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- Da Silva, Vinicius, et al.
(författare)
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Copy number variations associated with insect bite hypersensitivity in Friesian horses
- 2016
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Ingår i: Annual meeting of the European Association for Animal Production. - 1382-6077. ; , s. 286-286
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Copy number variations (CNVs) are the largest source of genetic variation that has been identified in the equine genome so far. CNV-based GWAS could therefore facilitate detection of genetic variation for traits of interest. The aim of our study was to identify, characterize and associate CNVs in Friesian horses with insect bite hypersensitivity (IBH), a common equine allergy to insects that causes intense itch and seriously reduces welfare. After pre-processing of raw intensity signals from 670,796 SNPs for 138 cases and 131 controls, CNVs were identified using PennCNV and merged into CNV regions (CNVRs) using CNVRuler. A SNP-based GWAS performed beforehand (chi squared test with 1df) showed a clear association between the ELA region on ECA20 and IBH in Friesian horses. Regions identified on ECA9, 11 and 20 have rather consistently been associated with IBH across equine breeds investigated so far. Currently, the CNV analysis is at an early stage and different strategies to improve the SNP array overall signal quality are being tested. The preliminary CNV-based GWAS, which analysed gains and losses separately by logistic regression, indicated a loss in the ELA region significantly more frequent in affected horses. CNVRs significantly associated with IBH could point to genes involved in this complex polygenic disease. Our study will increase the knowledge on CNVs in horses and will highlight which genes and pathways are affected by CNVs. Moreover, it will facilitate in our attempt to improve selection against IBH.
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- Eriksson, Susanne, et al.
(författare)
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A genome-wide association study of young horse test traits in Swedish Warmblood
- 2016
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Ingår i: Book of Abstracts, EAAP. - 1382-6077. ; 22, s. 576-576
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Tests of three-year-old Swedish Warmblood (SWB) horses include traditional subjective assessments on a ten point scale of the quality of the horses in relation to the breeding goal. In 2013 a complementary linear scoring of the horses on a nine point scale from one extreme to the other was introduced. The horses are assessed for traits related to conformation, gaits and jumping ability. Also, deviations from normality are indicated for some traits (0/1). In this study we aimed to find genomic regions associated with these test traits. In total 380 SWB horses tested as three-year-olds in 2013 or 2014 were genotyped using the Affymetrix 670k SNP bead chip. After quality control the data set included 379 horses and 467,606 SNPs. Counting also traits recorded in only one of the years, the data included 97 traits. A fast score test for association in the R software GenAbel was used for a first set of analyses. The uncorrected lambda value was >1 for most traits so genomic control was used, and the model included year and place of the test and sex of the horse. Preliminary results validate findings in other horse breeds of a region on ECA3 highly significant for height at withers. SNP-associations significant after Bonferroni correction were also found for traditionally scored type of the horse, and linear measures of type (light - heavy built). Because the data was particularly stratified for jumping traits, analyses were also done within clusters of genomic relationship. Within one of the two clusters, significant associations were also found for jumping technique. Suggestive significant associations were found for several traits, and continued analyses including polygenic effects are in the pipeline.
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- Eriksson, Susanne, et al.
(författare)
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Yearling conformation and radiographic findings related to Swedish Standardbred trotter performance
- 2016
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Ingår i: Annual meeting of the European Association for Animal Production. - 1382-6077. ; , s. 580-580
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- When breeding Swedish Standardbred trotters, the goal is well-tempered, sustainable and competitive racing horses. Conformation traits are believed to be important for a high performance and a long career, but conformation has not routinely been assessed in young Swedish Standardbreds. To enable studies of the relationship between conformation, leg health and later trotting performance, in total 1,125 Swedish Standardbred trotters born in 2011 and 2012 were assessed at Swedish yearling auctions. The conformation traits were subjectively described on a linear scale between two extremes. Results from radiographic examinations of fetlocks and hocks of most horses were also available. After data editing, 1,028 horses remained in the dataset. The conformation assessment scores and radiographic findings were statistically analyzed together with the performance of the horses as three-year-olds using SAS GLM. For horses born in 2011 also records of performance as four-year-olds were analyzed. The performance measures used were best racing time, earnings per start, percentage of placings (1-3) and number of starts. Radiographic findings of osteochondrosis and palmar/plantar osseous fragments were categorized according to a scale of severity and if the horse had had surgical treatment or not. Conformation traits assessed on yearlings with significant effects on their performance as three-year-olds were: body size, development, body direction, proportions (height vs length of body), muscularity of the neck, length and height of the withers, thoracic depth, front leg cannon bone length, and front and hind leg conformation from the side. Radiographic findings in yearlings significantly affected best racing time, earnings, number of starts and placings as three-year-olds (P<0.05). Our results suggest that conformation scores and radiographic findings in yearling Standardbred trotters could be useful indicators of trotting performance later in life.
