1. Detection of selection signatures in Limousin cattle using whole‐genome resequencing
- Author
-
Gilles Renand, Yuliaxis Ramayo-Caldas, Dominique Rocha, M. Mariadassou, Mathieu Charles, M. Féménia, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Animale et Biologie Intégrative (GABI), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute for Food and Agriculture Research and Technology (IRTA), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Université Paris-Saclay, APIS-GENE 01-2005-QualviGenA-02, INRAE, ANR-05-GANI-0005,Mugene,Approche intégrée combinant la génétique, la génomique et la biologie musculaire pour gérer la qualité de la viande bovine selon le potentiel de croissance des animaux et les facteurs d'élevage.(2005), ANR-05-GANI-0017,QualvigenA,Détection et validation de génes impliqués dans les qualités de la viande bovine des trois principales races à viande en France(2005), ANR-09-GENM-0011,Regulomix,Analyse à grande échelle des polymorphismes bovins affectant la régulation de gènes : un pas vers l'annotation fonctionnelle du génome bovin(2009), European Project: 6655919,P-Sphere, and AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
- Subjects
Male ,0301 basic medicine ,Candidate gene ,[SDV]Life Sciences [q-bio] ,whole-genome resequencing ,biology.animal_breed ,Single-nucleotide polymorphism ,Biology ,Quantitative trait locus ,Polymorphism, Single Nucleotide ,Genome ,03 medical and health sciences ,INDEL Mutation ,Genetics ,Animals ,Selection, Genetic ,Indel ,Limousin breed ,Selection (genetic algorithm) ,Limousin cattle ,[SDV.GEN]Life Sciences [q-bio]/Genetics ,Whole Genome Sequencing ,[SDV.BA]Life Sciences [q-bio]/Animal biology ,0402 animal and dairy science ,04 agricultural and veterinary sciences ,General Medicine ,040201 dairy & animal science ,signature of selection ,030104 developmental biology ,Cattle ,Animal Science and Zoology ,France ,polymorphisms ,Selective sweep - Abstract
International audience; Limousin, a renowned beef breed originating from central France, has been selectively bred over the last 100 years to improve economically important traits. We used whole-genome sequencing data from 10 unrelated Limousin bull calves to detect polymorphisms and identify regions under selection. A total of 13 943 766 variants were identified. Moreover, 311 852 bi-allelic SNPs and 92 229 indels located on autosomes were fixed for the alternative allele in all sequenced animals, including the previously reported missense deleterious F94L mutation inMSTN. We performed a whole-genome screen to discover genomic regions with excess homozygosity, using the pooled heterozygosity score and identified 171 different candidate selective sweeps. In total, 68 candidate genes were found in only 57 of these regions, indicating that a large fraction of the genome under selection might lie in non-coding regions and suggesting that a majority of adaptive mutations might be regulatory in nature. Many QTL were found within candidate selective sweep regions, including QTL associated with shear force or carcass weight. Among the putative selective sweeps, we located genes (MSTN,NCKAP5,RUNX2) that potentially contribute to important phenotypes in Limousin. Several candidate regions and genes under selection were also found in previous genome-wide selection scans performed in Limousin. In addition, we were able to pinpoint candidate causative regulatory polymorphisms inGRIK3andRUNX2that might have been under selection. Our results will contribute to improved understanding of the mechanisms and targets of artificial selection and will facilitate the interpretation of GWASs performed in Limousin.
- Published
- 2020