Parameters based on probabilities of gene origin were used to evaluate the genetic variability of... more Parameters based on probabilities of gene origin were used to evaluate the genetic variability of four Austrian cattle breeds. Effective numbers of founders, ancestors and remaining founder genomes showed that all four populations investigated are rather small genetically. Effective numbers of remaining founder genomes were 94 for Simmental, 41 for Braunvieh (Brown Swiss), 32 for Pinzgauer and 21 for Grauvieh (Grey cattle, a small mountain breed). As the value of 94 for Simmental was rather large in comparison with estimates from other populations in previous studies, the effect of population structure was investigated. A cosine measure of similarity based on differences in individual founder contributions to different subpopulations was defined and used for analysis. Subpopulations defined by regions were clearly more distinct for Simmental than for Braunvieh. The size of the cosine values depended on the method of calculating founder contributions and was overestimated when choosi...
SummaryLocal breeds can serve as an important source of genetic variability in domestic animal sp... more SummaryLocal breeds can serve as an important source of genetic variability in domestic animal species. This study aimed to assess the genetic diversity and population structure of Belarusian Red cattle and their differentiation from other European cattle populations based on genome‐wide SNP genotypes. Twenty pedigree‐recorded non‐closely related cows of Belarusian Red cattle were genotyped using the Illumina BovineHD BeadChip. Genotypes of 22 other European cattle breeds were included in the study for comparison. A total of 28 562 SNPs passed through the quality control checks and were selected for analysis. The Belarusian Red cattle displayed a moderate level of genetic variability (UHE = 0.341, HO = 0.368), and the highest heterozygote excess (UFIS = −0.066), among the studied breeds; this reflects the contribution of multiple breeds to their formation. The principal component analysis, FST‐based Neighbor‐Net tree and Admixture clustering, clearly distinguished the Belarusian Red...
SummaryIn the past two decades, average litter size (ALS) in Entlebucher Mountain dogs decreased ... more SummaryIn the past two decades, average litter size (ALS) in Entlebucher Mountain dogs decreased by approximately 0.8 puppies. We conducted a GWAS for ALS using the single‐step methodology to take advantage of 1632 pedigree records, 892 phenotypes and 372 genotypes (173 662 markers) for which only 12% of the dogs had both phenotypes and genotypes available. Our analysis revealed associations towards the growth differentiation factor 9 gene (GDF9), which is known to regulate oocyte maturation. The trait heritability was estimated at 43.1%, from which approximately 15% was accountable by the GDF9 locus alone. Therefore, markers flanking GDF9 explained approximately 6.5% of the variance in ALS. Analysis of WGSs revealed two missense substitutions in GDF9, one of which (g.11:21147009G>A) affected a highly conserved nucleotide in vertebrates. The derived allele A was validated in 111 dogs and shown to be associated with decreased ALS (−0.75 ± 0.22 puppies per litter). The variant was ...
Breeding values for length of productive life in Slovak Pinzgau cattle were estimated using survi... more Breeding values for length of productive life in Slovak Pinzgau cattle were estimated using survival analysis. As the results were corrected for milk production, the final breeding values represented the ability of cows to avoid culling from reasons other than milk production. In addition to the relative milk yield, the risk of culling was also studied in connection with the herd and year of calving, parity and stage of lactation, herd size change and age at the first calving. Among the fixed effects, the low milk production, high age at the first calving, and decreasing herd size were associated with increased risk of culling. The risk was non-linear for parity × stage of lactation classes, decreasing within the first parity and increasing during later parities. Two genetic random effects were considered in separate models: the sire of the cow and the animal itself, both with the corresponding pedigree records up to the third generation. The genetic effects were estimated in separa...
Genomic selection may accelerate genetic progress in breeding programs of indicine breeds when co... more Genomic selection may accelerate genetic progress in breeding programs of indicine breeds when compared with traditional selection methods. We present results of genomic predictions in Gyr (Bos indicus) dairy cattle of Brazil for milk yield (MY), fat yield (FY), protein yield (PY), and age at first calving using information from bulls and cows. Four different single nucleotide polymorphism (SNP) chips were studied. Additionally, the effect of the use of imputed data on genomic prediction accuracy was studied. A total of 474 bulls and 1,688 cows were genotyped with the Illumina BovineHD (HD; San Diego, CA) and BovineSNP50 (50K) chip, respectively. Genotypes of cows were imputed to HD using FImpute v2.2. After quality check of data, 496,606 markers remained. The HD markers present on the GeneSeek SGGP-20Ki (15,727; Lincoln, NE), 50K (22,152), and GeneSeek GGP-75Ki (65,018) were subset and used to assess the effect of lower SNP density on accuracy of prediction. Deregressed breeding va...
