| 1. |
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| 2. |
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| 3. |
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| 4. |
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| 5. |
- Andersson, Lisa, et al.
(author)
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The same ELA class II risk factors confer equine insect bite hypersensitivity in two distinct populations
- 2012
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In: Immunogenetics. - : Springer Science and Business Media LLC. - 0093-7711 .- 1432-1211. ; 64:3, s. 201-208
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Journal article (peer-reviewed)abstract
- Insect bite hypersensitivity (IBH) is a chronic allergic dermatitis common in horses. Affected horses mainly react against antigens present in the saliva from the biting midges, Culicoides ssp, and occasionally black flies, Simulium ssp. Because of this insect dependency, the disease is clearly seasonal and prevalence varies between geographical locations. For two distinct horse breeds, we genotyped four microsatellite markers positioned within the MHC class II region and sequenced the highly polymorphic exons two from DRA and DRB3, respectively. Initially, 94 IBH-affected and 93 unaffected Swedish born Icelandic horses were tested for genetic association. These horses had previously been genotyped on the Illumina Equine SNP50 BeadChip, which made it possible to ensure that our study did not suffer from the effects of stratification. The second population consisted of 106 unaffected and 80 IBH-affected Exmoor ponies. We show that variants in the MHC class II region are associated with disease susceptibility (p(raw)=2.34x10(-5)), with the same allele (COR112:274) associated in two separate populations. In addition, we combined microsatellite and sequencing data in order to investigate the pattern of homozygosity and show that homozygosity across the entire MHC class II region is associated with a higher risk of developing IBH (p=0.0013). To our knowledge this is the first time in any atopic dermatitis suffering species, including man, where the same risk allele has been identified in two distinct populations.
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| 6. |
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| 7. |
- Arvelius, Per, et al.
(author)
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Does the Swedish Armed Forces’ temperament test give information on genetic differences between dogs?
- 2013
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Conference paper (other academic/artistic)abstract
- With the purpose to select breeders and dogs for training, all German Shepherd dogs in the Swedish Armed Forces (SAF) breeding program go through a temperament test. During the test, the dog's behavioural responses are rated with two different methods. In a previous study, using PCA on the test items, five and three underlying behavioural dimensions from each rating method were defined. Three of the dimensions correlated significantly to training success. Using test results from 873 dogs, we estimated heritabilities of, and genetic correlations between, the 38 test items plus the eight underlying behavioural dimensions. Parameters were estimated using a linear animal model including fixed effects of sex, educational level, test age and interaction between test year and test arena, and random effect of litter, genetic effect of the individual and residual. Heritabilities ranged from 0.00 to 0.28 (SE=0.05- 0.10), which is similar to what has been reported in previous studies on traits defined and measured in a comparable way. Genetic correlations were high (rg=0.92-0.98, SE=0.08-0.12) between dimensions derived from each registration method and defined as confidence, engagement and aggressiveness, but relatively weak between these dimensions within registration method (rg=0.00-0.45, SE=0.29-0.41). Our results imply that the test measures three separate behavioural dimensions and that the SAF temperament test as a whole is possible to utilize for selection of dogs for breeding, but also that some test items should be measured differently to be meaningful for selection purposes. Furthermore, aggregating variables based on a PCA performed on phenotypic data might be sub-optimal when defining dimensions for breeding purposes.
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| 8. |
- Arvelius, Per, et al.
(author)
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Genetic analysis of a temperament test as a tool to select against everyday life fearfulness in Rough Collie
- 2014
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In: Journal of Animal Science. - : Oxford University Press (OUP). - 0021-8812 .- 1525-3163. ; 92, s. 4843-4855
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Journal article (peer-reviewed)abstract
- Fear-related problems are common among Rough Collies in Sweden. Annually, on average, >200 Rough Collies are subjected to the dog mentality assessment (DMA), a temperament test during which 33 behavioral reactions are rated. Previous research has shown that a dog's DMA result can be condensed into 5 underlying personality traits. The aim of the study was to evaluate if it is possible to use the DMA for selection for temperament in Swedish Rough Collies, in particular to decrease everyday life fearfulness. We also wanted to compare 2 methods to compute the personality traits: summated scales (SS) and factor scores (FS). The DMA data for 2,953 Rough Collies were used to estimate genetic parameters for the 5 personality traits (both SS and FS), using a linear animal model including fixed effects of sex, year and month of test, and random effects of litter, judge, test occasion, genetic effect of the individual, and residual. Age at test was included as linear and quadratic regressions. The DMA personality trait heritability estimates ranged from 0.13 to 0.25. The SS showed greater or equal heritability estimates compared with the FS. To validate the DMA, data on everyday life behavior of 1,738 Rough Collies were collected using an extended version of the Canine Behavioral Assessment and Research Questionnaire. Each dog's questionnaire result was condensed into 18 underlying behavioral subscales. Genetic parameters for the subscales were estimated using a linear animal model, including a fixed effect of sex and random genetic effect of the individual and residual. Age when the questionnaire was completed was included as linear and quadratic regressions. Heritability estimates for the questionnaire subscales were 0.06 to 0.36. There were high and significant genetic correlations between DMA personality traits and questionnaire subscales. For instance, the DMA personality trait Curiosity/Fearlessness correlated strongly genetically to the questionnaire subscale Non-social fear (-0.70), DMA Sociability to Stranger-directed interest (0.87) and Stranger-directed fear (-0.80), DMA Playfulness to Human-directed play interest (0.63), and DMA Chase-proneness to Chasing (0.73). We could not detect any obvious difference in validity between DMA SS and FS. We conclude that the DMA is an effective tool for selection of breeding animals with the goal to decrease everyday life fearfulness among Swedish Rough Collies. The DMA can also be used for breeding for other traits. The SS method seems to perform at least as good the FS method.
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| 9. |
- Arvelius, Per, et al.
