| 1. |
- Staiger, E. A., et al.
(författare)
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The evolutionary history of the DMRT3 'Gait keeper' haplotype
- 2017
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Ingår i: Animal Genetics. - : WILEY. - 0268-9146 .- 1365-2052. ; 48:5, s. 551-559
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Tidskriftsartikel (refereegranskat)abstract
- A previous study revealed a strong association between the DMRT3:Ser301STOP mutation in horses and alternate gaits as well as performance in harness racing. Several follow-up studies have confirmed a high frequency of the mutation in gaited horse breeds and an effect on gait quality. The aim of this study was to determine when and where the mutation arose, to identify additional potential causal mutations and to determine the coalescence time for contemporary haplotypes carrying the stop mutation. We utilized sequences from 89 horses representing 26 breeds to identify 102 SNPs encompassing the DMRT3 gene that are in strong linkage disequilibrium with the stop mutation. These 102 SNPs were genotyped in an additional 382 horses representing 72 breeds, and we identified 14 unique haplotypes. The results provided conclusive evidence that DMRT3: Ser301STOP is causal, as no other sequence polymorphisms showed an equally strong association to locomotion traits. The low sequence diversity among mutant chromosomes demonstrated that they must have diverged from a common ancestral sequence within the last 10 000 years. Thus, the mutation occurred either just before domestication or more likely some time after domestication and then spread across the world as a result of selection on locomotion traits.
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| 2. |
- Abebe Abiye, Shenkut, et al.
(författare)
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Genetic diversity of five local Swedish chicken breeds detected by microsatellite markers
- 2015
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- This study aimed at investigating the genetic diversity, relationship and population structure of 110 local Swedish chickens derived from five breeds (Gotlandshona, Hedemorahona, Olandsk dvarghona, Skansk blommehona, and Bohuslan-Dals svarthona, in the rest of the paper the shorter name Svarthona is used) using 24 microsatellite markers. In total, one hundred thirteen alleles were detected in all populations, with a mean of 4.7 alleles per locus. For the five chicken breeds, the observed and expected heterozygosity ranged from 0.225 to 0.408 and from 0.231 to 0.515, with the lowest scores for the Svarthona and the highest scores for the Skansk blommehona breeds, respectively. Similarly, the average within breed molecular kinship varied from 0.496 to 0.745, showing high coancestry, with Skansk blommehona having the lowest and Svarthona the highest coancestry. Furthermore, all breeds showed significant deviations from Hardy-Weinberg expectations. Across the five breeds, the global heterozygosity deficit (FIT) was 0.545, population differentiation index (F-ST) was 0.440, and the global inbreeding of individuals within breed (F-IS) was 0.187. The phylogenetic relationships of chickens were examined using neighbor-joining trees constructed at the level of breeds and individual samples. The neighbor-joining tree constructed at breed level revealed two main clusters, with Hedemorahona and Olandsk dvarghona breeds in one cluster, and Gotlandshona and Svarthona breeds in the second cluster leaving the Skansk blommehona in the middle. Based on the results of the STRUCTURE analysis, the most likely number of clustering of the five breeds was at K = 4, with Hedemorahona, Gotlandshona and Svarthona breeds forming their own distinct clusters, while Olandsk dvarghona and Skansk blommehona breeds clustered together. Losses in the overall genetic diversity of local Swedish chickens due to breeds extinction varied from -1.46% to -6.723%. The results of the current study can be used as baseline genetic information for genetic conservation program, for instance, to control inbreeding and to implement further genetic studies in local Swedish chickens.
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| 3. |
- Ablondi, Michela, et al.
