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Ogawa S, Taniguchi Y, Watanabe T, Iwaisaki H. Fitting Genomic Prediction Models with Different Marker Effects among Prefectures to Carcass Traits in Japanese Black Cattle. Genes (Basel) 2022; 14:24. [PMID: 36672767 PMCID: PMC9859149 DOI: 10.3390/genes14010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
We fitted statistical models, which assumed single-nucleotide polymorphism (SNP) marker effects differing across the fattened steers marketed into different prefectures, to the records for cold carcass weight (CW) and marbling score (MS) of 1036, 733, and 279 Japanese Black fattened steers marketed into Tottori, Hiroshima, and Hyogo prefectures in Japan, respectively. Genotype data on 33,059 SNPs was used. Five models that assume only common SNP effects to all the steers (model 1), common effects plus SNP effects differing between the steers marketed into Hyogo prefecture and others (model 2), only the SNP effects differing between Hyogo steers and others (model 3), common effects plus SNP effects specific to each prefecture (model 4), and only the effects specific to each prefecture (model 5) were exploited. For both traits, slightly lower values of residual variance than that of model 1 were estimated when fitting all other models. Estimated genetic correlation among the prefectures in models 2 and 4 ranged to 0.53 to 0.71, all <0.8. These results might support that the SNP effects differ among the prefectures to some degree, although we discussed the necessity of careful consideration to interpret the current results.
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Affiliation(s)
- Shinichiro Ogawa
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
- Division of Meat Animal and Poultry Research, Institute of Livestock and Grassland Science, Tsukuba 305-0901, Japan
| | - Yukio Taniguchi
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Toshio Watanabe
- National Livestock Breeding Center, Fukushima 961-8511, Japan
- Maebashi Institute of Animal Science, Livestock Improvement Association of Japan, Inc., Maebashi 371-0121, Japan
| | - Hiroaki Iwaisaki
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
- Sado Island Center for Ecological Sustainability, Niigata University, Niigata 952-0103, Japan
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Zhang P, Qiu X, Wang L, Zhao F. Progress in Genomic Mating in Domestic Animals. Animals (Basel) 2022; 12:ani12182306. [PMID: 36139166 PMCID: PMC9494983 DOI: 10.3390/ani12182306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/25/2022] Open
Abstract
Simple Summary Since animal domestication, breeders have been selecting candidates for breeding based on phenotypic performance. Estimating breeding values through the best linear unbiased prediction method represents a revolutionary shift in animal breeding. On this basis, selection and mating are utilized to improve the production level of animals. The application of genomic selection has once again revolutionized animal breeding methods. However, although this kind of truncated selection based on breeding values can significantly improve genetic gain, the genetic relationship between individuals with a high breeding value is usually closed, and the probability of being co-selected is greater, which will lead to a rapid increase in the rate of inbreeding in the population. Reduced genetic variation is not conducive to long-term sustainable breeding, so a trade-off between genetic gain and inbreeding is required. Genomic mating is the use of candidate individuals’ genomic information to implement optimized breeding and mating, which can effectively control the rate of inbreeding in the population and achieve long-term and sustainable genetic gain. It is more suitable for modern animal breeding, especially for conservation and genetic improvement of local domestic animal breeds. Abstract Selection is a continuous process that can influence the distribution of target traits in a population. From the perspective of breeding, elite individuals are selected for breeding, which is called truncated selection. With the introduction and application of the best linear unbiased prediction (BLUP) method, breeders began to use pedigree-based estimated breeding values (EBV) to select candidates for the genetic improvement of complex traits. Although truncated selection based on EBV can significantly improve the genetic progress, the genetic relationships between individuals with a high breeding value are usually closed, and the probability of being co-selected is greater, which will lead to a rapid increase in the level of inbreeding in the population. Reduced genetic variation is not conducive to long-term sustainable breeding, so a trade-off between genetic progress and inbreeding is required. As livestock and poultry breeding enters the genomic era, using genomic information to obtain optimal mating plans has formally been proposed by Akdemir et al., a method called genomic mating (GM). GM is more accurate and reliable than using pedigree information. Moreover, it can effectively control the inbreeding level of the population and achieve long-term and sustainable genetic gain. Hence, GM is more suitable for modern animal breeding, especially for local livestock and poultry breed conservation and genetic improvement. This review mainly summarized the principle of genomic mating, the methodology and usage of genomic mating, and the progress of its application in livestock and poultry.
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Affiliation(s)
- Pengfei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaotian Qiu
- National Animal Husbandry Service, Beijing 100125, China
| | - Lixian Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (L.W.); (F.Z.); Tel.: +86-010-6281-6011 (F.Z.)
| | - Fuping Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (L.W.); (F.Z.); Tel.: +86-010-6281-6011 (F.Z.)