(author)
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Good Possibilities to Select Against Fearfulness in Rough Collie
- 2014
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Other publication (other academic/artistic)abstract
- Fear-related problems are common among Swedish Rough Collies. Genetic analyses were performed on 4 composite behavioral traits based on 2953 Rough Collie results from a temperament test. Heritabilities ranged from 0.13-0.25. Validation of the test was done using a dog owner questionnaire, which generated information about everyday life behavior for 1738 Rough Collies. There were high and significant genetic correlations between traits measured in the test, and the everyday life behavior of the dogs as described by the owners. For instance, Curiosity/fearlessness in the test was negatively genetically correlated with Nonsocial fear in the questionnaire (-0.70, SE 0.10). We conclude that data from the analyzed test is possible to use for selection to decrease everyday life fearfulness in the Swedish Rough Collie population.
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| 10. |
- Arvelius, Per, et al.
(author)
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The Swedish Armed Forces temperament test gives information on genetic differences among dogs
- 2014
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In: Journal of Veterinary Behavior: Clinical Applications and Research. - : Elsevier BV. - 1558-7878 .- 1878-7517. ; 9, s. 281-289
-
Journal article (peer-reviewed)abstract
- With the dual purpose of selecting both breeding animals and dogs for training, all German shepherd dogs in the Swedish Armed Forces (SAF) breeding program are subjected to a temperament test. During the test, the dog's behavioral responses are rated with 2 different methods. In a previous study, using Principal Components Analysis (PCA) on the test items, 5 and 3 underlying behavioral dimensions from each rating method were defined. Three of the dimensions were reported to correlate significantly to training success. Using the test results from 873 dogs, we estimated heritabilities of, and genetic correlations among, the 38 test items and the 8 underlying behavioral dimensions. Parameters were estimated using a mixed linear animal model including fixed effects of sex, training level, test age and test year-location combination, and random effects of litter, genetic effect of the individual, and residual. Heritabilities ranged from 0.00 to 0.28 (standard error [SE] = 0.05-0.10), which is similar to what has been reported in previous studies of traits defined and measured in a comparable way. Genetic correlations were high (r(g) = 0.92-0.98, SE = 0.08-0.12) between dimensions derived from each rating method and defined as either confidence, engagement, or aggressiveness, but relatively weak among these dimensions within rating method (r(g) = 0.00-0.45, SE = 0.29-0.41). Our results imply that the test measures 3 separate behavioral dimensions and that the SAF temperament test as a whole is possible to use for selection of dogs for breeding, but also that some test items should be measured differently to be meaningful for genetic selection purposes. Furthermore, aggregating variables based on a PCA performed on phenotypic data might be suboptimal when defining dimensions for breeding purposes; taking genetic parameters into consideration resulted in generally higher heritabilities for the dimensions. (C) 2014 Elsevier Inc. All rights reserved.
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| 11. |
- Bengtsson, Christian, et al.
(author)
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Mating allocations in Nordic Red Dairy Cattle using genomic information
- 2022
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In: Journal of Dairy Science. - : American Dairy Science Association. - 0022-0302 .- 1525-3198. ; 105, s. 1281-1297
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Journal article (peer-reviewed)abstract
- In this study, we compared mating allocations in Nordic Red Dairy Cattle using genomic information. We used linear programming to optimize different economic scores within each herd, considering genetic level, semen cost, the economic impact of recessive genetic defects, and genetic relationships. We selected 9,841 genotyped females born in Denmark, Finland, or Sweden in 2019 for mating allocations. We used 2 different pedigree relationship coefficients, the first tracing the pedigree 3 generations back from the parents of the potential mating and the second based on all available pedigree information. We used 3 different genomic relationship coefficients, 1 SNP-by-SNP genomic relationship and 2 based on shared genomic segments. We found high correlations (≥0.83) between the pedigree and genomic relationship measures. The mating results showed that it was possible to reduce the different genetic relationships between parents with minimal effect on genetic level. Including the cost of known recessive genetic defects eliminated expression of genetic defects. It was possible to reduce genomic relationships between parents with pedigree measures, but it was best done with genomic measures. Linear programming maximized the economic score for all herds studied within seconds, which means that it is suitable for implementation in mating software to be used by advisors and farmers.
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| 12. |
- Clasen, Julie, et al.
(author)
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Conservation of a native dairy cattle breed through terminal crossbreeding with commercial dairy breeds
- 2021
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In: Acta Agriculturae Scandinavica, Section A - Animal Science. - : Informa UK Limited. - 0906-4702 .- 1651-1972. ; 70, s. 1-12
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Journal article (peer-reviewed)abstract
- Farmers play a key role in conserving native livestock breeds, but without economic support, farms with native breeds may not be viable. We hypothesized that terminal crossbreeding can improve herd economy and decrease the economic support needed from society. Three scenarios were simulated using SimHerd Crossbred: a herd of purebred Swedish Polled Cattle, a herd of purebred Swedish Red, and a herd of 75% Swedish Polled Cattle and 25% F1 crossbreds. The results showed annual contribution margin per cow in the herd can be increased by euro181 by crossbreeding compared with pure-breeding with the native breed, giving a 13.6% growth in contribution margin. However, the needed cost in subsidies paid by the government will remain unchanged if the population size of the native breed is to be maintained. Combining a crossbreeding strategy with the marketing of niche products may facilitate the conservation of native cattle.
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| 13. |
- Clasen, Julie, et al.