(författare)
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Performance of Swedish Warmblood fragile foal syndrome carriers and breeding prospects
- 2022
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Ingår i: Genetics Selection Evolution. - : Springer Science and Business Media LLC. - 0999-193X .- 1297-9686. ; 54
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Tidskriftsartikel (refereegranskat)abstract
- Background Warmblood fragile foal syndrome (WFFS) is a monogenetic defect caused by a recessive lethal missense point mutation in the procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 gene (PLOD1, c.2032G>A). The majority of homozygous WFFS horses are aborted during gestation. Clinical signs of affected horses include fragile skin, skin and mucosa lacerations, hyperextension of the articulations, and hematomas. In spite of its harmful effect, a relatively high frequency of WFFS carriers has been found in Warmblood horses, suggesting a heterozygote advantage. Thus, in this study our aims were to: (1) estimate the frequency of WFFS carriers in the Swedish Warmblood breed (SWB), (2) estimate the effect of WFFS carrier genotype on performance traits in two SWB subpopulations bred for different disciplines, and (3) simulate the potential effects of balancing selection and different selection strategies on the frequency of carriers. Methods In total, 2288 SWB sport horses born between 1971 and 2020 were tested for the WFFS mutation and had estimated breeding values (EBV) for ten traditional evaluating and 50 linear descriptive traits. Results The frequency of WFFS carriers calculated from a pool of 511 randomly selected SWB horses born in 2017 was equal to 7.4% and ranged from 0.0 to 12.0% among the whole set of tested SWB horses, starting from 1971 till 2020. The effect of the WFFS carrier genotype was significant for several EBV mainly related to movements and dressage traits and especially for horses not bred for the show jumping discipline. Using simulation, we showed that balancing selection can maintain a recessive lethal allele in populations such as the SWB breed over generations and that the frequency is expected to slowly decrease in absence of balancing selection. Finally, we showed that selection against carrier sires can result in a more rapid decrease of the frequency of the mutant allele over time. Conclusion Further research is needed to confirm the apparent association between equine performance and the WFFS carrier genotype. Identification of such associations or new causative mutations for horse performance traits can serve as new tools in horse breeding to select for healthy, sustainable, and better performing horses.
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| 4. |
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| 5. |
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| 6. |
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| 7. |
- Ablondi, Michela, et al.
(författare)
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Signatures of selection in the genome of Swedish warmblood horses selected for sport performance
- 2019
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 20
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Tidskriftsartikel (refereegranskat)abstract
- Background A growing demand for improved physical skills and mental attitude in modern sport horses has led to strong selection for performance in many warmblood studbooks. The aim of this study was to detect genomic regions with low diversity, and therefore potentially under selection, in Swedish Warmblood horses (SWB) by analysing high-density SNP data. To investigate if such signatures could be the result of selection for equestrian sport performance, we compared our SWB SNP data with those from Exmoor ponies, a horse breed not selected for sport performance traits. Results The genomic scan for homozygous regions identified long runs of homozygosity (ROH) shared by more than 85% of the genotyped SWB individuals. Such ROH were located on ECA4, ECA6, ECA7, ECA10 and ECA17. Long ROH were instead distributed evenly across the genome of Exmoor ponies in 77% of the chromosomes. Two population differentiation tests (F-ST and XP-EHH) revealed signatures of selection on ECA1, ECA4, and ECA6 in SWB horses. Conclusions Genes related to behaviour, physical abilities and fertility, appear to be targets of selection in the SWB breed. This study provides a genome-wide map of selection signatures in SWB horses, and ground for further functional studies to unravel the biological mechanisms behind complex traits in horses.
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| 8. |
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| 9. |
- Andersson, Lisa, et al.
(författare)
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Augendefekte bei windfarbenen Pferden
- 2012
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Ingår i: Eiðfaxi, Islandpferdemagazin. - 1023-3350. ; , s. 70-75
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Tidskriftsartikel (populärvet., debatt m.m.)
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| 10. |
- Andersson, Lisa, et al.
(författare)
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Augngallar í vindóttum hrossum
- 2012
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Ingår i: Eiðfaxi, Icelandic horse Magazine. - 1023-3342. ; , s. 42-47
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Tidskriftsartikel (populärvet., debatt m.m.)
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| 11. |
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| 12. |
- Andersson, Lisa, et al.
(författare)
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Genetic diversity in the modern horse illustrated from genome-wide SNP data
- 2013
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Horses were domesticated from the Eurasian steppes 5,000-6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. FST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection.
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| 13. |
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| 14. |
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| 15. |
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| 16. |
- Andersson, Lisa, et al.
(författare)
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Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice
- 2012
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 488:7413, s. 642-646
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Tidskriftsartikel (refereegranskat)abstract
- Locomotion in mammals relies on a central pattern-generating circuitry of spinal interneurons established during development that coordinates limb movement(1). These networks produce left-right alternation of limbs as well as coordinated activation of flexor and extensor muscles(2). Here we show that a premature stop codon in the DMRT3 gene has a major effect on the pattern of locomotion in horses. The mutation is permissive for the ability to perform alternate gaits and has a favourable effect on harness racing performance. Examination of wild-type and Dmrt3-null mice demonstrates that Dmrt3 is expressed in the dI6 subdivision of spinal cord neurons, takes part in neuronal specification within this subdivision, and is critical for the normal development of a coordinated locomotor network controlling limb movements. Our discovery positions Dmrt3 in a pivotal role for configuring the spinal circuits controlling stride in vertebrates. The DMRT3 mutation has had a major effect on the diversification of the domestic horse, as the altered gait characteristics of a number of breeds apparently require this mutation.