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Tiret M, Pégard M, Sánchez L. How to achieve a higher selection plateau in forest tree breeding? Fostering heterozygote × homozygote relationships in optimal contribution selection in the case study of Populus nigra. Evol Appl 2021; 14:2635-2646. [PMID: 34815744 PMCID: PMC8591327 DOI: 10.1111/eva.13300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 09/07/2021] [Indexed: 12/27/2022] Open
Abstract
In breeding, optimal contribution selection (OCS) is one of the most effective strategies to balance short- and long-term genetic responses, by maximizing genetic gain and minimizing global coancestry. Considering genetic diversity in the selection dynamic-through coancestry-is undoubtedly the reason for the success of OCS, as it avoids preliminary loss of favorable alleles. Originally formulated with the pedigree relationship matrix, global coancestry can nowadays be assessed with one of the possible formulations of the realized genomic relationship matrix. Most formulations were optimized for genomic evaluation, but few for the management of coancestry. We introduce here an alternative formulation specifically developed for genomic OCS (GOCS), intended to better control heterozygous loci, and thus better account for Mendelian sampling. We simulated a multigeneration breeding program with mate allocation and under GOCS for twenty generations, solved with quadratic programming. With the case study of Populus nigra, we have shown that, although the dynamic was mainly determined by the trade-off between genetic gain and genetic diversity, better formulations of the genomic relationship matrix, especially those fostering individuals carrying multiple heterozygous loci, can lead to better short-term genetic gain and a higher selection plateau.
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Affiliation(s)
- Mathieu Tiret
- BioForA, INRAE, ONFOrléansFrance
- Department of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Marie Pégard
- BioForA, INRAE, ONFOrléansFrance
- INRAE, BIOGECOUniv. BordeauxCestasFrance
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Villanueva B, Fernández A, Saura M, Caballero A, Fernández J, Morales-González E, Toro MA, Pong-Wong R. The value of genomic relationship matrices to estimate levels of inbreeding. Genet Sel Evol 2021; 53:42. [PMID: 33933002 PMCID: PMC8088726 DOI: 10.1186/s12711-021-00635-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 04/19/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Genomic relationship matrices are used to obtain genomic inbreeding coefficients. However, there are several methodologies to compute these matrices and there is still an unresolved debate on which one provides the best estimate of inbreeding. In this study, we investigated measures of inbreeding obtained from five genomic matrices, including the Nejati-Javaremi allelic relationship matrix (FNEJ), the Li and Horvitz matrix based on excess of homozygosity (FL&H), and the VanRaden (methods 1, FVR1, and 2, FVR2) and Yang (FYAN) genomic relationship matrices. We derived expectations for each inbreeding coefficient, assuming a single locus model, and used these expectations to explain the patterns of the coefficients that were computed from thousands of single nucleotide polymorphism genotypes in a population of Iberian pigs. RESULTS Except for FNEJ, the evaluated measures of inbreeding do not match with the original definitions of inbreeding coefficient of Wright (correlation) or Malécot (probability). When inbreeding coefficients are interpreted as indicators of variability (heterozygosity) that was gained or lost relative to a base population, both FNEJ and FL&H led to sensible results but this was not the case for FVR1, FVR2 and FYAN. When variability has increased relative to the base, FVR1, FVR2 and FYAN can indicate that it decreased. In fact, based on FYAN, variability is not expected to increase. When variability has decreased, FVR1 and FVR2 can indicate that it has increased. Finally, these three coefficients can indicate that more variability than that present in the base population can be lost, which is also unreasonable. The patterns for these coefficients observed in the pig population were very different, following the derived expectations. As a consequence, the rate of inbreeding depression estimated based on these inbreeding coefficients differed not only in magnitude but also in sign. CONCLUSIONS Genomic inbreeding coefficients obtained from the diagonal elements of genomic matrices can lead to inconsistent results in terms of gain and loss of genetic variability and inbreeding depression estimates, and thus to misleading interpretations. Although these matrices have proven to be very efficient in increasing the accuracy of genomic predictions, they do not always provide a useful measure of inbreeding.