(author)
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Dairy cattle farmers' preferences for different breeding tools
- 2021
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In: Animal. - : Elsevier BV. - 1751-7311 .- 1751-732X. ; 15
-
Journal article (peer-reviewed)abstract
- Breeding technologies play a significant role in improving dairy cattle production. Scientifically proven tools for improved management and genetic gain in dairy herds, such as sexed semen, beef semen, genomic testing, dairy crossbreeding, and multiple ovulation embryo transfer (MOET), are readily available to dairy farmers. However, despite good accessibility, decreasing costs, and continuous development of these tools, their use in Sweden is limited. This study investigated Swedish dairy farmers' preferences for breeding tools through a survey including a discrete choice experiment. The survey was distributed online to 1 521 Swedish farmers and by an open link published through a farming magazine. In total, the study included 204 completed responses. The discrete choice experiment consisted of 10 questions with two alternative combinations, which gave 48 combinations in total. Utility values and part-worth values were computed using a conditional logit model based on the responses in the discrete choice experiment for nine groups of respondents: one group with all respondents, two groups based on respondents using dairy crossbreeding or not within the past 12 months, two based on herd size, two based on respondent age, and two based on whether respondents had used breeding advisory services or not. The strongest preferences in all groups were for using sexed semen and beef semen. Genomic testing was also significantly preferred by all groups of respondents. Except in large herds, MOET on own animals was significantly and relatively strongly disfavoured by all groups. Buying embryos had no significant utility value to any group. Dairy crossbreeding had low and insignificant utility values in the group of all respondents, but it was strongly favoured by the group that had used dairy crossbreeding within the past 12 months, and it was disfavoured by the group that had not. Part-worth values of combined breeding tools showed that combinations of sexed and beef semen, alone or with genomic testing without dairy crossbreeding, were the most preferred tools. Compared with the most common combinations of breeding tools used in the past 12 months, the part-worth values indicated that Swedish dairy farmers may prefer to use breeding tools more than they do today. Statements on the different breeding tools indicated that the respondents agreed with the benefits attributed to the breeding tools, but these benefits may not be worth the cost of genomic testing and the time consumption of MOET. These valuable insights can be used for further development of breeding tools.
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| 14. |
- Clasen, Julie, et al.
(author)
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Genetic consequences of terminal crossbreeding, genomic test, sexed semen, and beef semen in dairy herds
- 2021
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In: Journal of Dairy Science. - : American Dairy Science Association. - 0022-0302 .- 1525-3198. ; 104, s. 8062-8075
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Journal article (peer-reviewed)abstract
- The development of breeding tools, such as genomic selection and sexed semen, has progressed rapidly in dairy cattle breeding during the past decades. In combination with beef semen, these tools are adopted increasingly at herd level. Dairy crossbreeding is emerging, but the economic and genetic consequences of combining it with the other breeding tools are relatively unknown. We investigated 5 different sexed semen schemes where 0, 50, and 90% of the heifers; 50% of the heifers + 25% of the first-parity cows; and 90% of the heifers + 45% of the first-parity cows were bred to sexed semen. The 5 schemes were combined in scenarios managing pure-breeding or terminal crossbreeding, including genomic testing of all newborn heifers or no testing, and keeping Swedish Red or Swedish Holstein as an initial breed. Thus, 40 scenarios were simulated, combining 2 stochastic simulation models: SimHerd Crossbred (operational returns) and ADAM (genetic returns). The sum of operational and genetic returns equaled the total economic return. Beef semen was used in all scenarios to limit the surplus of replacement heifers. Terminal crossbreeding implied having a nucleus of purebred females, where some were inseminated with semen of the opposite breed. The F-1 crossbred females were inseminated with beef semen. The reproductive performance played a role in improving the benefit of any of the tools. The most considerable total economic returns were achieved when all 4 breeding tools were combined. For Swedish Holstein, the highest total economic return compared with a pure-breeding scenario, without sexed semen and genomic test, was achieved when 90% sexed semen was used in heifers and 45% sexed semen was used for first-parity cows combined with genomic test and crossbreeding (+(sic)58, 33% crossbreds in the herd). The highest total economic return for Swedish Red compared with a pure-breeding scenario, without sexed semen and genomic test, was achieved when 90% sexed semen was used in heifers combined with genomic test and crossbreeding (+(sic)94, 46% crossbreds in the herd). Terminal crossbreeding resulted in lower genetic returns across the herd compared with the corresponding pure-breeding scenarios but was compensated by a higher operational return.
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| 15. |
- Clasen, Julie, et al.
(author)
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Korsning med mjölkkor – effekter på besättningsdynamik och ekonomiskt resultat
- 2020
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Reports (pop. science, debate, etc.)abstract
- I denna simuleringsstudie jämförs besättningsstruktur samt produktionsresultat och ekonomiskt resultat för besättningar med renrasiga kor och besättningar med korsningskor. Vi har använt medeltal från Kokontrollen som ingångsvärden till simuleringsprogrammet SimHerd Crossbred. Holsteinkor (SH), röda kor (SRB) och korsningskor från systematisk slutkorsning (enkelkorsning, terminal cross) ingick i studien. Fyra olika typer av besättningar studerades: bara renrasiga SRBkor, en kärna av renrasiga SRB-kor och SHxSRB-korsningskor, bara renrasiga SH-kor, samt en kärna av renrasiga SH-kor och SRBxSH-korsningskor. Resultaten presenteras både för konventionell och ekologisk produktion, eftersom medeltal för kornas resultat och kostnader och intäkter skiljer sig mellan dessa produktionssystem. Simuleringen visar att det ekonomiska resultatet för mjölkproducenter förbättras när man går från en renrasig besättning till en besättning med korsning och det gäller för såväl konventionell som ekologisk produktion. För besättningar med SRB-kärna blev förbättringen av det ekonomiska resultatet vid övergång till korsning större för ekologisk produktion än för konventionell produktion. Det är kopplat till ett högre avräkningspris för mjölk i ekologisk produktion. Besättningsstrukturen i en besättning med korsning påverkas av djurens reproduktion och funktionella egenskaper. Det medför att utrymmet för korsningskor är större i besättningar med SRB-kärna än i besättningar med SHkärna.
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| 16. |
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| 17. |
- Duchemin, Sandrine, et al.