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| 17. |
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| 18. |
- Andersson, Lisa, et al.
(författare)
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Targeted analysis of four breeds narrows equine Multiple Congenital Ocular Anomalies locus to 208 kilobases
- 2011
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Ingår i: Mammalian Genome. - : Springer Science and Business Media LLC. - 0938-8990 .- 1432-1777. ; 22, s. 353-360
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Tidskriftsartikel (refereegranskat)abstract
- The syndrome Multiple Congenital Ocular Anomalies (MCOA) is the collective name ascribed to heritable congenital eye defects in horses. Individuals homozygous for the disease allele (MCOA phenotype) have a wide range of eye anomalies, while heterozygous horses (Cyst phenotype) predominantly have cysts that originate from the temporal ciliary body, iris, and/or peripheral retina. MCOA syndrome is highly prevalent in the Rocky Mountain Horse but the disease is not limited to this breed. Affected horses most often have a Silver coat color; however, a pleiotropic link between these phenotypes is yet to be proven. Locating and possibly isolating these traits would provide invaluable knowledge to scientists and breeders. This would favor maintenance of a desirable coat color while addressing the health concerns of the affected breeds, and would also provide insight into the genetic basis of the disease. Identical-by-descent mapping was used to narrow the previous 4.6-Mb region to a 264-kb interval for the MCOA locus. One haplotype common to four breeds showed complete association to the disease (Cyst phenotype, = 246; MCOA phenotype, n = 83). Candidate genes from the interval, SMARCC2 and IKZF4, were screened for polymorphisms and genotyped, and segregation analysis allowed the MCOA syndrome region to be shortened to 208 kb. This interval also harbors PMEL17, the gene causative for Silver coat color. However, by shortening the MCOA locus by a factor of 20, 176 other genes have been unlinked from the disease and only 15 genes remain.
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| 19. |
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| 20. |
- Andersson, Lisa, et al.
(författare)
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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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Ingår i: Immunogenetics. - : Springer Science and Business Media LLC. - 0093-7711 .- 1432-1211. ; 64:3, s. 201-208
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Tidskriftsartikel (refereegranskat)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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| 21. |
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| 22. |
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| 23. |
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| 24. |
- Baltrusis, Paulius, et al.
(författare)
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Using droplet digital PCR for the detection of hco-acr-8b levamisole resistance marker in H. contortus
- 2021
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Ingår i: International Journal for Parasitology: Drugs and Drug Resistance. - : Elsevier BV. - 2211-3207. ; 15, s. 168-176
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Tidskriftsartikel (refereegranskat)abstract
- The nematode Haemonchus contortus is one of the most prevalent and pathogenic parasites in small ruminants. Although usually controlled using anthelmintics, the development of drug resistance by the parasite has become a major issue in livestock production. While the molecular detection of benzimidazole resistance in H. contortus is well developed, the molecular tools and protocols are far less advanced for the detection of levamisole resistance. The hco-acr-8 gene encodes a critical acetylcholine susceptible subunit that confers levamisole-sensitivity to the receptor. Here, we report the development of a droplet digital PCR assay as a molecular tool to detect a 63 bp deletion in the hco-acr-8 that has been previously associated with levamisole resistance. Sanger sequencing of single adult H. contortus yielded 56 high-quality consensus sequences surrounding the region containing the deletion. Based on the sequencing data, new primers and probes were designed and validated with a novel droplet digital PCR assay for the quantification of the deletion containing "resistant" allele in genomic DNA samples. Single adult worms from six phenotypically described isolates (n = 60) and from two Swedish sheep farms (n = 30) where levamisole was effective were tested. Even though a significant difference in genotype frequencies between the resistant and susceptible reference isolates was found (p = 0.01), the homozygous "resistant" genotype was observed to be abundantly present in both the susceptible isolates as well as in some Swedish H. contortus samples. Furthermore, field larval culture samples, collected pre- (n = 7) and post- (n = 6) levamisole treatment on seven Swedish sheep farms where levamisole was fully efficacious according to Fecal Egg Count Reduction Test results, were tested to evaluate the frequency of the "resistant" allele in each. Frequencies of the deletion ranged from 35 to 80% in the pre-treatment samples, whereas no amplifiable H. contortus genomic DNA was detected in the post-treatment samples. Together, these data reveal relatively high frequencies of the 63 bp deletion in the hco-acr-8 both on individual H. contortus and field larval culture scales, and cast doubt on the utility of the deletion in the hco-acr-8 as a molecular marker for levamisole resistance detection on sheep farms.
