Ruedi Fries
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View article: Unraveling Admixture, Inbreeding, and Recent Selection Signatures in West African Indigenous Cattle Populations in Benin
Unraveling Admixture, Inbreeding, and Recent Selection Signatures in West African Indigenous Cattle Populations in Benin Open
The Dwarf Lagune and the Savannah Somba cattle in Benin are typical representatives of the endangered West African indigenous Shorthorn taurine. The Lagune was previously exported to African and European countries and bred as Dahomey cattl…
View article: Whole genome sequencing reveals a complex introgression history and the basis of adaptation to subarctic climate in wild sheep
Whole genome sequencing reveals a complex introgression history and the basis of adaptation to subarctic climate in wild sheep Open
To predict species responses to anthropogenic disturbances and climate change, it is reasonable to use species with high sensitivity to such factors. Snow sheep ( Ovis nivicola ) could represent a good candidate for this; as the only large…
View article: Investigating the impact of reference assembly choice on genomic analyses in a cattle breed
Investigating the impact of reference assembly choice on genomic analyses in a cattle breed Open
Background Reference-guided read alignment and variant genotyping are prone to reference allele bias, particularly for samples that are greatly divergent from the reference genome. A Hereford-based assembly is the widely accepted bovine re…
View article: A nonsense mutation of bone morphogenetic protein-15 (BMP15) causes both infertility and increased litter size in pigs
A nonsense mutation of bone morphogenetic protein-15 (BMP15) causes both infertility and increased litter size in pigs Open
Background Atypical external genitalia are often a sign of reproductive organ pathologies and infertility with both environmental or genetic causes, including karyotypic abnormalities. Genome-wide association studies (GWAS) provide a means…
View article: Additional file 3 of Investigating the impact of reference assembly choice on genomic analyses in a cattle breed
Additional file 3 of Investigating the impact of reference assembly choice on genomic analyses in a cattle breed Open
Additional file 3 Table S3: Number of variants during the different filtering steps: from original variants to high-quality and non-fixed variants. Original variants are considered as the raw variants retrieved from GATK. Low quality varia…
View article: Additional file 2 of Investigating the impact of reference assembly choice on genomic analyses in a cattle breed
Additional file 2 of Investigating the impact of reference assembly choice on genomic analyses in a cattle breed Open
Additional file 2 Table S2: Number of mapped reads contained in the original files but not considered for our study. Number of reads mapped to sexual chromosomes and to unplaced contigs for both assemblies. Low quality mapping includes the…
View article: Additional file 6 of Investigating the impact of reference assembly choice on genomic analyses in a cattle breed
Additional file 6 of Investigating the impact of reference assembly choice on genomic analyses in a cattle breed Open
Additional file 6 Table S4: Density of high-quality and non-fixed variants per Kb along the autosomal genome. Unlike Table 3 in the main text, densities are calculated here when chromosome 12 is not considered.
View article: Additional file 9 of Investigating the impact of reference assembly choice on genomic analyses in a cattle breed
Additional file 9 of Investigating the impact of reference assembly choice on genomic analyses in a cattle breed Open
Additional file 9 Table S6: Summary of the annotated sequence ontology classes of SNPs and INDELs. SO terms are described by Ensembl. Total number of high-quality and non-fixed annotated SNPs and INDELs for both assemblies that were annota…
View article: Additional file 1 of A nonsense mutation of bone morphogenetic protein-15 (BMP15) causes both infertility and increased litter size in pigs
Additional file 1 of A nonsense mutation of bone morphogenetic protein-15 (BMP15) causes both infertility and increased litter size in pigs Open
Additional file 1.
View article: Additional file 4 of A nonsense mutation of bone morphogenetic protein-15 (BMP15) causes both infertility and increased litter size in pigs
Additional file 4 of A nonsense mutation of bone morphogenetic protein-15 (BMP15) causes both infertility and increased litter size in pigs Open
Additional file 4.
View article: Additional file 10 of Investigating the impact of reference assembly choice on genomic analyses in a cattle breed
Additional file 10 of Investigating the impact of reference assembly choice on genomic analyses in a cattle breed Open
Additional file 10 Table S7: Candidate selection signatures detected using ARS-UCD1.2 as reference. Genomic coordinates, CLR values, P-values and encompassed genes for 40 candidate selection signatures.
View article: Additional file 1 of Investigating the impact of reference assembly choice on genomic analyses in a cattle breed
Additional file 1 of Investigating the impact of reference assembly choice on genomic analyses in a cattle breed Open
Additional file 1 Table S1: BSW cattle IDs. Accession IDs of the 161 bovine samples used for our study.
View article: Additional file 7 of Investigating the impact of reference assembly choice on genomic analyses in a cattle breed
Additional file 7 of Investigating the impact of reference assembly choice on genomic analyses in a cattle breed Open
Additional file 7 Table S5: Number and percentage of multiallelic variants. Percentage of multiallelic variants is obtained from the division of multiallelic variants to non-fixed high-quality variants. Multiallelic variants are identified…
View article: Additional file 11 of Investigating the impact of reference assembly choice on genomic analyses in a cattle breed
Additional file 11 of Investigating the impact of reference assembly choice on genomic analyses in a cattle breed Open
Additional file 11 Table S8: Candidate selection signatures detected using UOA_Angus_1 as reference. Genomic coordinates, CLR values, P-values and encompassed genes for 33 candidate selection signatures.
