title: Genome-wide next-generation DNA and RNA sequencing reveals a mutation that perturbs splicing of the phosphatidylinositol glycan anchor biosynthesis class H gene (PIGH) and causes arthrogryposis in Belgian Blue cattle.
abstract: BACKGROUND
  Cattle populations are characterized by regular outburst of genetic defects as a result of the extensive use of elite sires. The causative genes and mutations can nowadays be rapidly identified by means of genome-wide association studies combined with next generation DNA sequencing, provided that the causative mutations are conventional loss-of-function variants. We show in this work how the combined use of next generation DNA and RNA sequencing allows for the rapid identification of otherwise difficult to identify splice-site variants.
  
  
  RESULTS
  We report the use of haplotype-based association mapping to identify a locus on bovine chromosome 10 that underlies autosomal recessive arthrogryposis in Belgian Blue Cattle. We identify 31 candidate mutations by resequencing the genome of four cases and 15 controls at ~10-fold depth. By analyzing RNA-Seq data from a carrier fetus, we observe skipping of the second exon of the PIGH gene, which we confirm by RT-PCR to be fully penetrant in tissues from affected calves. We identify - amongst the 31 candidate variants - a C-to-G transversion in the first intron of the PIGH gene (c211-10C > G) that is predicted to affect its acceptor splice-site. The resulting PIGH protein is likely to be non-functional as it lacks essential domains, and hence to cause arthrogryposis.
  
  
  CONCLUSIONS
  This work illustrates how the growing arsenal of genome exploration tools continues to accelerate the identification of an even broader range of disease causing mutations, therefore improving the management and control of genetic defects in livestock.
authors.affiliation: GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium. asartelet@ulg.ac.be.
authors.forename: Arnaud
authors.initials: A
authors.lastname: Sartelet
authors.affiliation: GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium. li.wanbo.ulg@gmail.com.
authors.forename: Wanbo
authors.initials: W
authors.lastname: Li
authors.affiliation: INRA, UMR 1198, Biologie du Développement et Reproduction, F-78350, Jouy-en-Josas, France. eric.pailhoux@jouy.inra.fr.
authors.forename: Eric
authors.initials: E
authors.lastname: Pailhoux
authors.affiliation: INRA, UMR 1198, Biologie du Développement et Reproduction, F-78350, Jouy-en-Josas, France. christophe.richard@jouy.inra.fr.
authors.forename: Christophe
authors.initials: C
authors.lastname: Richard
authors.affiliation: GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium. nico.tamma@ulg.ac.be.
authors.forename: Nico
authors.initials: N
authors.lastname: Tamma
authors.affiliation: GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium. lkarim@ulg.ac.be.|GIGA Genomic Platform, GIGA, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium. lkarim@ulg.ac.be.
authors.forename: Latifa
authors.initials: L
authors.lastname: Karim
authors.affiliation: GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium. corinne.fasquelle@ulg.ac.be.
authors.forename: Corinne
authors.initials: C
authors.lastname: Fasquelle
authors.affiliation: GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium. tom.druet@ulg.ac.be.
authors.forename: Tom
authors.initials: T
authors.lastname: Druet
authors.affiliation: GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium. wouter.coppieters@ulg.ac.be.|GIGA Genomic Platform, GIGA, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium. wouter.coppieters@ulg.ac.be.
authors.forename: Wouter
authors.initials: W
authors.lastname: Coppieters
authors.affiliation: GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium. michel.georges@ulg.ac.be.
authors.forename: Michel
authors.initials: M
authors.lastname: Georges
authors.affiliation: GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium. carole.charlier@ulg.ac.be.
authors.forename: Carole
authors.initials: C
authors.lastname: Charlier
mesh_terms: D000818:Animals; D001176:Arthrogryposis / Q000209:etiology / Q000235:genetics* / Q000662:veterinary; D001530:Belgium; D002417:Cattle; D002874:Chromosome Mapping; D005091:Exons; D016678:Genome; D055106:Genome-Wide Association Study; D005838:Genotype; D017261:Glycosylphosphatidylinositols / Q000378:metabolism; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing; D007438:Introns; D008565:Membrane Proteins / Q000235:genetics* / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D022821:RNA Splice Sites; D012326:RNA Splicing; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA
chemical_list: D017261:Glycosylphosphatidylinositols; D008565:Membrane Proteins; D022821:RNA Splice Sites