Template-Type: ReDIF-Article 1.0
Author-Name: Ludmila Zavadilová
Author-Name: Josef Přibyl
Author-Workplace-Name: Department of Animal Genetic and Breeding, Institute of Animal Science, Prague - Uhříněves, Czech Republic
Title: Prof. Václav Jakubec, DrSc. - 90th birthday
Journal: Czech Journal of Animal Science
Pages: 443-444
Volume: 65
Issue: 12
Year: 2020
DOI: 10.17221/282/2020-CJAS
File-URL: http://cjas.agriculturejournals.cz/doi/10.17221/282/2020-CJAS.html
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Handle: RePEc:caa:jnlcjs:v:65:y:2020:i:12:id:282-2020-CJAS

Template-Type: ReDIF-Article 1.0
Author-Name: Anita Klímová
Author-Workplace-Name: Department of Genetics and Breeding, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague - Suchdol, Czech Republic
Author-Workplace-Name: Department of Genetics and Breeding of Farm Animals, Institute of Animal Science, Prague - Uhříněves, Czech Republic
Author-Name: Eva Kašná
Author-Workplace-Name: Department of Genetics and Breeding of Farm Animals, Institute of Animal Science, Prague - Uhříněves, Czech Republic
Author-Name: Karolína Machová
Author-Workplace-Name: Department of Genetics and Breeding, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague - Suchdol, Czech Republic
Author-Name: Michaela Brzáková
Author-Workplace-Name: Department of Genetics and Breeding of Farm Animals, Institute of Animal Science, Prague - Uhříněves, Czech Republic
Author-Name: Josef Přibyl
Author-Workplace-Name: Department of Genetics and Breeding of Farm Animals, Institute of Animal Science, Prague - Uhříněves, Czech Republic
Author-Name: Luboš Vostrý
Author-Workplace-Name: Department of Genetics and Breeding, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague - Suchdol, Czech Republic
Title: The use of genomic data and imputation methods in dairy cattle breeding
Abstract: The inclusion of animal genotype data has contributed to the development of genomic selection. Animals are selected not only based on pedigree and phenotypic data but also on the basis of information about their genotypes. Genomic information helps to increase the accuracy of selection of young animals and thus enables a reduction of the generation interval. Obtaining information about genotypes in the form of SNPs (single nucleotide polymorphisms) has led to the development of new chips for genotyping. Several methods of genomic comparison have been developed as a result. One of the methods is data imputation, which allows the missing SNPs to be calculated using low-density chips to high-density chips. Through imputations, it is possible to combine information from diverse sets of chips and thus obtain more information about genotypes at a lower cost. Increasing the amount of data helps increase the reliability of predicting genomic breeding values. Imputation methods are increasingly used in genome-wide association studies. When classical genotyping and genome-wide sequencing data are combined, this option helps to increase the chances of identifying loci that are associated with economically significant traits.
Keywords: genomic breeding values, genomic selection, genotyping, microarray, SNP
Journal: Czech Journal of Animal Science
Pages: 445-453
Volume: 65
Issue: 12
Year: 2020
DOI: 10.17221/83/2020-CJAS
File-URL: http://cjas.agriculturejournals.cz/doi/10.17221/83/2020-CJAS.html
File-Format: text/html
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Handle: RePEc:caa:jnlcjs:v:65:y:2020:i:12:id:83-2020-CJAS

Template-Type: ReDIF-Article 1.0
Author-Name: Zuzana Krupová
Author-Name: Emil Krupa
Author-Workplace-Name: Institute of Animal Science, Prague - Uhříněves, Czech Republic
Author-Name: Ludmila Zavadilová
Author-Workplace-Name: Institute of Animal Science, Prague - Uhříněves, Czech Republic
Author-Name: Eva Kašná
Author-Workplace-Name: Institute of Animal Science, Prague - Uhříněves, Czech Republic
Author-Name: Eliška Žáková
Author-Workplace-Name: Institute of Animal Science, Prague - Uhříněves, Czech Republic
Title: Current challenges for trait economic values in animal breeding
Abstract: Modern selection approaches are expected to bring about the cumulative and permanent improvement of animal performance and profitability of animal production. Breeding values of traits along with trait economic values (EVs) are utilised for economic selection purposes with many species all over the world. Currently, some challenges related to trait EVs in animal breeding should be considered. First, the selection response based on the higher accuracy of genomic selection may be reduced due to improper weighting of the trait breeding values of selection candidates. A comprehensive approach applied in bioeconomic models allows suitable trait EV calculations. Further challenges comprise the new breeding objectives associated with climate change, environmental mitigation and animal adaptability. The estimation of EVs for traits influencing greenhouse gas (GHG) emissions has been mostly based on including the value of CO2 emission equivalent in the trait EVs, on calculating EVs for feed efficiency traits and on methane yield as a direct trait of GHG emission. Genetic improvement of production, functional, feed efficiency and methane traits through the application of multi-trait selection indices was found to be crucial for mitigation of emissions and farm profitability. Defining the non-market values of traits connected with climate protection could be a useful solution for including these traits in an economic breeding objective. While GHG emissions mostly change the costs per unit of production, animal adaptability in its complexity influences animal performance. Clear definitions of disease, fertility, mortality and other breeding objective traits allow the proper calculation of trait EVs, and an accurate estimation of trait genetic parameters could lead to sufficient economic selection response. This complex approach could be beneficial for more effective utilisation of inputs and overall economic and environmental sustainability of animal production.
Keywords: breeding objectives, selection index, bioeconomic model, climate change, emission mitigation, heat tolerance
Journal: Czech Journal of Animal Science
Pages: 454-462
Volume: 65
Issue: 12
Year: 2020
DOI: 10.17221/161/2020-CJAS
File-URL: http://cjas.agriculturejournals.cz/doi/10.17221/161/2020-CJAS.html
File-Format: text/html
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Handle: RePEc:caa:jnlcjs:v:65:y:2020:i:12:id:161-2020-CJAS