To estimate nonlinear genetic relationships between traits, formulas based on the paternal halfsi... more To estimate nonlinear genetic relationships between traits, formulas based on the paternal halfsib analysis theory were derived. To illustrate the usefulness of the formulas, a series of data sets with halfsib structure for some preselected parameters and sample size situations were generated by means of Monte Carlo techniques. When a nonlinear relationship in the form of a polynomial relationship of degree two is present, the linear and quadratic regression coefficients can be estimated from a paternal halfsib analysis without bias. Some of the traditional linear genetic parameters need correction; however, their value is limited if the relationship between two traits is nonlinear. Although regression coefficients may be estimated appropriately in many situations, the application of the described method is restricted to situations in which the causal flow between the traits involved is clear and the heritability of the determining trait is larger than approximately .10. Further work should be directed to investigation of possibilities for including such parameters in selection decisions in a formalized way.
Semen production data from an Austrian AI centre collected between 2000 and 2004 were analysed. I... more Semen production data from an Austrian AI centre collected between 2000 and 2004 were analysed. In total, 12,746 ejaculates from 301 AI bulls were examined considering different effects on ejaculate volume, sperm concentration, percentage of viable spermatozoa in the ejaculate, total spermatozoa per ejaculate and motility. The model included the fixed effects of age of bull, collection interval, number of collections on collection day, bull handler, semen collector, year and month of collection, and a random additive genetic component. Age of bull, collection interval, number of collection on collection day, and year and month significantly affected most semen quality traits. The collection team (bull handler and semen collector) had relevant effects on semen traits. All semen production traits were moderately heritable and correlated. Heritabilities for volume, concentration, percentage of viable spermatozoa, total spermatozoa and motility were 0.18, 0.14, 0.10, 0.22 and 0.04, respectively. Correlations between estimated breeding values of sperm quality traits and routinely estimated breeding values for male fertility were low and ranged from 0.10 to 0.20.
Parameters based on probabilities of gene origin were used to evaluate the genetic variability of... more Parameters based on probabilities of gene origin were used to evaluate the genetic variability of four Austrian cattle breeds. Effective numbers of founders, ancestors and remaining founder genomes showed that all four populations investigated are rather small genetically. Effective numbers of remaining founder genomes were 94 for Simmental, 41 for Braunvieh (Brown Swiss), 32 for Pinzgauer and 21 for Grauvieh (Grey cattle, a small mountain breed). As the value of 94 for Simmental was rather large in comparison with estimates from other populations in previous studies, the effect of population structure was investigated. A cosine measure of similarity based on differences in individual founder contributions to different subpopulations was defined and used for analysis. Subpopulations defined by regions were clearly more distinct for Simmental than for Braunvieh. The size of the cosine values depended on the method of calculating founder contributions and was overestimated when choosi...
SummaryLocal breeds can serve as an important source of genetic variability in domestic animal sp... more SummaryLocal breeds can serve as an important source of genetic variability in domestic animal species. This study aimed to assess the genetic diversity and population structure of Belarusian Red cattle and their differentiation from other European cattle populations based on genome‐wide SNP genotypes. Twenty pedigree‐recorded non‐closely related cows of Belarusian Red cattle were genotyped using the Illumina BovineHD BeadChip. Genotypes of 22 other European cattle breeds were included in the study for comparison. A total of 28 562 SNPs passed through the quality control checks and were selected for analysis. The Belarusian Red cattle displayed a moderate level of genetic variability (UHE = 0.341, HO = 0.368), and the highest heterozygote excess (UFIS = −0.066), among the studied breeds; this reflects the contribution of multiple breeds to their formation. The principal component analysis, FST‐based Neighbor‐Net tree and Admixture clustering, clearly distinguished the Belarusian Red...
