Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences

Mekki Boussaha , Pauline Michot , Rabia Letaief , Chris Hozé , Sébastien Fritz , Cécile Grohs , Diane Esquerré , Amandine Duchesne , Romain Philippe , Véronique V. Blanquet , Florence Phocas , Sandrine Floriot , Dominique Rocha , Christophe C. Klopp , Aurélien Capitan , Didier Boichard

AbstractBackgroundIn 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.ResultsIn 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.ConclusionsTo 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.

Mots clés: bovin; single nucleotide polymorphism (SNP)

Mots clés: séquençage du génome; InDel

Domaines: Sciences du Vivant [q-bio]

Mekki Boussaha, Pauline Michot, Rabia Letaief, Chris Hozé, Sébastien Fritz, et al.. Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences. Genetics Selection Evolution, 2016, 48 (1), pp.87. ⟨10.1186/s12711-016-0268-z⟩. ⟨hal-01479216⟩