View article: A nonsense mutation of bone morphogenetic protein-15 (BMP15) causes both infertility and increased litter size in pigs.
A nonsense mutation of bone morphogenetic protein-15 (BMP15) causes both infertility and increased litter size in pigs. Open
Background Atypical external genitalia are often a sign of reproductive organ pathologies and infertility with both environmental or genetic causes, including karyotypic abnormalities. Genome-wide association studies (GWAS) provide a means…
View article: A nonsense mutation of bone morphogenetic protein-15 (BMP15) causes both infertility and increased litter size in pigs.
A nonsense mutation of bone morphogenetic protein-15 (BMP15) causes both infertility and increased litter size in pigs. Open
Background: Atypical external genitalia are often a sign of reproductive organ pathologies and infertility with both environmental or genetic causes, including karyotypic abnormalities. Genome-wide association studies (GWAS) provide a mean…
View article: A nonsense mutation of bone morphogenetic protein-15 (BMP15) causes both infertility and increased litter size in pigs.
A nonsense mutation of bone morphogenetic protein-15 (BMP15) causes both infertility and increased litter size in pigs. Open
Background: Atypical external genitalia are often a sign of reproductive organ pathologies and infertility with both environmental or genetic causes, including karyotypic abnormalities. Genome-wide association studies (GWAS) provide a mean…
View article: A nonsense mutation of bone morphogenetic protein-15 (BMP15) causes both infertility and increased litter size in pigs.
A nonsense mutation of bone morphogenetic protein-15 (BMP15) causes both infertility and increased litter size in pigs. Open
Background: Atypical external genitalia are often a sign of reproductive organ pathologies and infertility with both environmental or genetic causes, including karyotypic abnormalities. Genome-wide association studies (GWAS) provide a mean…
View article: A nonsense mutation of bone morphogenetic protein-15 (BMP15) causes both infertility and increased litter size in pigs
A nonsense mutation of bone morphogenetic protein-15 (BMP15) causes both infertility and increased litter size in pigs Open
Background Atypical external genitalia are often a sign of reproductive organ pathologies and infertility with both environmental or genetic causes, including karyotypic abnormalities. Genome-wide association studies (GWAS) provide a means…
View article: Activation of cryptic splicing in bovine WDR19 is associated with reduced semen quality and male fertility
Activation of cryptic splicing in bovine WDR19 is associated with reduced semen quality and male fertility Open
Cattle are ideally suited to investigate the genetics of male reproduction, because semen quality and fertility are recorded for all ejaculates of artificial insemination bulls. We analysed 26,090 ejaculates of 794 Brown Swiss bulls to ass…
View article: Deletion of porcine BOLL causes defective acrosomes and subfertility in Yorkshire boars
Deletion of porcine BOLL causes defective acrosomes and subfertility in Yorkshire boars Open
This datset contains plink binaries (final_recode_ID.bed, final_recode_ID.bim, final_recode_ID.fam) that contain array-derived genotypes for 35 Yorkshire boars. 12 boars produced sperm with defective acrosomes. The case/control status (1-u…
View article: Deletion of porcine BOLL causes defective acrosomes and subfertility in Yorkshire boars
Deletion of porcine BOLL causes defective acrosomes and subfertility in Yorkshire boars Open
This datset contains plink binaries (final_recode_ID.bed, final_recode_ID.bim, final_recode_ID.fam) that contain array-derived genotypes for 35 Yorkshire boars. 12 boars produced sperm with defective acrosomes. The case/control status (1-u…
View article: Deletion of porcine BOLL causes defective acrosomes and subfertility in Yorkshire boars
Deletion of porcine BOLL causes defective acrosomes and subfertility in Yorkshire boars Open
This datset contains plink binaries (final_recode_ID.bed, final_recode_ID.bim, final_recode_ID.fam) that contain array-derived genotypes for 35 Yorkshire boars. 12 boars produced sperm with defective acrosomes. The case/control status (1-u…
View article: Deletion of porcine<i>BOLL</i>causes defective acrosomes and subfertility in Yorkshire boars
Deletion of porcine<i>BOLL</i>causes defective acrosomes and subfertility in Yorkshire boars Open
Summary A recessively inherited sperm defect of Finnish Yorkshire boars was detected more than a decade ago. Affected boars produce ejaculates that contain many spermatozoa with defective acrosomes resulting in low fertility and small litt…
View article: Candidate genes and gene markers for the resistance to porcine pleuropneumonia
Candidate genes and gene markers for the resistance to porcine pleuropneumonia Open
Actinobacillus ( A .) pleuropneumoniae is one of the most important respiratory pathogens in global pig production. Antimicrobial treatment and vaccination provide only limited protection, but genetic disease resistance is a very promising…
View article: Activation of cryptic splicing in bovine<i>WDR19</i>is associated with reduced semen quality and male fertility
Activation of cryptic splicing in bovine<i>WDR19</i>is associated with reduced semen quality and male fertility Open
Cattle are ideally suited to investigate the genetics of male reproduction, because semen quality and fertility are recorded for all ejaculates of artificial insemination bulls. We analysed 26,090 ejaculates of 794 Brown Swiss bulls to ass…
View article: Genetics of adaptation in modern chicken
Genetics of adaptation in modern chicken Open
We carried out whole genome resequencing of 127 chicken including red jungle fowl and multiple populations of commercial broilers and layers to perform a systematic screening of adaptive changes in modern chicken (Gallus gallus domesticus)…