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Ruedi Fries - One of the best experts on this subject based on the ideXlab platform.
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a frameshift mutation in armc3 is associated with a tail stump sperm defect in swedish red bos taurus Cattle
BMC Genetics, 2016Co-Authors: Hubert Pausch, Heli Venhoranta, Christine Wurmser, Kalle Hakala, Terhi Isotouru, Anu Sironen, Rikke K Vingborg, Hannes Lohi, L Soderquist, Ruedi FriesAbstract:Artificial insemination is widely used in many Cattle Breeding programs. Semen samples of Breeding bulls are collected and closely examined immediately after collection at artificial insemination centers. Only ejaculates without anomalous findings are retained for artificial insemination. Although morphological aberrations of the spermatozoa are a frequent reason for discarding ejaculates, the genetic determinants underlying poor semen quality are scarcely understood. A tail stump sperm defect was observed in three bulls of the Swedish Red Cattle Breed. The spermatozoa of affected bulls were immotile because of severely disorganized tails indicating disturbed spermatogenesis. We genotyped three affected bulls and 18 unaffected male half-sibs at 46,035 SNPs and performed homozygosity mapping to map the fertility disorder to an 8.42 Mb interval on bovine chromosome 13. The analysis of whole-genome re-sequencing data of an affected bull and 300 unaffected animals from eleven Cattle Breeds other than Swedish Red revealed a 1 bp deletion (Chr13: 24,301,425 bp, ss1815612719) in the eleventh exon of the armadillo repeat containing 3-encoding gene (ARMC3) that was compatible with the supposed recessive mode of inheritance. The deletion is expected to alter the reading frame and to induce premature translation termination (p.A451fs26). The mutated protein is shortened by 401 amino acids (46 %) and lacks domains that are likely essential for normal protein function. We report the phenotypic and genetic characterization of a sterilizing tail stump sperm defect in the Swedish Red Cattle Breed. Exploiting high-density genotypes and massive re-sequencing data enabled us to identify the most likely causal mutation for the fertility disorder in bovine ARMC3. Our results provide the basis for monitoring the mutated variant in the Swedish Red Cattle population and for the early identification of infertile animals.
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A frameshift mutation in ARMC3 is associated with a tail stump sperm defect in Swedish Red (Bos taurus) Cattle
BMC Genetics, 2016Co-Authors: Hubert Pausch, Heli Venhoranta, Christine Wurmser, Kalle Hakala, Anu Sironen, Rikke K Vingborg, Hannes Lohi, L Soderquist, Terhi Iso-touru, Ruedi FriesAbstract:Background Artificial insemination is widely used in many Cattle Breeding programs. Semen samples of Breeding bulls are collected and closely examined immediately after collection at artificial insemination centers. Only ejaculates without anomalous findings are retained for artificial insemination. Although morphological aberrations of the spermatozoa are a frequent reason for discarding ejaculates, the genetic determinants underlying poor semen quality are scarcely understood. Results A tail stump sperm defect was observed in three bulls of the Swedish Red Cattle Breed. The spermatozoa of affected bulls were immotile because of severely disorganized tails indicating disturbed spermatogenesis. We genotyped three affected bulls and 18 unaffected male half-sibs at 46,035 SNPs and performed homozygosity mapping to map the fertility disorder to an 8.42 Mb interval on bovine chromosome 13. The analysis of whole-genome re-sequencing data of an affected bull and 300 unaffected animals from eleven Cattle Breeds other than Swedish Red revealed a 1 bp deletion (Chr13: 24,301,425 bp, ss1815612719) in the eleventh exon of the armadillo repeat containing 3-encoding gene ( ARMC3 ) that was compatible with the supposed recessive mode of inheritance. The deletion is expected to alter the reading frame and to induce premature translation termination (p.A451fs26). The mutated protein is shortened by 401 amino acids (46 %) and lacks domains that are likely essential for normal protein function. Conclusions We report the phenotypic and genetic characterization of a sterilizing tail stump sperm defect in the Swedish Red Cattle Breed. Exploiting high-density genotypes and massive re-sequencing data enabled us to identify the most likely causal mutation for the fertility disorder in bovine ARMC3 . Our results provide the basis for monitoring the mutated variant in the Swedish Red Cattle population and for the early identification of infertile animals.