SummaryIn the past two decades, average litter size (ALS) in Entlebucher Mountain dogs decreased ... more SummaryIn the past two decades, average litter size (ALS) in Entlebucher Mountain dogs decreased by approximately 0.8 puppies. We conducted a GWAS for ALS using the single‐step methodology to take advantage of 1632 pedigree records, 892 phenotypes and 372 genotypes (173 662 markers) for which only 12% of the dogs had both phenotypes and genotypes available. Our analysis revealed associations towards the growth differentiation factor 9 gene (GDF9), which is known to regulate oocyte maturation. The trait heritability was estimated at 43.1%, from which approximately 15% was accountable by the GDF9 locus alone. Therefore, markers flanking GDF9 explained approximately 6.5% of the variance in ALS. Analysis of WGSs revealed two missense substitutions in GDF9, one of which (g.11:21147009G>A) affected a highly conserved nucleotide in vertebrates. The derived allele A was validated in 111 dogs and shown to be associated with decreased ALS (−0.75 ± 0.22 puppies per litter). The variant was ...
Breeding values for length of productive life in Slovak Pinzgau cattle were estimated using survi... more Breeding values for length of productive life in Slovak Pinzgau cattle were estimated using survival analysis. As the results were corrected for milk production, the final breeding values represented the ability of cows to avoid culling from reasons other than milk production. In addition to the relative milk yield, the risk of culling was also studied in connection with the herd and year of calving, parity and stage of lactation, herd size change and age at the first calving. Among the fixed effects, the low milk production, high age at the first calving, and decreasing herd size were associated with increased risk of culling. The risk was non-linear for parity × stage of lactation classes, decreasing within the first parity and increasing during later parities. Two genetic random effects were considered in separate models: the sire of the cow and the animal itself, both with the corresponding pedigree records up to the third generation. The genetic effects were estimated in separa...
Genomic selection may accelerate genetic progress in breeding programs of indicine breeds when co... more Genomic selection may accelerate genetic progress in breeding programs of indicine breeds when compared with traditional selection methods. We present results of genomic predictions in Gyr (Bos indicus) dairy cattle of Brazil for milk yield (MY), fat yield (FY), protein yield (PY), and age at first calving using information from bulls and cows. Four different single nucleotide polymorphism (SNP) chips were studied. Additionally, the effect of the use of imputed data on genomic prediction accuracy was studied. A total of 474 bulls and 1,688 cows were genotyped with the Illumina BovineHD (HD; San Diego, CA) and BovineSNP50 (50K) chip, respectively. Genotypes of cows were imputed to HD using FImpute v2.2. After quality check of data, 496,606 markers remained. The HD markers present on the GeneSeek SGGP-20Ki (15,727; Lincoln, NE), 50K (22,152), and GeneSeek GGP-75Ki (65,018) were subset and used to assess the effect of lower SNP density on accuracy of prediction. Deregressed breeding va...
To estimate nonlinear genetic relationships between traits, formulas based on the paternal halfsi... more To estimate nonlinear genetic relationships between traits, formulas based on the paternal halfsib analysis theory were derived. To illustrate the usefulness of the formulas, a series of data sets with halfsib structure for some preselected parameters and sample size situations were generated by means of Monte Carlo techniques. When a nonlinear relationship in the form of a polynomial relationship of degree two is present, the linear and quadratic regression coefficients can be estimated from a paternal halfsib analysis without bias. Some of the traditional linear genetic parameters need correction; however, their value is limited if the relationship between two traits is nonlinear. Although regression coefficients may be estimated appropriately in many situations, the application of the described method is restricted to situations in which the causal flow between the traits involved is clear and the heritability of the determining trait is larger than approximately .10. Further work should be directed to investigation of possibilities for including such parameters in selection decisions in a formalized way.
Semen production data from an Austrian AI centre collected between 2000 and 2004 were analysed. I... more Semen production data from an Austrian AI centre collected between 2000 and 2004 were analysed. In total, 12,746 ejaculates from 301 AI bulls were examined considering different effects on ejaculate volume, sperm concentration, percentage of viable spermatozoa in the ejaculate, total spermatozoa per ejaculate and motility. The model included the fixed effects of age of bull, collection interval, number of collections on collection day, bull handler, semen collector, year and month of collection, and a random additive genetic component. Age of bull, collection interval, number of collection on collection day, and year and month significantly affected most semen quality traits. The collection team (bull handler and semen collector) had relevant effects on semen traits. All semen production traits were moderately heritable and correlated. Heritabilities for volume, concentration, percentage of viable spermatozoa, total spermatozoa and motility were 0.18, 0.14, 0.10, 0.22 and 0.04, respectively. Correlations between estimated breeding values of sperm quality traits and routinely estimated breeding values for male fertility were low and ranged from 0.10 to 0.20.
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