(author)
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Identification of QTL on chromosome 18 associated with non-coagulating milk in Swedish Red cows
- 2016
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In: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 7
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Journal article (peer-reviewed)abstract
- Non-coagulating (NC) milk, defined as milk not coagulating within 40 min after rennet-addition, can have a negative influence on cheese production. Its prevalence is estimated at 18% in the Swedish Red (SR) cow population. Our study aimed at identifying genomic regions and causal variants associated with NC milk in SR cows, by doing a GWAS using 777k SNP genotypes and using imputed sequences to fine map the most promising genomic region. Phenotypes were available from 382 SR cows belonging to 21 herds in the south of Sweden, from which individual morning milk was sampled. NC milk was treated as a binary trait, receiving a score of one in case of non-coagulation within 40 min. For all 382 SR cows, 777k SNP genotypes were available as well as the combined genotypes of the genetic variants of as1-β-κ-caseins. In addition, whole-genome sequences from the 1000 Bull Genome Consortium (Run 3) were available for 429 animals of 15 different breeds. From these sequences, 33 sequences belonged to SR and Finish Ayrshire bulls with a large impact in the SR cow population. Single-marker analyses were run in ASReml using an animal model. After fitting the casein loci, 14 associations at -Log10(P-value) > 6 identified a promising region located on BTA18. We imputed sequences to the 382 genotyped SR cows using Beagle 4 for half of BTA18, and ran a region-wide association study with imputed sequences. In a seven mega base-pairs region on BTA18, our strongest association with NC milk explained almost 34% of the genetic variation in NC milk. Since it is possible that multiple QTL are in strong LD in this region, 59 haplotypes were built, genetically differentiated by means of a phylogenetic tree, and tested in phenotype-genotype association studies. Haplotype analyses support the existence of one QTL underlying NC milk in SR cows. A candidate gene of interest is the VPS35 gene, for which one of our strongest association is an intron SNP in this gene. The VPS35 gene belongs to the mammary gene sets of pre-parturient and of lactating cows.
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| 18. |
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| 19. |
- Eken Asp, Helena, et al.
(author)
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Breed differences in everyday behaviour of dogs
- 2015
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In: Applied Animal Behaviour Science. - : Elsevier BV. - 0168-1591 .- 1872-9045. ; 169, s. 69-77
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Journal article (peer-reviewed)abstract
- The domestication of the dog and the ensuing breed creation has resulted in a plethora of dog breeds that differ not only in morphology but also in terms of behaviour. In addition, a majority of the dogs today are no longer utilized for their working ability, but are mainly kept as companion animals. The main aim of this study was to estimate breed differences in everyday behaviour traits, as well as to study the phenotypic correlations between these traits. Dog owners described their dogs' everyday behaviour in a questionnaire. The responses to the questions were combined into 18 behavioural subscale scores (BSS). After editing, the material included dog owner responses for 3591 dogs from 20 different breeds. The breeds represent both working and non-working breeds.We can conclude that breed (and grouping into working vs non-working breeds), age and sex had significant effects on many everyday behaviour traits. The working breeds were about 10% more trainable, showed 30% more interest in playing with humans and were 10-60% less fearful. Furthermore, our results showed that fearful dogs were more aggressive, whereas more social dogs were less fearful and less aggressive. We also found that dogs that were more eager to play with humans were also easier to train. (C) 2015 Elsevier B.V. All rights reserved.
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| 20. |
- Eken Asp, Helena, et al.
(author)
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Genetics of Aggression, Fear and Sociability in Everyday Life of Swedish Dogs
- 2014
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Conference paper (other academic/artistic)abstract
- Most potential dog owners are looking for a non-aggressive, non-fearful, social and easily trained dog that functions well in everyday life. Despite this, most studies of genetic components for behavior traits have mainly focused on analyzing results from behavior tests and not everyday behavior data. The aim of this study was to estimate genetic parameters for aggression, fear, sociability and trainability in everyday life by using a questionnaire to assess information of the dog's everyday behavior. The genetic analysis included 3128 records distributed over 14 breeds. The effect of breed, sex and age were adjusted for in the estimations of genetic parameters. The estimated heritabilities ranged between 0.08 and 0.38, with the highest heritability found for human-directed play interest. Positive genetic correlations were found between aggression and fear traits. Sociability traits showed a negative genetic correlation with both aggression and fear traits.
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| 21. |
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| 22. |
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| 23. |
- Eriksson, Susanne, et al.
(author)
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Genetic trends for fertility, udder health and protein yield in Swedish red cattle estimated with different models
- 2017
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In: Journal of Animal Breeding and Genetics. - : Wiley. - 0931-2668 .- 1439-0388. ; 134, s. 308-321
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Journal article (peer-reviewed)abstract
- The aim of this study was to estimate and compare genetic trends in Swedish Red cattle using a full multiple-trait (MT) model and trait-group-wise models for female fertility, udder health and protein yield. Field data for maiden heifers from 1989 and cows with a first and second lactation between 1990 and 2007 were included. (Co)variance components were estimated prior to prediction of breeding values. The estimated genetic trends were clearly favourable for protein yield and udder conformation, and in most cases neutral to favourable for clinical mastitis and calving to first insemination. In maiden heifers, the trends were neutral for number of inseminations per service period. Unfavourable genetic trends were estimated for number of inseminations in the first two lactations, but the trends seemed less unfavourable from evaluations within trait groups compared with when using the full MT model. Excluding maiden heifer data affected genetic trends less than using trait-group-wise analyses instead of a full MT model. Unfavourable genetic trends in functional traits may be missed unless the traits are evaluated in a MT model including traits under strong selection.
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| 24. |
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| 25. |
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| 26. |
- Fikse, Freddy
(author)
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Bayesian Analysis of Heterogeneous Residual Variance in Canine Behaviour
- 2014
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Conference paper (other academic/artistic)abstract
- Non-additive effects like for instance genotype-environment interactions and genetically structured heterogeneity of residual variance are notoriously dependent on scale: many statistical non-additive phenomena disappear after a careful choice of transformation of the phenotypic values. Particularly for behavioural measures, scale is a delicate matter. We present a novel Bayesian approach that assesses heterogeneity in environmental variance as a function of genetic effects, where the scale is defined by a psychometric model based on item-response theory. This makes analysis results independent of what items are in a particular test version. We apply the method to fearful behaviour in dogs and compare results with the more usual sum score approach.