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Affiliation(s)
- Beatriz Villanueva
- Departamento de Mejora Genética Animal, INIA, Ctra. de La Coruña, km 7.5, 28040 Madrid, Spain
| | - Almudena Fernández
- Departamento de Mejora Genética Animal, INIA, Ctra. de La Coruña, km 7.5, 28040 Madrid, Spain
| | - María Saura
- Departamento de Mejora Genética Animal, INIA, Ctra. de La Coruña, km 7.5, 28040 Madrid, Spain
| | - Armando Caballero
- Centro de Investigación Mariña, Universidade de Vigo, Departamento de Bioquímica, Genética E Inmunología, Campus de Vigo, 36310 Vigo, Spain
| | - Jesús Fernández
- Departamento de Mejora Genética Animal, INIA, Ctra. de La Coruña, km 7.5, 28040 Madrid, Spain
| | | | - Miguel A. Toro
- Departamento de Producción Agraria, ETSI Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Ricardo Pong-Wong
- Genetics and Genomics, The Roslin Institute and the R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
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Changes in Allele Frequencies When Different Genomic Coancestry Matrices Are Used for Maintaining Genetic Diversity. Genes (Basel) 2021; 12:genes12050673. [PMID: 33947136 PMCID: PMC8146037 DOI: 10.3390/genes12050673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/21/2021] [Accepted: 04/29/2021] [Indexed: 11/16/2022] Open
Abstract
A main objective in conservation programs is to maintain genetic variability. This can be achieved using the Optimal Contributions (OC) method that optimizes the contributions of candidates to the next generation by minimizing the global coancestry. However, it has been argued that maintaining allele frequencies is also important. Different genomic coancestry matrices can be used on OC and the choice of the matrix will have an impact not only on the genetic variability maintained, but also on the change in allele frequencies. The objective of this study was to evaluate, through stochastic simulations, the genetic variability maintained and the trajectory of allele frequencies when using two different genomic coancestry matrices in OC to minimize the loss of diversity: (i) the matrix based on deviations of the observed number of alleles shared between two individuals from the expected numbers under Hardy–Weinberg equilibrium (θLH); and (ii) the matrix based on VanRaden’s genomic relationship matrix (θVR). The results indicate that the use of θLH resulted in a higher genetic variability than the use of θVR. However, the use of θVR maintained allele frequencies closer to those in the base population than the use of θLH.
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Meuwissen THE, Sonesson AK, Gebregiwergis G, Woolliams JA. Management of Genetic Diversity in the Era of Genomics. Front Genet 2020; 11:880. [PMID: 32903415 PMCID: PMC7438563 DOI: 10.3389/fgene.2020.00880] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/17/2020] [Indexed: 12/27/2022] Open
Abstract
Management of genetic diversity aims to (i) maintain heterozygosity, which ameliorates inbreeding depression and loss of genetic variation at loci that may become of importance in the future; and (ii) avoid genetic drift, which prevents deleterious recessives (e.g., rare disease alleles) from drifting to high frequency, and prevents random drift of (functional) traits. In the genomics era, genomics data allow for many alternative measures of inbreeding and genomic relationships. Genomic relationships/inbreeding can be classified into (i) homozygosity/heterozygosity based (e.g., molecular kinship matrix); (ii) genetic drift-based, i.e., changes of allele frequencies; or (iii) IBD-based, i.e., SNPs are used in linkage analyses to identify IBD segments. Here, alternative measures of inbreeding/relationship were used to manage genetic diversity in genomic optimal contribution (GOC) selection schemes. Contrary to classic inbreeding theory, it was found that drift and homozygosity-based inbreeding could differ substantially in GOC schemes unless diversity management was based upon IBD. When using a homozygosity-based measure of relationship, the inbreeding management resulted in allele frequency changes toward 0.5 giving a low rate of increase in homozygosity for the panel used for management, but not for unmanaged neutral loci, at the expense of a high genetic drift. When genomic relationship matrices were based on drift, following VanRaden and as in GCTA, drift was low at the expense of a high rate of increase in homozygosity. The use of IBD-based relationship matrices for inbreeding management limited both drift and the homozygosity-based rate of inbreeding to their target values. Genetic improvement per percent of inbreeding was highest when GOC used IBD-based relationships irrespective of the inbreeding measure used. Genomic relationships based on runs of homozygosity resulted in very high initial improvement per percent of inbreeding, but also in substantial discrepancies between drift and homozygosity-based rates of inbreeding, and resulted in a drift that exceeded its target value. The discrepancy between drift and homozygosity-based rates of inbreeding was caused by a covariance between initial allele frequency and the subsequent change in frequency, which becomes stronger when using data from whole genome sequence.