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- Hong, Thu Le, et al.
(författare)
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Good legs means good stayability of the sows
- 2016
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Ingår i: Annual meeting of the European Association for Animal Production. - 1382-6077. ; , s. 378-378
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Leg weakness is one of the major reasons for culling of sows. Improvement of leg conformation is expected to improve both animal welfare and producers' profit. We summarize here the possibilities to breed for better legs/ gaits and the potential influence on reproduction and stayability, based on data on Landrace and Yorkshire sows in Sweden and Denmark. Purebred young pigs were scored for leg conformation traits at performance testing (5 months of age) in our studies. Leg conformation traits were analyzed together with litter size in parities 1 and 2 and stayability traits (culled or not culled after parity 1 or parity 2), recorded on purebred sows in nucleus and multiplier herds. Genetic (co)variances between traits were estimated. We estimated heritabilities for leg conformation traits ranging from 0.02 to 0.20 depending on breed and population. Estimated genetic correlations between leg conformation and litter size were favorable for Swedish Yorkshire (+0.15 to +0.42), but unfavorable in the Danish populations (-0.17 to -0.46). Estimated correlations between leg conformation and stayability were favorable in both Swedish Yorkshire and the Danish populations (0.12 to 0.42). Our results indicate that leg conformation can be improved by selection. Indirect selection for improved stayability based on leg conformation traits would be possible but influenced by the size of the genetic correlations between traits. Our ongoing project on genome wide association study using high density SNP chip is expected to identify chromosome regions associated with leg traits in three Danish pig populations (Landrace, Yorkshire and Duroc). Results from this study could be used as prior information in genomic selection, helping to more effectively improve leg conformation and accordingly improve sow longevity.
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- Ismael, Ahmed, et al.
(författare)
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Genotype by environment interaction for activity based estrus traits in Danish Holstein
- 2016
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Ingår i: Annual meeting of the European Association for Animal Production. - 1382-6077. ; 22, s. 311-311
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The objective of this study was to investigate whether genotype by environment interaction (G×E) exists for female fertility traits with regards to production level. The fertility traits considered were: (1) interval from calving to first high activity (CFHA); (2) duration of first estrus (DFE); and (3) strength of first estrus (SFE). Estrus traits were derived from electronic activity tags for 11,522 first parity cows housed in 125 herds. Data were analyzed using random regression animal model (RRM) by regressing the phenotypic performance on the average herd energy corrected milk yield as an environmental gradient. For validation of the random regression model results, data were further analyzed using a bivariate model (BM) considering the same trait in high and low production environments as different trait. The heritability estimate for CFHA decreased from 0.25 to 0.10 with increasing production level. For DFE, heritability estimate obtained by BM for the low producing herds were more than twice the estimates for high producing herds, this trend was however not detected by the RRM results. For SFE, heritability estimates decreased from 0.12 in the lowest environment to the minimum estimate of 0.03 before increasing gradually to 0.13 in the highest environmental scale. The genetic correlation of the same trait in low and high production environments was around 0.74 for CFHA, 0.22 for SFE and 1.00 for DFE using RRM with similar estimates using BM. These results indicated no evidence of G×E interaction effect on CFHA, DFE, while there was strong G×E for SFE, which indicate that G×E interaction should be included in the evaluation of this trait.
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- Johansson, Birgitta
(författare)
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Minerals in forage for dairy cows
- 2016
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Ingår i: Annual meeting of the European Association for Animal Production. - 1382-6077. ; , s. 411-411
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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- Jonas, Elisabeth
(författare)
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Identification of key contributors to increase phasing accuracy in complex population structures
- 2016
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Ingår i: Annual meeting of the European Association for Animal Production. - 1382-6077. ; , s. 341-341
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Knowledge of the genetic contribution of individuals is essential to select informative individuals for genotype imputation. Based on the Eigen Value Decomposition (EVD) of a relationship matrix we describe a novel approach to determine the genetic contribution of individuals within populations. The approach was applied and validated in four disparate datasets including simulated population, a highly structured experimental sheep population and two large complex pedigreed populations namely horse and cattle. In the simulated and sheep datasets, we identified all known key contributors within the populations, whilst in the horse and cattle dataset we applied the method to select small reference populations that increased phasing accuracy. Compared to commonly applied strategies to select informative individuals for genotype imputation including the identification of marginal gene contributions (PEDIG) and the optimization of genetic relatedness (REL) the selection of key contributors provided the highest phasing accuracies within the selected reference populations. Therefore, this method provides a valuable complement to common applied tools to select individuals for re-sequencing.
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