Template-Type: ReDIF-Article 1.0
Author-Name: Ludmila Zavadilová
Author-Workplace-Name: Institute of Animal Science, Prague - Uhříněves, Czech Republic
Author-Name: Eva Kašná
Author-Workplace-Name: Institute of Animal Science, Prague - Uhříněves, Czech Republic
Author-Name: Zuzana Krupová
Author-Workplace-Name: Institute of Animal Science, Prague - Uhříněves, Czech Republic
Author-Name: Michaela Brzáková
Author-Workplace-Name: Institute of Animal Science, Prague - Uhříněves, Czech Republic
Title: Genetic parameters for clinical mastitis in Czech Holstein cattle
Abstract: Genetic parameters were estimated for clinical mastitis in Czech Holstein cattle. The datasets included 14 329 cows with 28 626 lactations. Clinical mastitis was defined as 0/1 occurrence per lactation. Single- or multi-trait repeatability linear animal models were employed for estimation of (co)variances and prediction of conventional or genomic breeding values. The inclusion of the random herd-year-month effect in the model was analysed. The estimated heritability for clinical mastitis ranged from 2.10% to 2.72%, while permanent environmental variance ratios or random herd-year-month effect ratios were twice higher than heritability. In the multi-trait models, udder type traits, such as fore udder attachment, rear udder attachment, rear udder width, front teat placement and udder depth, were employed. The highest genetic correlations of clinical mastitis occurred with rear udder width (0.41) and the lowest with front teat placement (-0.10). Both the multi-trait model and the genomic model provided breeding value estimates with higher reliability. In contrast, the model with random herd-year-season effects provided breeding values with lower accuracy.
Keywords: dairy cow, udder health, heritability, genomic breeding values, multi-trait model
Journal: Czech Journal of Animal Science
Pages: 463-472
Volume: 65
Issue: 12
Year: 2020
DOI: 10.17221/151/2020-CJAS
File-URL: http://cjas.agriculturejournals.cz/doi/10.17221/151/2020-CJAS.html
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Handle: RePEc:caa:jnlcjs:v:65:y:2020:i:12:id:151-2020-CJAS

Template-Type: ReDIF-Article 1.0
Author-Name: Eva Kašná
Author-Name: Ludmila Zavadilová
Author-Workplace-Name: Institute of Animal Science, Prague - Uhříněves, Czech Republic
Author-Name: Emil Krupa
Author-Workplace-Name: Institute of Animal Science, Prague - Uhříněves, Czech Republic
Author-Name: Zuzana Krupová
Author-Workplace-Name: Institute of Animal Science, Prague - Uhříněves, Czech Republic
Author-Name: Anita Kranjčevičová
Author-Workplace-Name: Institute of Animal Science, Prague - Uhříněves, Czech Republic
Title: Evaluation of gestation length in Czech Holstein cattle
Abstract: An objective of our study was to evaluate gestation length and its genetic variability in the Czech Holstein population. Data set consisted of 770 865 records of gestation length in 375 574 Holstein cows and covered the period from 2012 to 2018. Mean gestation length was 277 ± 4.9 days, and it was 1.4 days longer in male calves compared to females, and 1.1 days longer in cows compared to heifers. Animal repeatability model with maternal effect was employed for variance component estimation. The direct genetic effect explained the highest proportion of variability, and it corresponded with moderate direct heritability (0.48), while maternal heritability was much lower (0.06). We estimated conventional and genomic breeding values with the genomic matrix based on 39 145 single nucleotide polymorphisms in 13 844 animals. Genomic breeding values were weakly (< 0.25) but significantly correlated with breeding values for type, production and fitness traits. Pearson correlations between breeding values indicated a negative association of direct gestation length with milk production, longevity and fertility of bulls, and a positive association of maternal gestation length with most of the type traits related to the body composition. Genetic trends for male and female parts of the population showed a tendency to the shortening of gestation, which should be of concern, as short gestation could be reflected in a negative indirect response in other correlated traits, such as the incidence of stillbirth, the health status of cows after calving, culling, or conception rate.
Keywords: genetic trend, genomic evaluation, heritability, pregnancy
Journal: Czech Journal of Animal Science
Pages: 473-481
Volume: 65
Issue: 12
Year: 2020
DOI: 10.17221/150/2020-CJAS
File-URL: http://cjas.agriculturejournals.cz/doi/10.17221/150/2020-CJAS.html
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Handle: RePEc:caa:jnlcjs:v:65:y:2020:i:12:id:150-2020-CJAS