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| 25. |
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| 26. |
- Brunberg, Emma, et al.
(författare)
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A missense mutation in PMEL17 is associated with the Silver coat color in the horse
- 2006
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Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 7, s. 46-
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Tidskriftsartikel (refereegranskat)abstract
- Background: The Silver coat color, also called Silver dapple, in the horse is characterized by dilution of the black pigment in the hair. This phenotype shows an autosomal dominant inheritance. The effect of the mutation is most visible in the long hairs of the mane and tail, which are diluted to a mixture of white and gray hairs. Herein we describe the identification of the responsible gene and a missense mutation associated with the Silver phenotype. Results: Segregation data on the Silver locus (Z) were obtained within one half-sib family that consisted of a heterozygous Silver colored stallion with 34 offspring and their 29 non-Silver dams. We typed 41 genetic markers well spread over the horse genome, including one single microsatellite marker (TKY284) close to the candidate gene PMEL17 on horse chromosome 6 (ECA6q23). Significant linkage was found between the Silver phenotype and TKY284 (theta = 0, z = 9.0). DNA sequencing of PMEL17 in Silver and non-Silver horses revealed a missense mutation in exon 11 changing the second amino acid in the cytoplasmic region from arginine to cysteine (Arg618Cys). This mutation showed complete association with the Silver phenotype across multiple horse breeds, and was not found among non-Silver horses with one clear exception; a chestnut colored individual that had several Silver offspring when mated to different non-Silver stallions also carried the exon 11 mutation. In total, 64 Silver horses from six breeds and 85 non-Silver horses from 14 breeds were tested for the exon 11 mutation. One additional mutation located in intron 9, only 759 bases from the missense mutation, also showed complete association with the Silver phenotype. However, as one could expect to find several non-causative mutations completely associated with the Silver mutation, we argue that the missense mutation is more likely to be causative. Conclusion: The present study shows that PMEL17 causes the Silver coat color in the horse and enable genetic testing for this trait.
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| 27. |
- Brunberg, Emma, et al.
(författare)
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Icelandic horses with the Silver coat colour show altered behaviour in a fear reaction test
- 2013
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Ingår i: Applied Animal Behaviour Science. - : Elsevier BV. - 0168-1591 .- 1872-9045. ; 146, s. 72-78
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Tidskriftsartikel (refereegranskat)abstract
- The colour of a horse's coat has long been discussed to reflect its temperament. One opinion is that Silver coloured horses are nervous, difficult to handle and react more strongly to different fear stimuli. The objective with the present study was to investigate if mutations associated with the Silver coat colour affect fear reactions in Icelandic horses. The hypothesis was that horses with the Silver mutation Arg618Cys in PMEL show stronger fear reactions than horses without the mutation (e.g. Black/Brown or Chestnut horses). Twenty-seven Icelandic horses (nine Silver, nine Chestnuts and nine Black/Brown) matched for sire, were exposed to the fear stimulus (a suddenly moving plastic bag) while feeding from a container. The test was repeated five times and behavioural responses and latency to return to the feed container were recorded. All horses were genotyped for the Silver mutation. The proportion of Silver horses that were hesitant to approach the test set-up before each trial was significantly higher (P < 0.05) than the proportion of non-Silver horses and this difference was most pronounced before the first two trials. No differences in reaction vigour or latency to resume feeding were found between the differently coloured horses. The results suggest that Silver horses are more cautious in novel situations rather than more reactive in fearful situations. One likely explanation for this difference is that the Silver mutation is associated with multiple congenital ocular anomalies (MCOA) syndrome and visual impairment. Furthermore, offspring (regardless of coat colour) from sires with a Best Linear Unbiased Prediction (BLUP, an index indicating which traits a horse will pass on to its offspring) value above 100 for the temperament trait 'Spirit', showed a greater fear reaction (P < 0.01) and reacted for a longer time (P < 0.01) than horses from sires with a lower (<100) index. These results indicate that horses with a high BLUP value for 'Spirit' seem to express stronger fear reactions. Breeding for Silver coat colour and the 'Spirit' trait, as it is currently defined, may need to be reconsidered if these results are confirmed in a larger cohort. (c) 2013 Elsevier B.V. All rights reserved.
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| 28. |
- Einarsson, Stig, et al.
(författare)
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The Origin of Amniotic Polymorphonuclear Leucocytes in the Mare
- 2013
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Ingår i: Reproduction in Domestic Animals. - : Wiley. - 0936-6768 .- 1439-0531. ; 48, s. e88-e89
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Tidskriftsartikel (refereegranskat)abstract
- Contents The objective of this study was to investigate the presence and origin of polymorphonuclear leucocytes (PMNLs) in the amniotic fluid of mares giving birth to healthy foals. Material from 25 mares was included. Amniotic fluid was collected during parturition before breakage of the amniotic vesicle. Manual microscopic cytologic evaluation was made on cytospin preparations after staining. PMNLs were found in all amniotic samples examined. The genomic DNA was extracted from 12 of the amniotic fluid samples and was genotyped. The results indicate that the PMNLs originate from the foetus.
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| 29. |
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| 30. |
- 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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| 31. |
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| 32. |
- Eriksson, Susanne, et al.
(författare)
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Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data
- 2020
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Ingår i: Animals. - : MDPI AG. - 2076-2615. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Simple Summary The Bardigiano horse is a native Italian breed bred for living in rural areas, traditionally used in agriculture. The breed counts about 3000 horses, and it is nowadays mainly used for recreational purposes. The relatively small size and the closed status of the breed raise the issue of monitoring genetic diversity. We therefore characterized the breed's genetic diversity based on molecular data. We showed a critical reduction of genetic variability mainly driven by past bottlenecks. We also highlighted homozygous genomic regions that might be the outcome of directional selection in recent years, in line with the conversion of Bardigiano horses from agricultural to riding purposes. Horses are nowadays mainly used for sport and leisure activities, and several local breeds, traditionally used in agriculture, have been exposed to a dramatic loss in population size and genetic diversity. The loss of genetic diversity negatively impacts individual fitness and reduces the potential long-term survivability of a breed. Recent advances in molecular biology and bioinformatics have allowed researchers to explore biodiversity one step further. This study aimed to evaluate the loss of genetic variability and identify genomic regions under selection pressure in the Bardigiano breed based on GGP Equine70k SNP data. The effective population size based on Linkage Disequilibrium (N-e) was equal to 39 horses, and it showed a decline over time. The average inbreeding based on runs of homozygosity (ROH) was equal to 0.17 (SD = 0.03). The majority of the ROH were relatively short (91% were <= 2 Mbp long), highlighting the occurrence of older inbreeding, rather than a more recent occurrence. A total of eight ROH islands, shared among more than 70% of the Bardigiano horses, were found. Four of them mapped to known quantitative trait loci related to morphological traits (e.g., body size and coat color) and disease susceptibility. This study provided the first genome-wide scan of genetic diversity and selection signatures in an Italian native horse breed.
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| 33. |
- Eriksson, Susanne, et al.
(författare)
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Haplotype blocks and heterozygosity rich regions on ECA2 in Swedish Warmblood horses
- 2022
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Konferensbidrag (refereegranskat)abstract
- The Fragile Foal Syndrome (FFS) is a disease caused by a recessive lethal missense mutation in the PLOD1 gene (ECA2). Despite its harmful effect, a relatively high frequency of the FFS allele carriers has been found in the Swedish Warmblood (SWB), suggesting a heterozygous advantage. Balancing selection can be further studied in haplotype blocks and increased heterozygosity around the target of selection. In this study we evaluated the presence of haplotype blocks and Runs of Heterozygosity on ECA2 in 380 SWB horses divided by sport discipline. In horses mainly bred for dressage a haplotype block comprising the FFS variant was found. On average 11.7 Runs of Heterozygosity were identified per horse on ECA2, with no significant difference in numbers between the sport disciplines. This study provides a preliminary characterization of haplotype blocks and heterozygosity rich regions on ECA2 which may further corroborate the potential presence of balancing selection for the FFS allele.
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| 34. |
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| 35. |
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| 36. |
- Francois, Liesbeth, et al.
