title: NGS-based reverse genetic screen for common embryonic lethal mutations compromising fertility in livestock.
abstract: We herein report the result of a large-scale, next generation sequencing (NGS)-based screen for embryonic lethal (EL) mutations in Belgian beef and New Zealand dairy cattle. We estimated by simulation that cattle might carry, on average, ∼0.5 recessive EL mutations. We mined exome sequence data from >600 animals, and identified 1377 stop-gain, 3139 frame-shift, 1341 splice-site, 22,939 disruptive missense, 62,399 benign missense, and 92,163 synonymous variants. We show that cattle have a comparable load of loss-of-function (LoF) variants (defined as stop-gain, frame-shift, or splice-site variants) as humans despite having a more variable exome. We genotyped >40,000 animals for up to 296 LoF and 3483 disruptive missense, breed-specific variants. We identified candidate EL mutations based on the observation of a significant depletion in homozygotes. We estimated the proportion of EL mutations at 15% of tested LoF and 6% of tested disruptive missense variants. We confirmed the EL nature of nine candidate variants by genotyping 200 carrier × carrier trios, and demonstrating the absence of homozygous offspring. The nine identified EL mutations segregate at frequencies ranging from 1.2% to 6.6% in the studied populations and collectively account for the mortality of ∼0.6% of conceptuses. We show that EL mutations preferentially affect gene products fulfilling basic cellular functions. The resulting information will be useful to avoid at-risk matings, thereby improving fertility.
authors.affiliation: Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium.
authors.forename: Carole
authors.initials: C
authors.lastname: Charlier
authors.affiliation: State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, P.R. China.
authors.forename: Wanbo
authors.initials: W
authors.lastname: Li
authors.affiliation: Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium; Livestock Improvement Corporation, Newstead, Hamilton 3240, New Zealand.
authors.forename: Chad
authors.initials: C
authors.lastname: Harland
authors.affiliation: Livestock Improvement Corporation, Newstead, Hamilton 3240, New Zealand.
authors.forename: Mathew
authors.initials: M
authors.lastname: Littlejohn
authors.affiliation: 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.forename: Wouter
authors.initials: W
authors.lastname: Coppieters
authors.affiliation: Livestock Improvement Corporation, Newstead, Hamilton 3240, New Zealand.
authors.forename: Frances
authors.initials: F
authors.lastname: Creagh
authors.affiliation: Livestock Improvement Corporation, Newstead, Hamilton 3240, New Zealand.
authors.forename: Steve
authors.initials: S
authors.lastname: Davis
authors.affiliation: Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium.
authors.forename: Tom
authors.initials: T
authors.lastname: Druet
authors.affiliation: Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium.
authors.forename: Pierre
authors.initials: P
authors.lastname: Faux
authors.affiliation: Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium.
authors.forename: François
authors.initials: F
authors.lastname: Guillaume
authors.affiliation: 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.forename: Latifa
authors.initials: L
authors.lastname: Karim
authors.affiliation: Livestock Improvement Corporation, Newstead, Hamilton 3240, New Zealand.
authors.forename: Mike
authors.initials: M
authors.lastname: Keehan
authors.affiliation: Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium.
authors.forename: Naveen Kumar
authors.initials: NK
authors.lastname: Kadri
authors.affiliation: Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium.
authors.forename: Nico
authors.initials: N
authors.lastname: Tamma
authors.affiliation: Livestock Improvement Corporation, Newstead, Hamilton 3240, New Zealand.
authors.forename: Richard
authors.initials: R
authors.lastname: Spelman
authors.affiliation: Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium.
authors.forename: Michel
authors.initials: M
authors.lastname: Georges
mesh_terms: D000818:Animals; D002417:Cattle / Q000196:embryology / Q000235:genetics* / Q000502:physiology; D005298:Fertility / Q000235:genetics*; D005804:Genes, Lethal; D005820:Genetic Testing / Q000379:methods; D006579:Heterozygote; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006720:Homozygote; D009154:Mutation; D059386:Reverse Genetics / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods