Identification of genes involved in meat quality in French beef cattle breeds

Les méthodes classiques de sélection animale ne permettent pas d’améliorer la qualité sensoriel et organoleptique de la viande vu la complexité de prise des mesures en routine de ces caractères. L’utilisation de la génomique pourrai donc être l’alternative pour améliorer ces caractères en cherchant des marqueurs moléculaires qui sont en fort déséquilibre de liaison avec les mutations causales qui expliquent une part de la variabilité phénotypique. Mais tout d’abord, une analyse de la structure du déséquilibre de liaison à l’échelle du génome pourra être intéressante d’un point de vu fondamental afin de comprendre à quel point les allèles sont transmis ensemble de génération en génération.Ma thèse consiste à réaliser une étude du déséquilibre de liaison à longue distance (LRLD) dans les principales races bovines allaitantes françaises (Charolaise, Limousine et Blonde d’Aquitaine). Le deuxième volet de ma thèse a consisté à rechercher des variants associés à la qualité de la viande et aux aptitudes bouchères chez les principales races bovines allaitantes françaises à l’aide des données de séquence du génome complet.Classical methods of animal selection do not improve the sensory and organoleptic quality of meat due to the complexity of taking routine measurements of these qualities. The use of genomics could therefore be the alternative to improve these traits by looking for molecular markers that are in strong linkage disequilibrium with the causal mutation that explains part of the phenotypic variability. But first of all, an analysis of the structure of the linkage disequilibrium at the genome level could be interesting from a fundamental point of view in order to understand to which extent the alleles are transmitted together from generation to generation.My PhD thesis consists of a study of long-range linkage disequilibrium (LRLD) in the main French beef cattle breeds (Charolaise, Limousine and Blonde d’Aquitaine), in the framework of the GEMBAL project. The second part of my thesis consisted in searching for variants associated with meat quality and meat aptitude in the main French beef cattle breeds using whole genome sequence data. in the main French beef cattle breeds, in the framework of the Qualvigène projec

Identification de gènes impliqués dans la qualité des viandes chez les bovins allaitants français

Classical methods of animal selection do not improve the sensory and organoleptic quality of meat due to the complexity of taking routine measurements of these qualities. The use of genomics could therefore be the alternative to improve these traits by looking for molecular markers that are in strong linkage disequilibrium with the causal mutation that explains part of the phenotypic variability. But first of all, an analysis of the structure of the linkage disequilibrium at the genome level could be interesting from a fundamental point of view in order to understand to which extent the alleles are transmitted together from generation to generation.My PhD thesis consists of a study of long-range linkage disequilibrium (LRLD) in the main French beef cattle breeds (Charolaise, Limousine and Blonde d’Aquitaine), in the framework of the GEMBAL project. The second part of my thesis consisted in searching for variants associated with meat quality and meat aptitude in the main French beef cattle breeds using whole genome sequence data. in the main French beef cattle breeds, in the framework of the Qualvigène projectLes méthodes classiques de sélection animale ne permettent pas d’améliorer la qualité sensoriel et organoleptique de la viande vu la complexité de prise des mesures en routine de ces caractères. L’utilisation de la génomique pourrai donc être l’alternative pour améliorer ces caractères en cherchant des marqueurs moléculaires qui sont en fort déséquilibre de liaison avec les mutations causales qui expliquent une part de la variabilité phénotypique. Mais tout d’abord, une analyse de la structure du déséquilibre de liaison à l’échelle du génome pourra être intéressante d’un point de vu fondamental afin de comprendre à quel point les allèles sont transmis ensemble de génération en génération.Ma thèse consiste à réaliser une étude du déséquilibre de liaison à longue distance (LRLD) dans les principales races bovines allaitantes françaises (Charolaise, Limousine et Blonde d’Aquitaine). Le deuxième volet de ma thèse a consisté à rechercher des variants associés à la qualité de la viande et aux aptitudes bouchères chez les principales races bovines allaitantes françaises à l’aide des données de séquence du génome complet

Contribution of linkage disequilibrium studies for fine-mapping QTL : case study : application to meat quality in French beef cattle breeds.

International audienc

Contribution of linkage disequilibrium for fine-mapping of QTL : application to meat quality in French beef cattle breeds

International audienc

Fine mapping of QTLs for meat quality traits in French Charolaise breed using HD SNP data

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Long-range linkage disequilibrium in French beef cattle breeds

International audienceBackground: Linkage disequilibrium (LD) is a key parameter to study the history of populations and to identify and fine map quantitative trait loci (QTL) and it has been studied for many years in animal populations. The advent of new genotyping technologies has allowed whole-genome LD studies in most cattle populations. However, to date, long-range LD (LRLD) between distant variants on the genome has not been investigated in detail in cattle. Here, we present the first comprehensive study of LRLD in French beef cattle by analysing data on 672 Charolais (CHA), 462 Limousine (LIM) and 326 Blonde d' Aquitaine (BLA) individuals that were genotyped on the Illumina BovineHD Beadchip. Furthermore, whole-genome LD and haplotype block structure were analysed in these three breeds. Results: We computed linkage disequilibrium (r 2) values for 5.9, 5.6 and 6.0 billion pairs of SNPs on the 29 autosomes of CHA, LIM and BLA, respectively. Mean r 2 values drop to less than 0.1 for distances between SNPs greater than 120 kb. However, for the first time, we detected the existence of LRLD in the three main French beef breeds. In total, 598, 266, and 795 LRLD events (r 2 ≥ 0.6) were detected in CHA, LIM and BLA, respectively. Each breed had predominantly population-specific LRLD interactions, although shared LRLD events occurred in a number of regions (55 LRLD events were shared between two breeds and nine between the three breeds). Examples of possible functional gene interactions and QTL co-location were observed with some of these LRLD events, which suggests epistatic selection. Conclusions: We identified long-range linkage disequilibrium for the first time in French beef cattle populations. Epistatic selection may be the main source of the observed LRLD events, but other forces may also be involved. LRLD information should be accounted for in genome-wide association studies

Survey of allele specific expression in bovine muscle

Abstract Allelic imbalance is a common phenomenon in mammals that plays an important role in gene regulation. An Allele Specific Expression (ASE) approach can be used to detect variants with a cis-regulatory effect on gene expression. In cattle, this type of study has only been done once in Holstein. In our study we performed a genome-wide analysis of ASE in 19 Limousine muscle samples. We identified 5,658 ASE SNPs (Single Nucleotide Polymorphisms showing allele specific expression) in 13% of genes with detectable expression in the Longissimus thoraci muscle. Interestingly we found allelic imbalance in AOX1, PALLD and CAST genes. We also found 2,107 ASE SNPs located within genomic regions associated with meat or carcass traits. In order to identify causative cis-regulatory variants explaining ASE we searched for SNPs altering binding sites of transcription factors or microRNAs. We identified one SNP in the 3’UTR region of PRNP that could be a causal regulatory variant modifying binding sites of several miRNAs. We showed that ASE is frequent within our muscle samples. Our data could be used to elucidate the molecular mechanisms underlying gene expression imbalance