Didier Boichard
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View article: Comprehensive detection of structural variations in long and short reads dataset of French cattle
Comprehensive detection of structural variations in long and short reads dataset of French cattle Open
Structural variants (SVs) correspond to different types of genomic variants larger than 50 bp. Many findings suggest the use of long-read (LR) rather than short-read (SR) sequencing to improve the accuracy of SVs detection. Here, we presen…
View article: Short communication: First insights into response to selection for reducing methane emissions in dairy cows
Short communication: First insights into response to selection for reducing methane emissions in dairy cows Open
Genetic selection against methane emissions is one of the levers to reduce the environmental impact of dairy production. Once genetic evaluation of methane emissions is available, the next step is to include this trait in breeding objectiv…
View article: Genetic regulation of sperm DNA methylation in cattle through meQTL mapping
Genetic regulation of sperm DNA methylation in cattle through meQTL mapping Open
Background DNA methylation (DNAm) plays an important functional role and is influenced by genetic variants known as methylation QTLs (meQTLs). The majority of meQTL studies have been conducted in human blood. Despite its unique landscape, …
View article: Deep Generative Models for Discrete Genotype Simulation
Deep Generative Models for Discrete Genotype Simulation Open
Deep generative models open new avenues for simulating realistic genomic data while preserving privacy and addressing data accessibility constraints. While previous studies have primarily focused on generating gene expression or haplotype …
View article: A novel reusable transcriptome-wide association study workflow used to map key genes linked to important cattle traits
A novel reusable transcriptome-wide association study workflow used to map key genes linked to important cattle traits Open
Transcriptome-wide association studies (TWAS) are a powerful approach for studying the genes underlying complex traits by directly integrating GWAS and gene expression datasets. In cattle, they have been previously applied to identify gene…
View article: Comprehensive detection of structural variations in long and short reads dataset of French cattle
Comprehensive detection of structural variations in long and short reads dataset of French cattle Open
Structural variants (SVs) correspond to different types of genomic variants larger than 50 bp. Many findings suggest the use of long rather than short reads to improve the accuracy of SV detection. Here, we present the results of an in-dep…
View article: Functional impact of splicing variants in the elaboration of complex traits in cattle
Functional impact of splicing variants in the elaboration of complex traits in cattle Open
GWAS conducted directly on imputed whole genome sequence have led to the identification of numerous genetic variants associated with agronomic traits in cattle. However, such variants are often simply markers in linkage disequilibrium with…
View article: Application of a French cattle pangenome, from structural variant discovery to association studies on key phenotypes
Application of a French cattle pangenome, from structural variant discovery to association studies on key phenotypes Open
Background The current cattle reference genome assembly, a pseudo-linear sequence produced using sequences from a single Hereford cow, represent a limit when performing genetic studies, especially when investigating the whole spectrum of g…
View article: Trajectories of genetic correlations in populations under selection: from theory to a case-study
Trajectories of genetic correlations in populations under selection: from theory to a case-study Open
Background Breeding programs select for multiple commercial traits, aiming to achieve genetic progress for all. Often, selection is based on a selection index, i . e . a linear combination of traits with weights defined by, among other inf…
View article: Genetic parameters for methane production, intensity, and yield predicted from milk mid-infrared spectra throughout lactation in Holstein dairy cows
Genetic parameters for methane production, intensity, and yield predicted from milk mid-infrared spectra throughout lactation in Holstein dairy cows Open
Genetic selection to reduce CH4 emissions is a promising solution for reducing the environmental impact of dairy cattle production. Before such a selection program can be implemented, however, it is necessary to have a better understanding…
View article: Long-lasting effects of in utero heat stress on subsequent performances of heifers and primiparous cows
Long-lasting effects of in utero heat stress on subsequent performances of heifers and primiparous cows Open
The performance of an adult dairy cow may be influenced by heat stress that occurs during her gestation. The present study investigated potential effects of temperature-humidity index (THI) experienced by a cow during pregnancy on the gest…
View article: Anticipating future genetic needs for French dairy and suckler cattle sectors.
Anticipating future genetic needs for French dairy and suckler cattle sectors. Open
Session 58. The role of breeding and genetics in the sustainable transformation of the livestock sector
View article: Genetic parameters for methane production, intensity, and yield predicted from milk mid-infrared spectra throughout the lactation in Montbeliarde cows.
Genetic parameters for methane production, intensity, and yield predicted from milk mid-infrared spectra throughout the lactation in Montbeliarde cows. Open
Session 1. Integrating mitigation and adaptation breeding strategies
View article: Sequence-based GWAS of heat tolerance traits in Holstein and Montbeliarde cattle.
Sequence-based GWAS of heat tolerance traits in Holstein and Montbeliarde cattle. Open
Session 1. Integrating mitigation and adaptation breeding strategies
View article: The construction of a cattle pangenome for 14 French dairy and beef breeds provides new insights into their genetic diversity.
The construction of a cattle pangenome for 14 French dairy and beef breeds provides new insights into their genetic diversity. Open
Session 15. Role of bioinformatics applied to livestock data - Exploiting structural variation and pangenome-based techniques forlivestock
View article: Genetic determinism of sperm DNA methylation in French Holstein cattle
Genetic determinism of sperm DNA methylation in French Holstein cattle Open
Session 69. Epigenetics, adaptation and intergenerational transmission
View article: Genomic prediction using functional annotations and QTL features in dairy and beef cattle.breeds
Genomic prediction using functional annotations and QTL features in dairy and beef cattle.breeds Open
Session 15. Role of bioinformatics applied to livestock data - Exploitingstructural variation and pangenome-based techniques for livestock
View article: Genetic parameters, genome-wide association study, and selection perspective on gestation length in 16 French cattle breeds
Genetic parameters, genome-wide association study, and selection perspective on gestation length in 16 French cattle breeds Open
In this paper, we present a comprehensive study of gestation length (GL) in 16 cattle breeds by using large genotype and animal record databases. Data included over 20 million gestations since 2000 and genotypes from one million calves. Th…
View article: Detection and characterization of cytogenetic defects in cattle using large genotypic and phenotypic data sets generated for genomic evaluation
Detection and characterization of cytogenetic defects in cattle using large genotypic and phenotypic data sets generated for genomic evaluation Open
International audience
View article: A bovine model of rhizomelic chondrodysplasia punctata caused by a deep intronic splicing mutation in the<i>GNPAT</i>gene
A bovine model of rhizomelic chondrodysplasia punctata caused by a deep intronic splicing mutation in the<i>GNPAT</i>gene Open
Background Genetic defects that occur naturally in livestock species provide valuable models for investigating the molecular mechanisms underlying rare human diseases. Livestock breeds are subject to the regular emergence of recessive gene…
View article: WITHDRAWN: Genetic parameters, GWAS and selection perspective on gestation length in 16 French cattle breeds
WITHDRAWN: Genetic parameters, GWAS and selection perspective on gestation length in 16 French cattle breeds Open
In this paper, we present a comprehensive study of gestation length (GL) in 16 cattle breeds by using large genotype and animal record databases. Data included over 20 million gestations since 2000 and genotypes from one million calves. Th…