Using pre-selected variants from large-scale whole-genome sequence data for single-step genomic predictions in pigs
CONCLUSIONS: The benefit of using sequence data depends on the line, the size of the genotyped population, and how the WGS variants are preselected. When WGS data are available on hundreds of thousands of animals, using sequence data presents an advantage but this remains limited in pigs.PMID:37495982 | PMC:PMC10373252 | DOI:10.1186/s12711-023-00831-0 (Source: Genet Sel Evol)
Source: Genet Sel Evol - July 26, 2023 Category: Genetics & Stem Cells Authors: Sungbong Jang Roger Ros-Freixedes John M Hickey Ching-Yi Chen Justin Holl William O Herring Ignacy Misztal Daniela Lourenco Source Type: research
Using pre-selected variants from large-scale whole-genome sequence data for single-step genomic predictions in pigs
CONCLUSIONS: The benefit of using sequence data depends on the line, the size of the genotyped population, and how the WGS variants are preselected. When WGS data are available on hundreds of thousands of animals, using sequence data presents an advantage but this remains limited in pigs.PMID:37495982 | PMC:PMC10373252 | DOI:10.1186/s12711-023-00831-0 (Source: Genet Sel Evol)
Source: Genet Sel Evol - July 26, 2023 Category: Genetics & Stem Cells Authors: Sungbong Jang Roger Ros-Freixedes John M Hickey Ching-Yi Chen Justin Holl William O Herring Ignacy Misztal Daniela Lourenco Source Type: research
Using pre-selected variants from large-scale whole-genome sequence data for single-step genomic predictions in pigs
CONCLUSIONS: The benefit of using sequence data depends on the line, the size of the genotyped population, and how the WGS variants are preselected. When WGS data are available on hundreds of thousands of animals, using sequence data presents an advantage but this remains limited in pigs.PMID:37495982 | PMC:PMC10373252 | DOI:10.1186/s12711-023-00831-0 (Source: Genet Sel Evol)
Source: Genet Sel Evol - July 26, 2023 Category: Genetics & Stem Cells Authors: Sungbong Jang Roger Ros-Freixedes John M Hickey Ching-Yi Chen Justin Holl William O Herring Ignacy Misztal Daniela Lourenco Source Type: research
Using pre-selected variants from large-scale whole-genome sequence data for single-step genomic predictions in pigs
CONCLUSIONS: The benefit of using sequence data depends on the line, the size of the genotyped population, and how the WGS variants are preselected. When WGS data are available on hundreds of thousands of animals, using sequence data presents an advantage but this remains limited in pigs.PMID:37495982 | DOI:10.1186/s12711-023-00831-0 (Source: Genet Sel Evol)
Source: Genet Sel Evol - July 26, 2023 Category: Genetics & Stem Cells Authors: Sungbong Jang Roger Ros-Freixedes John M Hickey Ching-Yi Chen Justin Holl William O Herring Ignacy Misztal Daniela Lourenco Source Type: research
Combining host and rumen metagenome profiling for selection in sheep: prediction of methane, feed efficiency, production, and health traits
CONCLUSIONS: This paper shows the potential of using RE-RRS as a low-cost, high-throughput approach for generating metagenome profiles on thousands of animals for improved prediction of economically and environmentally important traits. A reference-free approach using a microbial relationship matrix from log10 proportions of each tag normalized within cohort (i.e., the group of animals sampled at the same time) is recommended for future predictions using RE-RRS metagenome profiles.PMID:37491204 | DOI:10.1186/s12711-023-00822-1 (Source: Genet Sel Evol)
Source: Genet Sel Evol - July 25, 2023 Category: Genetics & Stem Cells Authors: Melanie K Hess Larissa Zetouni Andrew S Hess Juliana Budel Ken G Dodds Hannah M Henry Rudiger Brauning Alan F McCulloch Sharon M Hickey Patricia L Johnson Sara Elmes Janine Wing Brooke Bryson Kevin Knowler Dianne Hyndman Hayley Baird Kathryn M McRae Arjan Source Type: research
Selection for social genetic effects in purebred pigs improves behaviour and handling of their crossbred progeny