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| 27. |
- Fikse, Freddy
(author)
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Can a model with Genetic Groups for Mendelian Sampling Deviations Correct for pre-selection bias?
- 2014
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Conference paper (peer-reviewed)abstract
- Pre-selection of animals in breeding schemes invalidates some of the assumptions necessary to maintain the unbiasedness property in genetic evaluations. In particular, the expected value of Mendelian sampling deviations is no longer zero, and the Mendelian sampling variance is reduced. This study investigated, using simulation, the possibility to attenuate bias due to preselection using a genetic evaluation model with genetic groups for Mendelian sampling deviations proposed some years ago. Two generations of data were simulated. Daughter yield deviations and yield deviations were simulated for males and females, resp., in generations 1 and 2. Males in generation 1 were pre-selected on estimated Mendelian sampling deviations. Accounting for preselection by including genetic groups for Mendelian sampling deviations did not remove bias in estimated breeding values. The reason was that pre-selection not only led to selection differential for Mendelian sampling deviations but also for parent averages, which the model failed to account for.
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| 28. |
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| 29. |
- Fikse, Freddy
(author)
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Detection of evaluation bias caused by genomic preselection
- 2018
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In: Journal of Dairy Science. - : American Dairy Science Association. - 0022-0302 .- 1525-3198. ; 101, s. 3155-3163
-
Journal article (peer-reviewed)abstract
- The aim of this simulation study was to investigate whether it is possible to detect the effect of genomic preselection on Mendelian sampling (MS) means or variances obtained by the MS validation test. Genomic preselection of bull calves is 1 additional potential source of bias in international evaluations unless adequately accounted for in national evaluations. Selection creates no bias in traditional breeding value evaluation if the data of all animals are included. However, this is not the case with genomic preselection, as it excludes culled bulls. Genomic breeding values become biased if calculated using a multistep procedure instead of, for example, a single-step method. Currently, about 60% of the countries participating in international bull evaluations have already adopted genomic selection in their breeding schemes. The data sent for multiple across-country evaluation can, therefore, be very heterogeneous, and a proper validation method is needed to ensure a fair comparison of the bulls included in international genetic evaluations. To study the effect of genomic preselection, we generated a total of 50 replicates under control and genomic preselection schemes using the structures of the real data and pedigree from a medium-size cow population. A genetic trend of 15% of the genetic standard deviation was created for both schemes. In carrying out the analyses, we used 2 different heritabilities: 0.25 and 0.10. From the start of genomic preselection, all bulls were genomically preselected. Their MS deviations were inflated with a value corresponding to selection of the best 10% of genomically tested bull calves. For cows, the MS deviations were unaltered. The results revealed a clear underestimation of bulls' breeding values (BV) after genomic preselection started, as well as a notable deviation from zero both in true and estimated MS means. The software developed recently for the MS validation test already produces yearly MS means, and they can be used to devise an appropriate test. Mean squared true MS of genomically preselected bulls was clearly inflated. After correcting for the simulated preselection bias, the true genetic variance was smaller than the parametric value used to simulate BV, and also below the variance based on the estimated BV. Based on this study, the lower the trait's heritability, the stronger the bias in estimated BV and MS means and variances. Daughters of genomically preselected bulls had higher true and estimated BV compared with the control scheme and only slightly elevated MS means, but no effect on genetic variances was observed.
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| 30. |
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| 31. |
- Fikse, Freddy
(author)
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Fuzzy classification of phantom parent groups in an animal model
- 2009
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In: Genetics Selection Evolution. - : Springer Science and Business Media LLC. - 0999-193X .- 1297-9686. ; 41
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Journal article (peer-reviewed)abstract
- Conclusion: Fuzzy-classification provides the potential to describe the genetic level of unknown parents in a more parsimonious and structured manner, and thereby increases the precision of predicted breeding values.
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| 32. |
- Fikse, Freddy, et al.
(author)
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Genetic evaluation of claw health traits accounting for potential preselection of cows to be trimmed
- 2017
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In: Journal of Dairy Science. - : American Dairy Science Association. - 0022-0302 .- 1525-3198. ; 100, s. 8197-8204
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Journal article (peer-reviewed)abstract
- Claw lesions are one of the most important health issues in dairy cattle. Although the frequency of claw lesions depends greatly on herd management, the frequency can be lowered through genetic selection. A genetic evaluation could be developed based on trimming records collected by claw trimmers; however, not all cows present in a herd are usually selected by the breeder to be trimmed. The objectives of this study were to investigate the importance of the preselection of cows for trimming, to account for this preselection, and to estimate genetic parameters of claw health traits. The final data set contained 25,511 trimming records of French Holstein cows. Analyzed claw lesion traits were digital dermatitis, heel horn erosion, inter digital hyperplasia, sole hemorrhage circumscribed, sole hemorrhage diffused, sole ulcer, and white line fissure. All traits were analyzed as binary traits in a multitrait linear animal model. Three scenarios were considered: including only trimmed cows in a 7-trait model (scenario 1); or trimmed cows and contemporary cows not trimmed but present at the time of a visit (considering that nontrimmed cows were healthy) in a 7-trait model (scenario 2); or trimmed cows and contemporary cows not trimmed but present at the time of a visit (considering lesion records for trimmed cows only), in an 8-trait model, including a 0/1 trimming status trait (scenario 3). For scenario 3, heritability estimates ranged from 0.02 to 0.09 on the observed scale. Genetic correlations clearly revealed 2 groups of traits (digital dermatitis, heel horn erosion, and interdigital hyperplasia on the one hand, and sole hemorrhage circumscribed, sole hemorrhage diffused, sole ulcer, and white line fissure on the other hand). Heritabilities on the underlying scale did not vary much depending on the scenario: the effect of the preselection of cows for trimming on the estimation of heritabilities appeared to be negligible. However, including untrimmed cows as healthy caused bias in the estimation of genetic correlations. The use of a trimming status trait to account for preselection appears promising, as it allows consideration of the exhaustive population of cows present at the time a trimmer visited a farm without causing bias in genetic parameters.