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Affiliation(s)
- Theo H E Meuwissen
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
| | | | | | - John A Woolliams
- The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
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7
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Gebregiwergis GT, Sørensen AC, Henryon M, Meuwissen T. Controlling Coancestry and Thereby Future Inbreeding by Optimum-Contribution Selection Using Alternative Genomic-Relationship Matrices. Front Genet 2020; 11:345. [PMID: 32425971 PMCID: PMC7212439 DOI: 10.3389/fgene.2020.00345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 03/23/2020] [Indexed: 11/28/2022] Open
Abstract
We tested the consequences of using alternative genomic relationship matrices to predict genomic breeding values (GEBVs) and control of coancestry in optimum contribution selection, where the relationship matrix used to calculate GEBVs was not necessarily the same as that used to control coancestry. A stochastic simulation study was carried out to investigate genetic gain and true genomic inbreeding in breeding schemes that applied genomic optimum contribution selection (GOCS) with different genomic relationship matrices. Three genomic-relationship matrices were used to predict the GEBVs based on three information sources: markers (GM), QTL (GQ), and markers and QTL (GA). Strictly, GQ is not possible to implement in practice since we do not know the quantitative trait loci (QTL) positions, but more and more information is becoming available especially about the largest QTL. Two genomic-relationship matrices were used to control coancestry: GM and GA. Three genetic architectures were simulated: with 7702, 1000, and 500 QTLs together with 54,218 markers. Selection was for a single trait with heritability 0.2. All selection candidates were phenotyped and genotyped before selection. With 7702 QTL, there were no significant differences in rates of genetic gain at the same rate of true inbreeding using different genomic relationship matrices in GOCS. However, as the number of QTLs was reduced to 1000, prediction of GEBVs using a genomic relationship matrix constructed based on GQ and control of coancestry using GM realized 29.7% higher genetic gain than using GM for both prediction and control of coancestry. Forty-three percent of this increased rate of genetic gain was due to increased accuracies of GEBVs. These findings indicate that with large numbers of QTL, it is not critical what information, i.e., markers or QTL, is used to construct genomic-relationship matrices. However, it becomes critical with small numbers of QTL. This highlights the importance of using genomic-relationship matrices that focus on QTL regions for GEBV estimation when the number of QTL is small in GOCS. Relationships used to control coancestry are preferably based on marker data.
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Affiliation(s)
- G T Gebregiwergis
- Department of Animal and Aquaculture Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Anders C Sørensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Mark Henryon
- Seges, Copenhagen, Denmark.,School of Agriculture and Environment, University of Western Australia, Crawley, WA, Australia
| | - Theo Meuwissen
- Department of Animal and Aquaculture Sciences, Norwegian University of Life Sciences, Ås, Norway
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Toro MA, Villanueva B, Fernández J. The concept of effective population size loses its meaning in the context of optimal management of diversity using molecular markers. J Anim Breed Genet 2019; 137:345-355. [PMID: 31713272 DOI: 10.1111/jbg.12455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/03/2019] [Accepted: 10/11/2019] [Indexed: 11/28/2022]
Abstract
Effective population size is a key parameter in conservation genetics. In the management of conservation programs using pedigree information, there is a consensus that the optimal method for maximizing effective population size is to calculate the contribution of each potential parent (the number of offspring that each individual leaves to the next generation) by minimizing the global pedigree-based coancestry between potential parents weighted by their contributions. When using molecular data, the optimal method for managing genetic diversity will remain the same but now the molecular coancestry calculated from markers will replace the pedigree-based coancestry. However, in this situation, the concept of effective population size loses its meaning because with optimal molecular management, genetic diversity increases in early generations and therefore effective population size takes negative values. Furthermore, in the long term, the molecular effective population size does not attain an asymptotic value but it shows an unpredictable behaviour.
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Affiliation(s)
- Miguel A Toro
- Departamento de Producción Agraria, Universidad Politécnica de Madrid, Madrid, Spain
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Doublet AC, Croiseau P, Fritz S, Michenet A, Hozé C, Danchin-Burge C, Laloë D, Restoux G. The impact of genomic selection on genetic diversity and genetic gain in three French dairy cattle breeds. Genet Sel Evol 2019; 51:52. [PMID: 31547802 PMCID: PMC6757367 DOI: 10.1186/s12711-019-0495-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 09/11/2019] [Indexed: 11/23/2022] Open
Abstract
Background In France, implementation of genomic evaluations in dairy cattle breeds started in 2009 and this has modified the breeding schemes drastically. In this context, the goal of our study was to understand the impact of genomic selection on the genetic diversity of bulls from three French dairy cattle breeds born between 2005 and 2015 (Montbéliarde, Normande and Holstein) and the factors that are involved. Methods We compared annual genetic gains, inbreeding rates based on runs of homozygosity (ROH) and pedigree data, and mean ROH length within breeds, before and after the implementation of genomic selection. Results Genomic selection induced an increase in mean annual genetic gains of 50, 71 and 33% for Montbéliarde, Normande and Holstein bulls, respectively, and in parallel, the generation intervals were reduced by a factor of 1.7, 1.9 and 2, respectively. We found no significant change in inbreeding rate for the two national breeds, Montbéliarde and Normande, and a significant increase in inbreeding rate for the Holstein international breed, which is now as high as 0.55% per year based on ROH and 0.49% per year based on pedigree data (equivalent to a rate of 1.36 and 1.39% per generation, respectively). The mean ROH length was longer for bulls from the Holstein breed than for those from the other two breeds. Conclusions With the implementation of genomic selection, the annual genetic gain increased for bulls from the three major French dairy cattle breeds. At the same time, the annual loss of genetic diversity increased for Holstein bulls, possibly because of the massive use of a few elite bulls in this breed, but not for Montbéliarde and Normande bulls. The increase in mean ROH length in Holstein may reflect the occurrence of recent inbreeding. New strategies in breeding schemes, such as female donor stations and embryo transfer, and recent implementation of genomic evaluations in small regional breeds should be studied carefully in order to ensure the sustainability of breeding schemes in the future.
