Spelman
authors: Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000 Liège, Belgium.
authors: Carole
authors: C
authors: Charlier
authors: Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000 Liège, Belgium.
authors: Michel
authors: M
authors: Georges
authors: Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000 Liège, Belgium.
authors: Tom
authors: T
authors: Druet
mesh_terms: D000818:Animals; D002417:Cattle / Q000235:genetics*; D005260:Female; D055106:Genome-Wide Association Study; D005854:Germ Cells / Q000166:cytology / Q000378:metabolism; D059765:Homologous Recombination; D008297:Male; D008540:Meiosis / Q000235:genetics; D009154:Mutation; D011110:Polymorphism, Genetic; D040641:Quantitative Trait Loci; D012737:Sex Factors