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| 33. |
- Fikse, Freddy, et al.
(author)
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Genetic parameters for carcass cuts in Irish cattle
- 2009
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In: Book of abstracts of the ... Annual meeting of the European Association for Animal Production. - 1382-6077. ; 15, s. 141-
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Conference paper (other academic/artistic)
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| 34. |
- Fikse, Freddy, et al.
(author)
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Genetic variation in wholesale carcass cuts predicted from digital images in cattle
- 2011
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In: Animal. - 1751-7311 .- 1751-732X. ; 5, s. 1720-1727
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Journal article (peer-reviewed)abstract
- The objective of this study was to quantify the genetic variation in carcass cuts predicted using digital image analysis in commercial cross-bred cattle. The data set comprised 38 404 steers and 14 318 heifers from commercial Irish herds. The traits investigated included the weights of lower value cuts (LVC), medium value cuts (MVC), high value cuts (HVC), very high value cuts (VHVC) and total meat weight. In addition, the weights of total fat and total bones were available on the steers. Heritability of carcass cut weights, within gender, was estimated using an animal linear model, whereas genetic and phenotypic correlations among cuts were estimated using a sire linear model. Carcass weight was included as a covariate in all models. In the steers, heritability ranged from 0.13 (s.e. = 50.02) for VHVC to 0.49 (s.e. = 50.03) for total bone weight, and in the heifers heritability ranged from 0.15 (s.e. = 50.04) for MVC to 0.72 (s.e. = 50.06) for total meat weight. The coefficient of genetic variation for the different cuts varied from 1.4% to 3.6%. Genetic correlations between the different cut weights were all positive and ranged from 0.45 (s.e. = 50.08) to 0.89 (s.e. = 50.03) in the steers, and from 0.47 (s.e. = 50.14) to 0.82 (s.e. = 50.06) in the heifers. Genetic correlations between the wholesale cut weights and carcass conformation ranged from 0.32 (s.e. = 50.06) to 0.45 (s.e. = 50.07) in the steers, and from 0.10 (s.e. = 50.12) to 0.38 (s.e. = 50.09) in the heifers. Genetic correlations between the same wholesale cut traits in steers and heifers ranged from 0.54 (s.e. = 50.14) for MVC to 0.79 (s.e. = 50.06) for total meat weight; genetic correlations between carcass weight and carcass classification for conformation and fat score in both genders varied from 0.80 to 0.87. The existence of genetic variation in carcass cut traits, coupled with the routine availability of predicted cut weights from digital image analysis, clearly shows the potential to genetically improve carcass value.
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| 35. |
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| 36. |
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| 37. |
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| 38. |
- Fikse, Freddy
(author)
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Opportunities for international collaboration in dog breeding from the sharing of pedigree and health data
- 2013
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In: Veterinary Journal. - : Elsevier BV. - 1090-0233 .- 1532-2971. ; 197, s. 873-875
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Journal article (peer-reviewed)abstract
- Pooling of pedigree and phenotype data from different countries may improve the accuracy of derived indicators of both genetic diversity and genetic merit of traits of interest. This study demonstrates significant migration of individuals of four pedigree dog breeds between Sweden and the United Kingdom. Correlations of estimates of genetic merit (estimated breeding values, EBVs) for the Federation Cynologique Internationale and the British Veterinary Association and Kennel Club evaluations of hip dysplasia (HD) were strong and favourable, indicating that both scoring schemes capture substantially the same genetic trait. Therefore pooled use of phenotypic data on hip dysplasia would be expected to improve the accuracy of EBV for HD in both countries due to increased sample data. (C) 2013 Published by Elsevier Ltd.
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| 39. |
- Fikse, Freddy, et al.
(author)
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Principal component and factor analytic models in international sire evaluation
- 2011
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In: Genetics Selection Evolution. - : Springer Science and Business Media LLC. - 0999-193X .- 1297-9686. ; 43
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Journal article (peer-reviewed)abstract
- Background: Interbull is a non-profit organization that provides internationally comparable breeding values for globalized dairy cattle breeding programmes. Due to different trait definitions and models for genetic evaluation between countries, each biological trait is treated as a different trait in each of the participating countries. This yields a genetic covariance matrix of dimension equal to the number of countries which typically involves high genetic correlations between countries. This gives rise to several problems such as over-parameterized models and increased sampling variances, if genetic (co) variance matrices are considered to be unstructured.Methods: Principal component (PC) and factor analytic (FA) models allow highly parsimonious representations of the (co) variance matrix compared to the standard multi-trait model and have, therefore, attracted considerable interest for their potential to ease the burden of the estimation process for multiple-trait across country evaluation (MACE). This study evaluated the utility of PC and FA models to estimate variance components and to predict breeding values for MACE for protein yield. This was tested using a dataset comprising Holstein bull evaluations obtained in 2007 from 25 countries.Results: In total, 19 principal components or nine factors were needed to explain the genetic variation in the test dataset. Estimates of the genetic parameters under the optimal fit were almost identical for the two approaches. Furthermore, the results were in a good agreement with those obtained from the full rank model and with those provided by Interbull. The estimation time was shortest for models fitting the optimal number of parameters and prolonged when under-or over-parameterized models were applied. Correlations between estimated breeding values (EBV) from the PC19 and PC25 were unity. With few exceptions, correlations between EBV obtained using FA and PC approaches under the optimal fit were >= 0.99. For both approaches, EBV correlations decreased when the optimal model and models fitting too few parameters were compared.Conclusions: Genetic parameters from the PC and FA approaches were very similar when the optimal number of principal components or factors was fitted. Over-fitting increased estimation time and standard errors of the estimates but did not affect the estimates of genetic correlations or the predictions of breeding values, whereas fitting too few parameters affected bull rankings in different countries.