(författare)
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Conformation Traits and Gaits in the Icelandic Horse are Associated with Genetic Variants in Myostatin (MSTN)
- 2016
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Ingår i: Journal of Heredity. - : Oxford University Press (OUP). - 0022-1503 .- 1465-7333. ; 107:5, s. 431-437
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Tidskriftsartikel (refereegranskat)abstract
- Many genes are known to have an influence on conformation and performance traits; however, the role of one gene, Myostatin (MSTN), has been highlighted in recent studies on horses. Myostatin acts as a repressor in the development and regulation of differentiation and proliferative growth of skeletal muscle. Several studies have examined the link between MSTN, conformation, and performance in racing breeds, but no studies have investigated the relationship in Icelandic horses. Icelandic horses, a highly unique breed, are known both for their robust and compact conformation as well as their additional gaits tolt and pace. Three SNPs (g.65868604G>T [PR8604], g.66493737C>T [PR3737], and g.66495826A>G [PR5826]) flanking or within equine MSTN were genotyped in 195 Icelandic horses. The SNPs and haplotypes were analyzed for association with official estimated breeding values (EBV) for conformation traits (n = 11) and gaits (n = 5). The EBV for neck, withers, and shoulders was significantly associated with both PR8604 and PR3737 (P < 0.05). PR8604 was also associated with EBV for total conformation (P = 0.05). These associations were all supported by the haplotype analysis. However, while SNP PR5826 showed a significant association with EBVs for leg stance and hooves (P < 0.05), haplotype analyses for these traits failed to fully support these associations. This study demonstrates the possible role of MSTN on both the form and function of horses from non-racing breeds. Further analysis of Icelandic horses as well as other non-racing breeds would be beneficial and likely help to completely understand the influence of MSTN on conformation and performance in horses.
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| 37. |
- Getman, Yaroslav, et al.
(författare)
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Developing an AI-Assisted Low-Resource Spoken Language Learning App for Children
- 2023
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Ingår i: IEEE Access. - : Institute of Electrical and Electronics Engineers (IEEE). - 2169-3536. ; 11, s. 86025-86037
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Tidskriftsartikel (refereegranskat)abstract
- Computer-assisted Language Learning (CALL) is a rapidly developing area accelerated by advancements in the field of AI. A well-designed and reliable CALL system allows students to practice language skills, like pronunciation, any time outside of the classroom. Furthermore, gamification via mobile applications has shown encouraging results on learning outcomes and motivates young users to practice more and perceive language learning as a positive experience. In this work, we adapt the latest speech recognition technology to be a part of an online pronunciation training system for small children. As part of our gamified mobile application, our models will assess the pronunciation quality of young Swedish children diagnosed with Speech Sound Disorder, and participating in speech therapy. Additionally, the models provide feedback to young non-native children learning to pronounce Swedish and Finnish words. Our experiments revealed that these new models fit into an online game as they function as speech recognizers and pronunciation evaluators simultaneously. To make our systems more trustworthy and explainable, we investigated whether the combination of modern input attribution algorithms and time-aligned transcripts can explain the decisions made by the models, give us insights into how the models work and provide a tool to develop more reliable solutions.
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| 38. |
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| 39. |
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| 40. |
- Imsland, Freyja, et al.
(författare)
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Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation underlying Dun camouflage colour in horses
- 2016
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 48:2, s. 152-158
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Tidskriftsartikel (refereegranskat)abstract
- Dun is a wild-type coat color in horses characterized by pigment dilution with a striking pattern of dark areas termed primitive markings. Here we show that pigment dilution in Dun horses is due to radially asymmetric deposition of pigment in the growing hair caused by localized expression of the T-box 3 (TBX3) transcription factor in hair follicles, which in turn determines the distribution of hair follicle melanocytes. Most domestic horses are non-dun, a more intensely pigmented phenotype caused by regulatory mutations impairing TBX3 expression in the hair follicle, resulting in a more circumferential distribution of melanocytes and pigment granules in individual hairs. We identified two different alleles (non-dun1 and non-dun2) causing non-dun color. non-dun2 is a recently derived allele, whereas the Dun and non-dun1 alleles are found in ancient horse DNA, demonstrating that this polymorphism predates horse domestication. These findings uncover a new developmental role for T-box genes and new aspects of hair follicle biology and pigmentation.
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| 41. |
- Jäderkvist Fegraeus, Kim, et al.