Ivica Medugorac - One of the best experts on this subject based on the ideXlab platform.
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Mapping of a milk production quantitative trait locus to a 1.056 Mb region on bovine chromosome 5 in the Fleckvieh dual purpose Cattle Breed
Genetics Selection Evolution, 2011Co-Authors: Ashraf Awad, Martin Förster, Ingolf Russ, Ivica MedugoracAbstract:Background In a previous study in the Fleckvieh dual purpose Cattle Breed, we mapped a quantitative trait locus (QTL) affecting milk yield (MY1), milk protein yield (PY1) and milk fat yield (FY1) during first lactation to the distal part of bovine chromosome 5 (BTA5), but the confidence interval was too large for positional cloning of the causal gene. Our objective here was to refine the position of this QTL and to define the candidate region for high-throughput sequencing.
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confirmation and refinement of a qtl on bta5 affecting milk production traits in the fleckvieh dual purpose Cattle Breed
Animal Genetics, 2010Co-Authors: Ashraf Awad, Ingolf Russ, R Emmerling, M Forste, Ivica MedugoracAbstract:Summary We analysed a QTL affecting milk yield (MY), milk protein yield (PY) and milk fat yield (FY) in the dual purpose Cattle Breed Fleckvieh on BTA5. Twenty-six microsatellite markers covering 135 cM were selected to analyse nine half-sib families containing 605 sons in a granddaughter design. We thereby assigned two new markers to the public linkage map using the CRI-MAP program. Phenotypic records were daughter yield deviations (DYD) originating from the routinely performed genetic evaluations of Breeding animals. To determine the position of the QTL, three different approaches were applied: interval mapping (IM), linkage analysis by variance component analysis (LAVC), and combined linkage disequilibrium (LD) and linkage (LDL) analysis. All three methods mapped the QTL in the same marker interval (BM2830-ETH152) with the greatest test-statistic value at 118, 119.33 and 119.33 cM respectively. The positive QTL allele simultaneously increases DYD in the first lactation by 272 kg milk, 7.1 kg milk protein and 7.0 kg milk fat. Although the mapping accuracy and the significance of a QTL effect increased from IM over LAVC to LDL, the confidence interval was large (13, 20 and 24 cM for FY, MY and PY respectively) for the positional cloning of the causal gene. The estimated averages of pair wise marker LD with a distance <5 cM were low (0.107) and reflect the large effective population size of the Fleckvieh subpopulation analysed. This low level of LD suggests a need for increase in marker density in following fine mapping steps.
Larserik Holm - One of the best experts on this subject based on the ideXlab platform.
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deep sequencing of danish holstein dairy Cattle for variant detection and insight into potential loss of function variants in protein coding genes
BMC Genomics, 2015Co-Authors: Ashutosh Das, Frank Panitz, Vivi Raundahl Gregersen, Christian Bendixen, Larserik HolmAbstract:Background Over the last few years, continuous development of high-throughput sequencing platforms and sequence analysis tools has facilitated reliable identification and characterization of genetic variants in many Cattle Breeds. Deep sequencing of entire genomes within a Cattle Breed that has not been thoroughly investigated would be imagined to discover functional variants that are underlying phenotypic differences. Here, we sequenced to a high coverage the Danish Holstein Cattle Breed to detect and characterize single nucleotide polymorphisms (SNPs), insertion/deletions (Indels), and loss-of-function (LoF) variants in protein-coding genes in order to provide a comprehensive resource for subsequent detection of causal variants for recessive traits.
