title: Genome-Wide Study of Structural Variants in Bovine Holstein, Montbéliarde and Normande Dairy Breeds.
abstract: High-throughput sequencing technologies have offered in recent years new opportunities to study genome variations. These studies have mostly focused on single nucleotide polymorphisms, small insertions or deletions and on copy number variants. Other structural variants, such as large insertions or deletions, tandem duplications, translocations, and inversions are less well-studied, despite that some have an important impact on phenotypes. In the present study, we performed a large-scale survey of structural variants in cattle. We report the identification of 6,426 putative structural variants in cattle extracted from whole-genome sequence data of 62 bulls representing the three major French dairy breeds. These genomic variants affect DNA segments greater than 50 base pairs and correspond to deletions, inversions and tandem duplications. Out of these, we identified a total of 547 deletions and 410 tandem duplications which could potentially code for CNVs. Experimental validation was carried out on 331 structural variants using a novel high-throughput genotyping method. Out of these, 255 structural variants (77%) generated good quality genotypes and 191 (75%) of them were validated. Gene content analyses in structural variant regions revealed 941 large deletions removing completely one or several genes, including 10 single-copy genes. In addition, some of the structural variants are located within quantitative trait loci for dairy traits. This study is a pan-genome assessment of genomic variations in cattle and may provide a new glimpse into the bovine genome architecture. Our results may also help to study the effects of structural variants on gene expression and consequently their effect on certain phenotypes of interest.
authors: INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France; AgroParisTech, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France.
authors: Mekki
authors: M
authors: Boussaha
authors: INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, France.
authors: Diane
authors: D
authors: Esquerré
authors: INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, France.
authors: Johanna
authors: J
authors: Barbieri
authors: INRA, SIGENAE, UR 875, INRA Auzeville, BP 52627, Castanet-Tolosan, France.
authors: Anis
authors: A
authors: Djari
authors: INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, France.
authors: Alain
authors: A
authors: Pinton
authors: INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France; AgroParisTech, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France.
authors: Rabia
authors: R
authors: Letaief
authors: INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, France.
authors: Gérald
authors: G
authors: Salin
authors: INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, France.
authors: Frédéric
authors: F
authors: Escudié
authors: INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, France.
authors: Alain
authors: A
authors: Roulet
authors: INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France; AgroParisTech, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France; Union Nationale des Coopératives Agricoles d'Elevage et d'Insémination Animale, Paris, France.
authors: Sébastien
authors: S
authors: Fritz
authors: INRA, UR1077, Mathématique Informatique et Génome, Domaine de Vilvert, Jouy-en-Josas, France.
authors: Franck
authors: F
authors: Samson
authors: INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France; AgroParisTech, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France.
authors: Cécile
authors: C
authors: Grohs
authors: INRA, SIGENAE, UR 875, INRA Auzeville, BP 52627, Castanet-Tolosan, France.
authors: Maria
authors: M
authors: Bernard
authors: INRA, SIGENAE, UR 875, INRA Auzeville, BP 52627, Castanet-Tolosan, France.
authors: Christophe
authors: C
authors: Klopp
authors: INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France; AgroParisTech, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France.
authors: Didier
authors: D
authors: Boichard
authors: INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France; AgroParisTech, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France.
authors: Dominique
authors: D
authors: Rocha
mesh_terms: D000818:Animals; D017849:Animals, Inbred Strains; D002417:Cattle / Q000235:genetics*; D003612:Dairying; D055106:Genome-Wide Association Study; D056914:Genomic Structural Variation; D005838:Genotype; D040641:Quantitative Trait Loci