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| 40. |
- Fikse, Freddy, et al.
(author)
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Principal component approach in variance component estimation for international sire evaluation
- 2011
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In: Genetics Selection Evolution. - : Springer Science and Business Media LLC. - 0999-193X .- 1297-9686. ; 43
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Journal article (peer-reviewed)abstract
- Background: The dairy cattle breeding industry is a highly globalized business, which needs internationally comparable and reliable breeding values of sires. The international Bull Evaluation Service, Interbull, was established in 1983 to respond to this need. Currently, Interbull performs multiple-trait across country evaluations (MACE) for several traits and breeds in dairy cattle and provides international breeding values to its member countries. Estimating parameters for MACE is challenging since the structure of datasets and conventional use of multiple-trait models easily result in over-parameterized genetic covariance matrices. The number of parameters to be estimated can be reduced by taking into account only the leading principal components of the traits considered. For MACE, this is readily implemented in a random regression model.Methods: This article compares two principal component approaches to estimate variance components for MACE using real datasets. The methods tested were a REML approach that directly estimates the genetic principal components (direct PC) and the so-called bottom-up REML approach (bottom-up PC), in which traits are sequentially added to the analysis and the statistically significant genetic principal components are retained. Furthermore, this article evaluates the utility of the bottom-up PC approach to determine the appropriate rank of the (co)variance matrix.Results: Our study demonstrates the usefulness of both approaches and shows that they can be applied to large multi-country models considering all concerned countries simultaneously. These strategies can thus replace the current practice of estimating the covariance components required through a series of analyses involving selected subsets of traits. Our results support the importance of using the appropriate rank in the genetic (co) variance matrix. Using too low a rank resulted in biased parameter estimates, whereas too high a rank did not result in bias, but increased standard errors of the estimates and notably the computing time.Conclusions: In terms of estimation's accuracy, both principal component approaches performed equally well and permitted the use of more parsimonious models through random regression MACE. The advantage of the bottom-up PC approach is that it does not need any previous knowledge on the rank. However, with a predetermined rank, the direct PC approach needs less computing time than the bottom-up PC.
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| 41. |
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| 42. |
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| 43. |
- Fikse, Freddy
(author)
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Validation of consistency of Mendelian sampling variance
- 2018
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In: Journal of Dairy Science. - : American Dairy Science Association. - 0022-0302 .- 1525-3198. ; 101, s. 2187-2198
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Journal article (peer-reviewed)abstract
- Experiences from international sire evaluation indicate that the multiple-trait across-country evaluation method is sensitive to changes in genetic variance over time. Top bulls from birth year classes with inflated genetic variance will benefit, hampering reliable ranking of bulls. However, none of the methods available today enable countries to validate their national evaluation models for heterogeneity of genetic variance. We describe a new validation method to fill this gap comprising the following steps: estimating within-year genetic variances using Mendelian sampling and its prediction error variance, fitting a weighted linear regression between the estimates and the years under study, identifying possible outliers, and defining a 95% empirical confidence interval for a possible trend in the estimates. We tested the specificity and sensitivity of the proposed validation method with simulated data using a real data structure. Moderate (M) and small (S) size populations were simulated under 3 scenarios: a control with homogeneous variance and 2 scenarios with yearly increases in phenotypic variance of 2 and 10%, respectively. Results showed that the new method was able to estimate genetic variance accurately enough to detect bias in genetic variance. Under the control scenario, the trend in genetic variance was practically zero in setting M. Testing cows with an average birth year class size of more than 43,000 in setting M showed that tolerance values are needed for both the trend and the outlier tests to detect only cases with a practical effect in larger data sets. Regardless of the magnitude (yearly increases in phenotypic variance of 2 or 10%) of the generated trend, it deviated statistically significantly from zero in all data replicates for both cows and bulls in setting M. In setting S with a mean of 27 bulls in a year class, the sampling error and thus the probability of a false-positive result clearly increased. Still, overall estimated genetic variance was close to the parametric value. Only rather strong trends in genetic variance deviated statistically significantly from zero in setting S. Results also showed that the new method was sensitive to the quality of the approximated reliabilities of breeding values used in calculating the prediction error variance. Thus, we recommend that only animals with a reliability of Mendelian sampling higher than 0.1 be included in the test and that low heritability traits be analyzed using bull data sets only.
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| 44. |
- Forabosco, Flavio, et al.
(author)
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Assessment of the value of international genetic evaluations for yield in predicting domestic breeding values for foreign Holstein bulls
- 2011
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In: Journal of Dairy Science. - : American Dairy Science Association. - 0022-0302 .- 1525-3198. ; 94, s. 2601-2612
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Journal article (peer-reviewed)abstract
- International genetic evaluations are a valuable source of information for decisions about the importation of (the semen of) foreign bulls. This study analyzed data from 6 countries (Australia, Canada, Italy, France, the Netherlands, and the United States) and compared international evaluations for production traits of foreign bulls (i.e., when no national daughter information was available) to their national breeding values in August 2009, which were based only on domestic daughters' data. A total of 821 bulls with highly reliable estimated breeding values (EBV) for milk, fat, and protein yield were analyzed. No evidence of systematic over- or underestimation was found in most of the countries analyzed. Observed correlations between national and international evaluations were close to 0.9 and, for most countries, generally close to their expected values (calculated from national and international EBV reliabilities). In Italy, however, higher differences between observed and expected correlations and significant mean differences between EBV for more than one trait were observed in bulls progeny-tested in the United States and in other European countries (with differences up to 33.1% of the genetic standard deviation). These results were probably induced by a relatively recent change in the model for national evaluation. The findings in this study reflect a conservative estimate of the real value of international evaluations, as changes in methodologies in either the national or the international evaluations decreased the ability of past international evaluations to predict current national evaluations. Nevertheless, our results indicate that international evaluations based on foreign information for Holstein bulls were reasonably accurate predictors of the future national breeding values based only upon domestic daughters.