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deep sequencing of danish holstein dairy Cattle for variant detection and insight into potential loss of function variants in protein coding genes
BMC Genomics, 2015Co-Authors: Ashutosh Das, Frank Panitz, Vivi Raundahl Gregersen, Christian Bendixen, Larserik HolmAbstract:Over the last few years, continuous development of high-throughput sequencing platforms and sequence analysis tools has facilitated reliable identification and characterization of genetic variants in many Cattle Breeds. Deep sequencing of entire genomes within a Cattle Breed that has not been thoroughly investigated would be imagined to discover functional variants that are underlying phenotypic differences. Here, we sequenced to a high coverage the Danish Holstein Cattle Breed to detect and characterize single nucleotide polymorphisms (SNPs), insertion/deletions (Indels), and loss-of-function (LoF) variants in protein-coding genes in order to provide a comprehensive resource for subsequent detection of causal variants for recessive traits. We sequenced four genetically unrelated Danish Holstein cows with a mean coverage of 27X using an Illumina Hiseq 2000. Multi-sample SNP calling identified 10,796,794 SNPs and 1,295,036 indels whereof 482,835 (4.5 %) SNPs and 231,359 (17.9 %) indels were novel. A comparison between sequencing-derived SNPs and genotyping from the BovineHD BeadChip revealed a concordance rate of 99.6–99.8 % for homozygous SNPs and 93.3–96.5 % for heterozygous SNPs. Annotation of the SNPs discovered 74,886 SNPs and 1937 indels affecting coding sequences with 2145 being LoF mutations. The frequency of LoF variants differed greatly across the genome, a hot spot with a strikingly high density was observed in a 6 Mb region on BTA18. LoF affected genes were enriched for functional categories related to olfactory reception and underrepresented for genes related to key cellular constituents and cellular and biological process regulation. Filtering using sequence derived genotype data for 288 Holstein animals from the 1000 bull genomes project removing variants containing homozygous individuals retained 345 of the LoF variants as putatively deleterious. A substantial number of the putative deleterious LoF variants had a minor allele frequency >0.05 in the 1000 bull genomes data set. Deep sequencing of Danish Holstein genomes enabled us to identify 12.1 million variants. An investigation into LoF variants discovered a set of variants predicted to disrupt protein-coding genes. This catalog of variants will be a resource for future studies to understand variation underlying important phenotypes, particularly recessively inherited lethal phenotypes.
Hubert Pausch - One of the best experts on this subject based on the ideXlab platform.
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a frameshift mutation in armc3 is associated with a tail stump sperm defect in swedish red bos taurus Cattle
BMC Genetics, 2016Co-Authors: Hubert Pausch, Heli Venhoranta, Christine Wurmser, Kalle Hakala, Terhi Isotouru, Anu Sironen, Rikke K Vingborg, Hannes Lohi, L Soderquist, Ruedi FriesAbstract:Artificial insemination is widely used in many Cattle Breeding programs. Semen samples of Breeding bulls are collected and closely examined immediately after collection at artificial insemination centers. Only ejaculates without anomalous findings are retained for artificial insemination. Although morphological aberrations of the spermatozoa are a frequent reason for discarding ejaculates, the genetic determinants underlying poor semen quality are scarcely understood. A tail stump sperm defect was observed in three bulls of the Swedish Red Cattle Breed. The spermatozoa of affected bulls were immotile because of severely disorganized tails indicating disturbed spermatogenesis. We genotyped three affected bulls and 18 unaffected male half-sibs at 46,035 SNPs and performed homozygosity mapping to map the fertility disorder to an 8.42 Mb interval on bovine chromosome 13. The analysis of whole-genome re-sequencing data of an affected bull and 300 unaffected animals from eleven Cattle Breeds other than Swedish Red revealed a 1 bp deletion (Chr13: 24,301,425 bp, ss1815612719) in the eleventh exon of the armadillo repeat containing 3-encoding gene (ARMC3) that was compatible with the supposed recessive mode of inheritance. The deletion is expected to alter the reading frame and to induce premature translation termination (p.A451fs26). The mutated protein is shortened by 401 amino acids (46 %) and lacks domains that are likely essential for normal protein function. We report the phenotypic and genetic characterization of a sterilizing tail stump sperm defect in the Swedish Red Cattle Breed. Exploiting high-density genotypes and massive re-sequencing data enabled us to identify the most likely causal mutation for the fertility disorder in bovine ARMC3. Our results provide the basis for monitoring the mutated variant in the Swedish Red Cattle population and for the early identification of infertile animals.