CONCLUSIONS: After 7 weeks in the finisher unit, crossbred progeny with high SBV were calmer in the weighing crate and had fewer ear lesions. These results indicate that selection of purebred parents for SBV for growth rate will increase welfare in their crossbred progeny by decreasing the number of ear lesions and making them easier to handle.PMID:37491205 | DOI:10.1186/s12711-023-00828-9 (Source: Genet Sel Evol)
Source: Genet Sel Evol - July 25, 2023 Category: Genetics & Stem Cells Authors: Bjarne Nielsen Lizette Vestergaard Horndrup Simon P Turner Ole Fredslund Christensen Hanne Marie Nielsen Birgitte Ask Source Type: research
The WUR0000125 PRRS resilience SNP had no apparent effect on pigs' infectivity and susceptibility in a novel transmission trial
CONCLUSIONS: The novel design demonstrated that it is possible to estimate genotype effects on Shedder pig infectivity and Contact pig susceptibility that are not confounded by family effects. The study, however, provided no supportive evidence that genetic selection on WUR genotype would affect PRRSV-2 transmission. The results of this study need to be independently validated in a larger trial using different PRRSV strains before dismissing the effects of the WUR marker or the previously detected GBP5 gene on PRRSV transmission.PMID:37488481 | PMC:PMC10364427 | DOI:10.1186/s12711-023-00824-z (Source: Genet Sel Evol)
Source: Genet Sel Evol - July 24, 2023 Category: Genetics & Stem Cells Authors: Margo Chase-Topping Graham Plastow Jack Dekkers Yanhua Li Ying Fang Volker Gerdts Jill Van Kessel John Harding Tanja Opriessnig Andrea Doeschl-Wilson Source Type: research
Using social interaction models for genetic analysis of skin damage in gilts
CONCLUSIONS: Combined skin damage is heritable, and genetic selection against this trait will increase the welfare of animals in the long term. Combined skin damage is affected by social genetic effects, and modeling this trait with a social interaction model increases the potential for genetic improvement. Including genomic information increases the prediction accuracy of estimated breeding values and reduces their bias and dispersion, although some biases persist. The results of the genome-wide association study indicate that CSD has a polygenic architecture and no major quantitative trait locus was detected.PMID:3748848...
Source: Genet Sel Evol - July 24, 2023 Category: Genetics & Stem Cells Authors: Nat ália Galoro Leite Egbert Knol Shogo Tsuruta Stefanie Nuphaus Roos Vogelzang Daniela Lourenco Source Type: research
The WUR0000125 PRRS resilience SNP had no apparent effect on pigs' infectivity and susceptibility in a novel transmission trial
CONCLUSIONS: The novel design demonstrated that it is possible to estimate genotype effects on Shedder pig infectivity and Contact pig susceptibility that are not confounded by family effects. The study, however, provided no supportive evidence that genetic selection on WUR genotype would affect PRRSV-2 transmission. The results of this study need to be independently validated in a larger trial using different PRRSV strains before dismissing the effects of the WUR marker or the previously detected GBP5 gene on PRRSV transmission.PMID:37488481 | PMC:PMC10364427 | DOI:10.1186/s12711-023-00824-z (Source: Genet Sel Evol)
Source: Genet Sel Evol - July 24, 2023 Category: Genetics & Stem Cells Authors: Margo Chase-Topping Graham Plastow Jack Dekkers Yanhua Li Ying Fang Volker Gerdts Jill Van Kessel John Harding Tanja Opriessnig Andrea Doeschl-Wilson Source Type: research
Using social interaction models for genetic analysis of skin damage in gilts
CONCLUSIONS: Combined skin damage is heritable, and genetic selection against this trait will increase the welfare of animals in the long term. Combined skin damage is affected by social genetic effects, and modeling this trait with a social interaction model increases the potential for genetic improvement. Including genomic information increases the prediction accuracy of estimated breeding values and reduces their bias and dispersion, although some biases persist. The results of the genome-wide association study indicate that CSD has a polygenic architecture and no major quantitative trait locus was detected.PMID:3748848...