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| 45. |
- Forabosco, Flavio, et al.
(author)
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International genetic evaluation for direct longevity in dairy bulls
- 2009
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In: Journal of Dairy Science. - : American Dairy Science Association. - 0022-0302 .- 1525-3198. ; 92, s. 2338-2347
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Journal article (peer-reviewed)abstract
- The aims of this study were to document, present, and discuss the procedure used to calculate the international estimated breeding value (EBV) for longevity for Brown Swiss, Guernsey, Holstein, Jersey, Red Dairy Cattle, and Simmental breeds. Data from 19 countries and 123,833 national sires' breeding value were used for this purpose. Trait definitions and national genetic evaluation procedures were first summarized; and this showed that differences among countries existed. International breeding values for direct longevity were calculated using a multi-trait across-country evaluation model. The data editing method was identical to the one used for the February 2007 routine international genetic evaluation. Estimated genetic correlations presented in this study were similar to those presented in the literature and, in general, differed from unity because of differences in trait definitions, culling reasons, data included, evaluation procedures, genotype-environment interactions, and weak genetic ties among countries. The average genetic correlations for Holstein ranged from 0.49 to 0.76. The genetic correlations for Brown Swiss and Guernsey ranged from 0.29 to 0.95 and from 0.30 to 0.89, respectively. For Jersey and Red Dairy Cattle the genetic correlations ranged from 0.39 to 0.61 and from 0.30 to 0.96, respectively. For Simmental the genetic correlation was 0.59. Different predictors were used at national levels to define combined longevity. These predictors were combined using economic and empirical weights. Three out of 15 countries published international EBV of direct longevity only and 12 out of 15 countries combined direct longevity with predictors (combined longevity). International breeding values for longevity were combined into the total merit index by most of the member organizations and made available to breeders across the world through magazines and Web sites. Even if some breeders are not familiar with longevity EBV, they will select for this trait automatically if they use the published total merit indexes.
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| 46. |
- Gustavsson, Frida, et al.
(author)
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Genetic parameters for rennet- and acid-induced coagulation properties in milk from Swedish Red dairy cows.
- 2014
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In: Journal of Dairy Science. - : American Dairy Science Association. - 1525-3198 .- 0022-0302. ; 97:8, s. 5219-5229
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Journal article (peer-reviewed)abstract
- Milk coagulation is an important processing trait, being the basis for production of both cheese and fermented products. There is interest in including technological properties of these products in the breeding goal for dairy cattle. The aim of the present study was therefore to estimate genetic parameters for milk coagulation properties, including both rennet- and acid-induced coagulation, in Swedish Red dairy cattle using genomic relationships. Morning milk samples and blood samples were collected from 395 Swedish Red cows that were selected to be as genetically unrelated as possible. Using a rheometer, milk samples were analyzed for rennet- and acid-induced coagulation properties, including gel strength (G'), coagulation time, and yield stress (YS). In addition to the technological traits, milk composition was analyzed. A binary trait was created to reflect that milk samples that had not coagulated 40 min after rennet addition were considered noncoagulating milk. The cows were genotyped by using the Illumina BovineHD BeadChip (Illumina Inc., San Diego, CA). Almost 600,000 markers remained after quality control and were used to construct a matrix of genomic relationships among the cows. Multivariate models including fixed effects of herd, lactation stage, and parity were fitted using the ASReml software to obtain estimates of heritabilities and genetic and phenotypic correlations. Heritability estimates (h(2)) for G' and YS in rennet and acid gels were found to be high (h(2) = 0.38-0.62) and the genetic correlations between rennet-induced and acid-induced coagulation properties were weak but favorable, with the exception of YSrennet with G'acid and YSacid, both of which were strong. The high heritability (h(2) = 0.45) for milk coagulating ability expressed as a binary trait suggests that noncoagulation could be eliminated through breeding. Additionally, the results indicated that the current breeding objective could increase the frequency of noncoagulating milk and lead to deterioration of acid-induced coagulation through unfavorable genetic associations with protein content (0.38) and milk yield (-0.61 to -0.71), respectively. The outcome of this study suggests that by including more detailed compositional traits genetically associated with milk coagulation or by including milk coagulation properties directly within the breeding goal, it appears possible to breed cows that produce milk better suited for production of cheese and fermented products.
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| 47. |
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| 48. |
- Halkjer Jakobsen, Jette, et al.
(author)
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Detection of Genomic Pre-Selection with Mendelian Sampling Variance Test
- 2013
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In: Interbull bulletin. - 2001-340X. ; 47, s. 197-202
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Conference paper (other academic/artistic)abstract
- Genomic pre-selection of bull calves is potentially one additional source of bias in the international evaluations, given it has not been adequately accounted for in the national evaluations. The aim of this simulation study was to investigate whether it is possible to detect the effect of genomic pre-selection in the MS means or variances obtained by the MS-trend validation test. In total, 50 replicates were generated under control and genomic pre-selection schemes utilizing structures of the real data and pedigree from a medium size cow population during a 20-year time interval. All bulls in the last 10 birth year classes were assumed to be genomically pre-selected. Therefore, their Mendelian sampling terms were inflated with a value corresponding to the selection of best 10% of the genomically tested bull calves. After start of genomic pre-selection, both the true and estimated means of Mendelian sampling terms and breeding values rose sharply in bulls, although the effects of estimated means were more moderate. A clear decrease was found in true and estimated genetic variances of bulls, but the effect was temporary and thus hard to exploit. Daughters of genomically pre-selected bulls had higher true and estimated breeding values compared to the control scheme, only slightly elevated MS means and no effect in the genetic variances.
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| 49. |
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| 50. |
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