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A frameshift mutation in ARMC3 is associated with a tail stump sperm defect in Swedish Red (Bos taurus) Cattle
BMC Genetics, 2016Co-Authors: Hubert Pausch, Heli Venhoranta, Christine Wurmser, Kalle Hakala, Anu Sironen, Rikke K Vingborg, Hannes Lohi, L Soderquist, Terhi Iso-touru, Ruedi FriesAbstract:Background Artificial insemination is widely used in many Cattle Breeding programs. Semen samples of Breeding bulls are collected and closely examined immediately after collection at artificial insemination centers. Only ejaculates without anomalous findings are retained for artificial insemination. Although morphological aberrations of the spermatozoa are a frequent reason for discarding ejaculates, the genetic determinants underlying poor semen quality are scarcely understood. Results A tail stump sperm defect was observed in three bulls of the Swedish Red Cattle Breed. The spermatozoa of affected bulls were immotile because of severely disorganized tails indicating disturbed spermatogenesis. We genotyped three affected bulls and 18 unaffected male half-sibs at 46,035 SNPs and performed homozygosity mapping to map the fertility disorder to an 8.42 Mb interval on bovine chromosome 13. The analysis of whole-genome re-sequencing data of an affected bull and 300 unaffected animals from eleven Cattle Breeds other than Swedish Red revealed a 1 bp deletion (Chr13: 24,301,425 bp, ss1815612719) in the eleventh exon of the armadillo repeat containing 3-encoding gene ( ARMC3 ) that was compatible with the supposed recessive mode of inheritance. The deletion is expected to alter the reading frame and to induce premature translation termination (p.A451fs26). The mutated protein is shortened by 401 amino acids (46 %) and lacks domains that are likely essential for normal protein function. Conclusions We report the phenotypic and genetic characterization of a sterilizing tail stump sperm defect in the Swedish Red Cattle Breed. Exploiting high-density genotypes and massive re-sequencing data enabled us to identify the most likely causal mutation for the fertility disorder in bovine ARMC3 . Our results provide the basis for monitoring the mutated variant in the Swedish Red Cattle population and for the early identification of infertile animals.
Ashraf Awad - One of the best experts on this subject based on the ideXlab platform.
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Mapping of a milk production quantitative trait locus to a 1.056 Mb region on bovine chromosome 5 in the Fleckvieh dual purpose Cattle Breed
Genetics Selection Evolution, 2011Co-Authors: Ashraf Awad, Martin Förster, Ingolf Russ, Ivica MedugoracAbstract:Background In a previous study in the Fleckvieh dual purpose Cattle Breed, we mapped a quantitative trait locus (QTL) affecting milk yield (MY1), milk protein yield (PY1) and milk fat yield (FY1) during first lactation to the distal part of bovine chromosome 5 (BTA5), but the confidence interval was too large for positional cloning of the causal gene. Our objective here was to refine the position of this QTL and to define the candidate region for high-throughput sequencing.
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confirmation and refinement of a qtl on bta5 affecting milk production traits in the fleckvieh dual purpose Cattle Breed
Animal Genetics, 2010Co-Authors: Ashraf Awad, Ingolf Russ, R Emmerling, M Forste, Ivica MedugoracAbstract:Summary We analysed a QTL affecting milk yield (MY), milk protein yield (PY) and milk fat yield (FY) in the dual purpose Cattle Breed Fleckvieh on BTA5. Twenty-six microsatellite markers covering 135 cM were selected to analyse nine half-sib families containing 605 sons in a granddaughter design. We thereby assigned two new markers to the public linkage map using the CRI-MAP program. Phenotypic records were daughter yield deviations (DYD) originating from the routinely performed genetic evaluations of Breeding animals. To determine the position of the QTL, three different approaches were applied: interval mapping (IM), linkage analysis by variance component analysis (LAVC), and combined linkage disequilibrium (LD) and linkage (LDL) analysis. All three methods mapped the QTL in the same marker interval (BM2830-ETH152) with the greatest test-statistic value at 118, 119.33 and 119.33 cM respectively. The positive QTL allele simultaneously increases DYD in the first lactation by 272 kg milk, 7.1 kg milk protein and 7.0 kg milk fat. Although the mapping accuracy and the significance of a QTL effect increased from IM over LAVC to LDL, the confidence interval was large (13, 20 and 24 cM for FY, MY and PY respectively) for the positional cloning of the causal gene. The estimated averages of pair wise marker LD with a distance <5 cM were low (0.107) and reflect the large effective population size of the Fleckvieh subpopulation analysed. This low level of LD suggests a need for increase in marker density in following fine mapping steps.