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Affiliation(s)
- Anna-Charlotte Doublet
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France. .,ALLICE, Paris, France.
| | - Pascal Croiseau
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Sébastien Fritz
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,ALLICE, Paris, France
| | - Alexis Michenet
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,ALLICE, Paris, France
| | - Chris Hozé
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,ALLICE, Paris, France
| | | | - Denis Laloë
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Gwendal Restoux
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
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10
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Wellmann R, Bennewitz J. Key Genetic Parameters for Population Management. Front Genet 2019; 10:667. [PMID: 31475027 PMCID: PMC6707806 DOI: 10.3389/fgene.2019.00667] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 06/25/2019] [Indexed: 11/13/2022] Open
Abstract
Population management has the primary task of maximizing the long-term competitiveness of a breed. Breeds compete with each other for being able to supply consumer demands at low costs and also for funds from conservation programs. The competition for consumer preference is won by breeds with high genetic gain for total merit who maintained a sufficiently high genetic diversity, whereas the competition for funds is won by breeds with high conservation value. The conservation value of a breed could be improved by increasing its contribution to the gene pool of the species. This may include the recovery of its original genetic background and the maintenance of a high genetic diversity at native haplotype segments. The primary objective of a breeding program depends on the genetic state of the population and its intended usage. In this paper, we review the key genetic parameters that are relevant for population management, compare the methods for estimating them, derive the formulas for predicting their value at a future time, and clarify their usage in various types of breeding programs that differ in their main objectives. These key parameters are kinships, native kinships, breeding values, Mendelian sampling variances, native contributions, and mutational effects. Population management currently experiences a transition from using pedigree-based estimates to marker-based estimates, which improves the accuracies of these estimates and thereby increases response to selection. In addition, improved measures of the factors that determine the competitiveness of a breed and utilize auxiliary parameters, such as Mendelian sampling variances, mutational effects, and native kinships, enable to improve further upon historic recommendations for genetic population management.
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Affiliation(s)
- Robin Wellmann
- Animal Genetics and Breeding, Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Jörn Bennewitz
- Animal Genetics and Breeding, Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
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11
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Doekes HP, Veerkamp RF, Bijma P, Hiemstra SJ, Windig JJ. Trends in genome-wide and region-specific genetic diversity in the Dutch-Flemish Holstein-Friesian breeding program from 1986 to 2015. Genet Sel Evol 2018; 50:15. [PMID: 29642838 PMCID: PMC5896142 DOI: 10.1186/s12711-018-0385-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 03/27/2018] [Indexed: 12/19/2022] Open
Abstract
Background In recent decades, Holstein–Friesian (HF) selection schemes have undergone profound changes, including the introduction of optimal contribution selection (OCS; around 2000), a major shift in breeding goal composition (around 2000) and the implementation of genomic selection (GS; around 2010). These changes are expected to have influenced genetic diversity trends. Our aim was to evaluate genome-wide and region-specific diversity in HF artificial insemination (AI) bulls in the Dutch-Flemish breeding program from 1986 to 2015. Methods Pedigree and genotype data (~ 75.5 k) of 6280 AI-bulls were used to estimate rates of genome-wide inbreeding and kinship and corresponding effective population sizes. Region-specific inbreeding trends were evaluated using regions of homozygosity (ROH). Changes in observed allele frequencies were compared to those expected under pure drift to identify putative regions under selection. We also investigated the direction of changes in allele frequency over time. Results Effective population size estimates for the 1986–2015 period ranged from 69 to 102. Two major breakpoints were observed in genome-wide inbreeding and kinship trends. Around 2000, inbreeding and kinship levels temporarily dropped. From 2010 onwards, they steeply increased, with pedigree-based, ROH-based and marker-based inbreeding rates as high as 1.8, 2.1 and 2.8% per generation, respectively. Accumulation of inbreeding varied substantially across the genome. A considerable fraction of markers showed changes in allele frequency that were greater than expected under pure drift. Putative selected regions harboured many quantitative trait loci (QTL) associated to a wide range of traits. In consecutive 5-year periods, allele frequencies changed more often in the same direction than in opposite directions, except when comparing the 1996–2000 and 2001–2005 periods. Conclusions Genome-wide and region-specific diversity trends reflect major changes in the Dutch-Flemish HF breeding program. Introduction of OCS and the shift in breeding goal were followed by a drop in inbreeding and kinship and a shift in the direction of changes in allele frequency. After introduction of GS, rates of inbreeding and kinship increased substantially while allele frequencies continued to change in the same direction as before GS. These results provide insight in the effect of breeding practices on genomic diversity and emphasize the need for efficient management of genetic diversity in GS schemes. Electronic supplementary material The online version of this article (10.1186/s12711-018-0385-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Harmen P Doekes
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands. .,Centre for Genetic Resources the Netherlands, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands.
