title: Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences.
abstract: In recent years, several bovine genome sequencing projects were carried out with the aim of developing genomic tools to improve dairy and beef production efficiency and sustainability.
  
  
  
  In this study, we describe the first French cattle genome variation dataset obtained by sequencing 274 whole genomes representing several major dairy and beef breeds. This dataset contains over 28 million single nucleotide polymorphisms (SNPs) and small insertions and deletions. Comparisons between sequencing results and SNP array genotypes revealed a very high genotype concordance rate, which indicates the good quality of our data.
  
  
  
  To our knowledge, this is the first large-scale catalog of small genomic variations in French dairy and beef cattle. This resource will contribute to the study of gene functions and population structure and also help to improve traits through genotype-guided selection.
authors.affiliation: GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France. mekki.boussaha@inra.fr.
authors.forename: Mekki
authors.initials: M
authors.lastname: Boussaha
authors.affiliation: GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.|Allice, Maison Nationale des Eleveurs, 75012, Paris, France.
authors.forename: Pauline
authors.initials: P
authors.lastname: Michot
authors.affiliation: GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
authors.forename: Rabia
authors.initials: R
authors.lastname: Letaief
authors.affiliation: GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.|Allice, Maison Nationale des Eleveurs, 75012, Paris, France.
authors.forename: Chris
authors.initials: C
authors.lastname: Hozé
authors.affiliation: GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.|Allice, Maison Nationale des Eleveurs, 75012, Paris, France.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Fritz
authors.affiliation: GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
authors.forename: Cécile
authors.initials: C
authors.lastname: Grohs
authors.affiliation: GenPhySE, INRA, INPT, ENVT, Université de Toulouse, Castanet Tolosan, France.
authors.forename: Diane
authors.initials: D
authors.lastname: Esquerré
authors.affiliation: GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
authors.forename: Amandine
authors.initials: A
authors.lastname: Duchesne
authors.affiliation: GMA, INRA, Université de Limoges, 87060, Limoges Cedex, France.
authors.forename: Romain
authors.initials: R
authors.lastname: Philippe
authors.affiliation: GMA, INRA, Université de Limoges, 87060, Limoges Cedex, France.
authors.forename: Véronique
authors.initials: V
authors.lastname: Blanquet
authors.affiliation: GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
authors.forename: Florence
authors.initials: F
authors.lastname: Phocas
authors.affiliation: GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Floriot
authors.affiliation: GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
authors.forename: Dominique
authors.initials: D
authors.lastname: Rocha
authors.affiliation: SIGENAE, UR 875, INRA, 31362, Castanet-Tolosan, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Klopp
authors.affiliation: GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.|Allice, Maison Nationale des Eleveurs, 75012, Paris, France.
authors.forename: Aurélien
authors.initials: A
authors.lastname: Capitan
authors.affiliation: GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
authors.forename: Didier
authors.initials: D
authors.lastname: Boichard
mesh_terms: D000818:Animals; D001947:Breeding; D002417:Cattle; D002874:Chromosome Mapping; D003612:Dairying; D005260:Female; D014644:Genetic Variation; D016678:Genome; D005838:Genotype; D054643:INDEL Mutation; D008297:Male; D059645:Mutation Rate; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D000069466:Red Meat