Source: Genet Sel Evol - July 24, 2023 Category: Genetics & Stem Cells Authors: Nat ália Galoro Leite Egbert Knol Shogo Tsuruta Stefanie Nuphaus Roos Vogelzang Daniela Lourenco Source Type: research
Taming transposable elements in livestock and poultry: a review of their roles and applications
Genet Sel Evol. 2023 Jul 21;55(1):50. doi: 10.1186/s12711-023-00821-2.ABSTRACTLivestock and poultry play a significant role in human nutrition by converting agricultural by-products into high-quality proteins. To meet the growing demand for safe animal protein, genetic improvement of livestock must be done sustainably while minimizing negative environmental impacts. Transposable elements (TE) are important components of livestock and poultry genomes, contributing to their genetic diversity, chromatin states, gene regulatory networks, and complex traits of economic value. However, compared to other species, research on TE i...
Source: Genet Sel Evol - July 21, 2023 Category: Genetics & Stem Cells Authors: Pengju Zhao Chen Peng Lingzhao Fang Zhengguang Wang George E Liu Source Type: research
Taming transposable elements in livestock and poultry: a review of their roles and applications
Genet Sel Evol. 2023 Jul 21;55(1):50. doi: 10.1186/s12711-023-00821-2.ABSTRACTLivestock and poultry play a significant role in human nutrition by converting agricultural by-products into high-quality proteins. To meet the growing demand for safe animal protein, genetic improvement of livestock must be done sustainably while minimizing negative environmental impacts. Transposable elements (TE) are important components of livestock and poultry genomes, contributing to their genetic diversity, chromatin states, gene regulatory networks, and complex traits of economic value. However, compared to other species, research on TE i...
Source: Genet Sel Evol - July 21, 2023 Category: Genetics & Stem Cells Authors: Pengju Zhao Chen Peng Lingzhao Fang Zhengguang Wang George E Liu Source Type: research
Taming transposable elements in livestock and poultry: a review of their roles and applications
Genet Sel Evol. 2023 Jul 21;55(1):50. doi: 10.1186/s12711-023-00821-2.ABSTRACTLivestock and poultry play a significant role in human nutrition by converting agricultural by-products into high-quality proteins. To meet the growing demand for safe animal protein, genetic improvement of livestock must be done sustainably while minimizing negative environmental impacts. Transposable elements (TE) are important components of livestock and poultry genomes, contributing to their genetic diversity, chromatin states, gene regulatory networks, and complex traits of economic value. However, compared to other species, research on TE i...
Source: Genet Sel Evol - July 21, 2023 Category: Genetics & Stem Cells Authors: Pengju Zhao Chen Peng Lingzhao Fang Zhengguang Wang George E Liu Source Type: research
Dimensionality of genomic information and its impact on genome-wide associations and variant selection for genomic prediction: a simulation study
CONCLUSIONS: Accurately identifying causative variants from sequence data depends on the effective population size and, therefore, on the dimensionality of genomic information. This dimensionality can help identify the most suitable sample size for GWA and could be considered for variant selection, especially when resources are restricted. Even when variants are accurately identified, their inclusion in prediction models has limited benefits.PMID:37460964 | PMC:PMC10351171 | DOI:10.1186/s12711-023-00823-0 (Source: Genet Sel Evol)
Source: Genet Sel Evol - July 17, 2023 Category: Genetics & Stem Cells Authors: Sungbong Jang Shogo Tsuruta Natalia Galoro Leite Ignacy Misztal Daniela Lourenco Source Type: research
Impact of kinship matrices on genetic gain and inbreeding with optimum contribution selection in a genomic dairy cattle breeding program
CONCLUSIONS: Using genomic relationships for OCS realizes more genetic gain for a given amount of kinship and inbreeding than using pedigree relationships when the number of sires is fixed. For a small genomic dairy cattle breeding program, we recommend that the implementation of OCS uses VR1 with reference allele frequencies estimated either from base animals or old genotyped animals.PMID:37460999 | PMC:PMC10351146 | DOI:10.1186/s12711-023-00826-x (Source: Genet Sel Evol)
Source: Genet Sel Evol - July 17, 2023 Category: Genetics & Stem Cells Authors: Egill Gautason Goutam Sahana Bernt Guldbrandtsen Peer Berg Source Type: research