| | - Roel F Veerkamp
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Piter Bijma
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Sipke J Hiemstra
- Centre for Genetic Resources the Netherlands, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Jack J Windig
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands.,Centre for Genetic Resources the Netherlands, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
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12
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Druml T, Neuditschko M, Grilz-Seger G, Horna M, Ricard A, Mesarič M, Cotman M, Pausch H, Brem G. Population Networks Associated with Runs of Homozygosity Reveal New Insights into the Breeding History of the Haflinger Horse. J Hered 2017; 109:384-392. [DOI: 10.1093/jhered/esx114] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/23/2017] [Indexed: 02/04/2023] Open
Affiliation(s)
- Thomas Druml
- Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Vienna, Austria
| | | | | | - Michaela Horna
- Department of Animal Husbandry, Slovak University of Agriculture in Nitra, Nitra-Chrenová, Slovak Republic
| | - Anne Ricard
- Institut National de la Recherche Agronomique, UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
- Institut Français du Cheval et de l’Equitation, Recherche et Innovation, Exmes, France
| | - Matjaz Mesarič
- Clinic for Reproduction and Large Animals, Veterinary Faculty, University of Lubljana, Cesta v Mestni log, Ljubljana, Slovenia
| | - Marco Cotman
- Institute of Preclinical Sciences, Veterinary Faculty, University of Ljubljana, Cesta v Mestni log, Ljubljana, Slovenia
| | | | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Vienna, Austria
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13
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Howard JT, Pryce JE, Baes C, Maltecca C. Invited review: Inbreeding in the genomics era: Inbreeding, inbreeding depression, and management of genomic variability. J Dairy Sci 2017; 100:6009-6024. [DOI: 10.3168/jds.2017-12787] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/25/2017] [Indexed: 11/19/2022]
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14
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Wang Y, Bennewitz J, Wellmann R. Novel optimum contribution selection methods accounting for conflicting objectives in breeding programs for livestock breeds with historical migration. Genet Sel Evol 2017; 49:45. [PMID: 28499352 PMCID: PMC5427594 DOI: 10.1186/s12711-017-0320-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 05/03/2017] [Indexed: 11/10/2022] Open
Abstract
Background Optimum contribution selection (OCS) is effective for increasing genetic gain, controlling the rate of inbreeding and enables maintenance of genetic diversity. However, this diversity may be caused by high migrant contributions (MC) in the population due to introgression of genetic material from other breeds, which can threaten the conservation of small local populations. Therefore, breeding objectives should not only focus on increasing genetic gains but also on maintaining genetic originality and diversity of native alleles. This study aimed at investigating whether OCS was improved by including MC and modified kinships that account for breed origin of alleles. Three objective functions were considered for minimizing kinship, minimizing MC and maximizing genetic gain in the offspring generation, and we investigated their effects on German Angler and Vorderwald cattle. Results In most scenarios, the results were similar for Angler and Vorderwald cattle. A significant positive correlation between MC and estimated breeding values of the selection candidates was observed for both breeds, thus traditional OCS would increase MC. Optimization was performed under the condition that the rate of inbreeding did not exceed 1% and at least 30% of the maximum progress was achieved for all other criteria. Although traditional OCS provided the highest breeding values under restriction of classical kinship, the magnitude of MC in the progeny generation was not controlled. When MC were constrained or minimized, the kinship at native alleles increased compared to the reference scenario. Thus, in addition to constraining MC, constraining kinship at native alleles is required to ensure that native genetic diversity is maintained. When kinship at native alleles was constrained, the classical kinship was automatically lowered in most cases and more sires were selected. However, the average breeding value in the next generation was also lower than that obtained with traditional OCS. Conclusions For local breeds with historical introgressions, current breeding programs should focus on increasing genetic gain and controlling inbreeding, as well as maintaining the genetic originality of the breeds and the diversity of native alleles via the inclusion of MC and kinship at native alleles in the OCS process. Electronic supplementary material The online version of this article (doi:10.1186/s12711-017-0320-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yu Wang
- Institute of Animal Science, University of Hohenheim, 70593, Stuttgart, Germany.