Template-Type: ReDIF-Article 1.0
Author-Name: Michaela Přibáňová
Author-Name: Daniela Schroffelová
Author-Workplace-Name: Czech-Moravian Breeders' Corporation, a.s., Hradištko, Czech Republic
Author-Name: David Lipovský
Author-Workplace-Name: Czech-Moravian Breeders' Corporation, a.s., Hradištko, Czech Republic
Author-Name: Josef Kučera
Author-Workplace-Name: Czech-Moravian Breeders' Corporation, a.s., Hradištko, Czech Republic
Author-Name: Vladimír Šteiger
Author-Workplace-Name: Czech-Moravian Breeders' Corporation, a.s., Hradištko, Czech Republic
Author-Name: Jarmila Hromádková
Author-Workplace-Name: Czech-Moravian Breeders' Corporation, a.s., Hradištko, Czech Republic
Author-Name: Lucie Němcová
Author-Workplace-Name: Czech-Moravian Breeders' Corporation, a.s., Hradištko, Czech Republic
Title: Use of SNPs from Illumina BovineSNP50K BeadChip v3 for imputation of microsatellite alleles for parentage verification and QTL reporting
Abstract: The present study aimed to test the possibility of avoiding expensive retesting of the whole parental generation for single nucleotide polymorphisms (SNPs), to provide additional analysis of microsatellites in offspring in the transitional period and to analyse the likelihood of imputation of the International Society for Animal Genetics-recommended microsatellite markers from selected SNPs. The imputation and pedigree verification of 9 520 animals (representing 84 dairy bulls, 285 dairy cows, 3 202 beef bulls and 5 949 beef cows) were analysed by the method using 9 410 SNP haplotypes (incorporating an average of 73 SNPs per haplotype). The imputation method was confirmed to allow the parentage verification of up to 87% of the analysed animals without the need for retesting. The most problematic locus was TGLA53, with only 78% successful imputation. Seven loci (BM2113, ETH225, TGLA227, BM1824, SPS115, TGLA122 and TGLA126) had more than 90% imputing accuracy and success of imputation. The success of imputation also depends on the breed and the call rate of the test results. The highest imputation accuracy was found for the Holstein breed; the other six breeds had over 90% successful imputation rates, four breeds had imputation rates between 85.0 and 89.9%, and ten breeds (rarely bred in the Czech Republic) had imputation rates below 85.0%. A call rate of SNP tests lower than 90% indicates problems with haplotype construction and thus deterioration in the success of imputation. The analysis of a possibility of using all possible information from Illumina BovineSNP50K BeadChip v3 showed 109 SNPs encoding 51 quantitative trait loci markers. Haplotypes were designed for interpretation of the most important markers for diseases, exterior and performance. The most important markers for Holstein breeders were chosen as kappa- (variants A, B and E) and beta-casein (variants A1, A2), Holstein haplotypes affecting fertility (HH1, HH3, and HH4) and loci causing genetic defects, bovine leukocyte adhesion deficiency and deficiency of uridine monophosphate synthetase. The results estimated from bovine bead chips corresponded to the expected distribution of the incidence of these traits in the population and were verified by PCR-RFLP tests.
Keywords: kappa-casein, beta-casein, BLAD, DUMPS, Holstein fertility haplotypes, single nucleotide polymorphism, quantitative trait locus
Journal: Czech Journal of Animal Science
Pages: 482-490
Volume: 65
Issue: 12
Year: 2020
DOI: 10.17221/208/2020-CJAS
File-URL: http://cjas.agriculturejournals.cz/doi/10.17221/208/2020-CJAS.html
File-Format: text/html
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Handle: RePEc:caa:jnlcjs:v:65:y:2020:i:12:id:208-2020-CJAS