| | - Jörn Bennewitz
- Institute of Animal Science, University of Hohenheim, 70593, Stuttgart, Germany
| | - Robin Wellmann
- Institute of Animal Science, University of Hohenheim, 70593, Stuttgart, Germany
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15
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Howard JT, Tiezzi F, Pryce JE, Maltecca C. Geno-Diver: A combined coalescence and forward-in-time simulator for populations undergoing selection for complex traits. J Anim Breed Genet 2017; 134:553-563. [PMID: 28464287 DOI: 10.1111/jbg.12277] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/25/2017] [Indexed: 01/30/2023]
Abstract
Geno-Diver is a combined coalescence and forward-in-time simulator designed to simulate complex traits with a quantitative and/or fitness component and implement multiple selection and mating strategies utilizing pedigree or genomic information. The simulation is carried out in two steps. The first step generates whole-genome sequence data for founder individuals. A variety of trait architectures can be generated for quantitative and fitness traits along with their covariance. The second step generates new individuals forward-in-time based on a variety of selection and mating scenarios. Genetic values are predicted for individuals utilizing pedigree or genomic information. Relationship matrices and their associated inverses are generated using computationally efficient routines. We benchmarked Geno-Diver with a previous simulation program and described how to simulate a traditional quantitative trait along with a quantitative and fitness trait. A user manual with examples, source code in C++11 and executable versions of Geno-Diver for Linux are freely available at https://github.com/jeremyhoward/Geno-Diver.
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Affiliation(s)
- J T Howard
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | - F Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | - J E Pryce
- Department of Economic Development, Jobs, Transport and Resources and Dairy Futures Cooperative Research Centre, Bundoora, Vic., Australia.,La Trobe University, Bundoora, Vic., Australia
| | - C Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
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16
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Moving Beyond Managing Realized Genomic Relationship in Long-Term Genomic Selection. Genetics 2017; 206:1127-1138. [PMID: 28381589 DOI: 10.1534/genetics.116.194449] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 04/04/2017] [Indexed: 11/18/2022] Open
Abstract
Long-term genomic selection (GS) requires strategies that balance genetic gain with population diversity, to sustain progress for traits under selection, and to keep diversity for future breeding. In a simulation model for a recurrent selection scheme, we provide the first head-to-head comparison of two such existing strategies: genomic optimal contributions selection (GOCS), which limits realized genomic relationship among selection candidates, and weighted genomic selection (WGS), which upscales rare allele effects in GS. Compared to GS, both methods provide the same higher long-term genetic gain and a similar lower inbreeding rate, despite some inherent limitations. GOCS does not control the inbreeding rate component linked to trait selection, and, therefore, does not strike the optimal balance between genetic gain and inbreeding. This makes it less effective throughout the breeding scheme, and particularly so at the beginning, where genetic gain and diversity may not be competing. For WGS, truncation selection proved suboptimal to manage rare allele frequencies among the selection candidates. To overcome these limitations, we introduce two new set selection methods that maximize a weighted index balancing genetic gain with controlling expected heterozygosity (IND-HE) or maintaining rare alleles (IND-RA), and show that these outperform GOCS and WGS in a nearly identical way. While requiring further testing, we believe that the inherent benefits of the IND-HE and IND-RA methods will transfer from our simulation framework to many practical breeding settings, and are therefore a major step forward toward efficient long-term genomic selection.
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17
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Peripolli E, Munari DP, Silva MVGB, Lima ALF, Irgang R, Baldi F. Runs of homozygosity: current knowledge and applications in livestock. Anim Genet 2016; 48:255-271. [PMID: 27910110 DOI: 10.1111/age.12526] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2016] [Indexed: 12/17/2022]
Abstract
This review presents a broader approach to the implementation and study of runs of homozygosity (ROH) in animal populations, focusing on identifying and characterizing ROH and their practical implications. ROH are continuous homozygous segments that are common in individuals and populations. The ability of these homozygous segments to give insight into a population's genetic events makes them a useful tool that can provide information about the demographic evolution of a population over time. Furthermore, ROH provide useful information about the genetic relatedness among individuals, helping to minimize the inbreeding rate and also helping to expose deleterious variants in the genome. The frequency, size and distribution of ROH in the genome are influenced by factors such as natural and artificial selection, recombination, linkage disequilibrium, population structure, mutation rate and inbreeding level. Calculating the inbreeding coefficient from molecular information from ROH (FROH ) is more accurate for estimating autozygosity and for detecting both past and more recent inbreeding effects than are estimates from pedigree data (FPED ). The better results of FROH suggest that FROH can be used to infer information about the history and inbreeding levels of a population in the absence of genealogical information. The selection of superior animals has produced large phenotypic changes and has reshaped the ROH patterns in various regions of the genome. Additionally, selection increases homozygosity around the target locus, and deleterious variants are seen to occur more frequently in ROH regions. Studies involving ROH are increasingly common and provide valuable information about how the genome's architecture can disclose a population's genetic background. By revealing the molecular changes in populations over time, genome-wide information is crucial to understanding antecedent genome architecture and, therefore, to maintaining diversity and fitness in endangered livestock breeds.
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Affiliation(s)
- E Peripolli
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - D P Munari
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil.,Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil
| | - M V G B Silva
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil.,Embrapa Gado de Leite, Juiz de Fora, 36038-330, Brazil
| | - A L F Lima
- Departamento de Zootecnia e Desenvolvimento Rural, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Florianópolis, 88034-000, Brazil
| | - R Irgang
- Departamento de Zootecnia e Desenvolvimento Rural, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Florianópolis, 88034-000, Brazil
| | - F Baldi
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil.,Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil
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18
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Howard JT, Tiezzi F, Huang Y, Gray KA, Maltecca C. Characterization and management of long runs of homozygosity in parental nucleus lines and their associated crossbred progeny. Genet Sel Evol 2016; 48:91. [PMID: 27884108 PMCID: PMC5123398 DOI: 10.1186/s12711-016-0269-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 11/10/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND In nucleus populations, regions of the genome that have a high frequency of runs of homozygosity (ROH) occur and are associated with a reduction in genetic diversity, as well as adverse effects on fitness. It is currently unclear whether, and to what extent, ROH stretches persist in the crossbred genome and how genomic management in the nucleus population might impact low diversity regions and its implications on the crossbred genome. METHODS We calculated a ROH statistic based on lengths of 5 (ROH5) or 10 (ROH10) Mb across the genome for genotyped Landrace (LA), Large White (LW) and Duroc (DU) dams. We simulated crossbred dam (LA × LW) and market [DU × (LA × LW)] animal genotypes based on observed parental genotypes and the ROH frequency was tabulated. We conducted a simulation using observed genotypes to determine the impact of minimizing parental relationships on multiple diversity metrics within nucleus herds, i.e. pedigree-(A), SNP-by-SNP relationship matrix or ROH relationship matrix. Genome-wide metrics included, pedigree inbreeding, heterozygosity and proportion of the genome in ROH of at least 5 Mb. Lastly, the genome was split into bins of increasing ROH5 frequency and, within each bin, heterozygosity, ROH5 and length (Mb) of ROH were evaluated. RESULTS We detected regions showing high frequencies of either ROH5 and/or ROH10 across both LW and LA on SSC1, SSC4, and SSC14, and across all breeds on SSC9. Long haplotypes were shared across parental breeds and thus, regions of ROH persisted in crossbred animals. Averaged across replicates and breeds, progeny had higher levels of heterozygosity (0.0056 ± 0.002%) and lower proportion of the genome in a ROH of at least 5 Mb (-0.015 ± 0.003%) than their parental genomes when genomic relationships were constrained, while pedigree relationships resulted in negligible differences at the genomic level. Across all breeds, only genomic data was able to target low diversity regions. CONCLUSIONS We show that long stretches of ROH present in the parents persist in crossbred animals. Furthermore, compared to using pedigree relationships, using genomic information to constrain parental relationships resulted in maintaining more genetic diversity and more effectively targeted low diversity regions.
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Affiliation(s)
- Jeremy T Howard
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695-7627, USA.
| | - Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695-7627, USA
| | - Yijian Huang
- Smithfield Premium Genetics, Rose Hill, NC, 28458, USA
| | - Kent A Gray
- Smithfield Premium Genetics, Rose Hill, NC, 28458, USA
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695-7627, USA.,Genetics Program, North Carolina State University, Raleigh, NC, 27695-7627, USA
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