(författare)
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The DMRT3 'Gait keeper' mutation affects performance of Nordic and Standardbred trotters
- 2014
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Ingår i: Journal of Animal Science. - : Oxford University Press (OUP). - 0021-8812 .- 1525-3163. ; 92:10, s. 4279-4286
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Tidskriftsartikel (refereegranskat)abstract
- In a previous study it was shown that a nonsense mutation in the DMRT3 gene alters the pattern of locomotion in horses and that this mutation has a strong positive impact on trotting performance of Standardbreds. One aim of this study was to test if racing performance and trotting technique in the Nordic (Coldblood) trotters are also influenced by the DMRT3 genotype. Another aim was to further investigate the effect of the mutation on performance in Standardbreds, by using a within-family analysis and genotype-phenotype correlations in a larger horse material than in the previous study. We genotyped 427 Nordic trotters and 621 Standardbreds for the DMRT3 nonsense mutation and a SNP in strong linkage disequilibrium with it. In Nordic trotters, we show that horses homozygous for the DMRT3 mutation (A) had significantly higher EBV for trotting performance traits than heterozygous (CA) or homozygous wild-type (CC) horses (P = 0.001). Furthermore, AA homozygotes had a higher proportion of victories and top 3 placings than horses heterozygous or homozygous wild-type, when analyzing performance data for the period 3 to 6 yr of age (P = 0.06 and P = 0.05, respectively). Another finding in the Nordic trotters was that the DMRT3 mutation influenced trotting technique (P = 2.1 x 10(-8)). Standardbred horses homozygous AA had significantly higher EBV for all traits than horses with at least 1 wild-type allele (CA and CC; P = 1.6 x 10(-16)). In a within-family analysis of Standardbreds, we found significant differences in several traits (e. g., earnings, P = 0.002; number of entered races, P = 0.004; and fraction of offspring that entered races, P = 0.002) among paternal half-sibs with genotype AA or CA sired by a CA stallion. For most traits, we found significant differences at young ages. For Nordic trotters, most of the results were significant at 3 yr of age but not for the older ages, and for the Standardbreds most of the results for the ages 3 to 5 were significant. For Nordic trotters, the proportion of victories and placings were the only traits that were significant for other ages than 3 yr.
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| 42. |
- Karppinen, Jaro, et al.
(författare)
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Evaluation of training in guideline‐oriented biopsychosocial management of low back pain in occupational health services : Protocol of a cluster randomized trial
- 2021
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Ingår i: Health Science Reports. - : John Wiley & Sons. - 2398-8835. ; 4:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundTo prevent low back pain (LBP) from developing into a prolonged disabling condition, clinical guidelines advocate early stage assessment, risk‐screening, and tailored interventions. Occupational health services recommend guideline‐oriented biopsychosocial screening and individualized assessment and management. However, it is not known whether training a limited number of health care professionals improves the management process. The primary objective of this study is to investigate whether training in the biopsychosocial practice model is effective in reducing disability. Furthermore, we aim to evaluate health‐economic impacts of the training intervention in comparison to usual medical care.MethodsThe occupational health service units will be allocated into a training or control arm in a two‐arm cluster randomized controlled design. The training of occupational physiotherapists and physicians will include the assessment of pain‐related psychosocial factors using the STarT Back Tool and the short version of the Örebro Musculoskeletal Pain Screening Questionnaire, the use of an evidence‐based patient education booklet as part of the management of LBP, and tailored individualized management of LBP according to risk stratification. The control units will receive no training. The study population will include patients aged 18–65 with nonspecific LBP. The primary outcome is a patient‐reported Oswestry Disability Index from baseline to 12 months. By estimating group differences over time, we aim to evaluate the effectiveness of the training intervention in comparison to usual medical care, and to undertake an economic evaluation using individual patients' health care records (participant‐level data) and the participating units' registries (cluster‐level data). In addition, through interviews and questionnaires, we will explore the health care professionals' conceptions of the adoption of, the barriers to, and the facilitators of the implementation of the practice model.DiscussionThe evaluation of training in the guideline‐oriented biopsychosocial management of LBP in occupational health services is justified because LBP represents an enormous burden in terms of work disability.
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| 43. |
- Kelkka, Tiina, et al.
(författare)
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Adult-Onset Anti-Citrullinated Peptide Antibody-Negative Destructive Rheumatoid Arthritis Is Characterized by a Disease-Specific CD8+T Lymphocyte Signature
- 2020
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Ingår i: Frontiers in Immunology. - : FRONTIERS MEDIA SA. - 1664-3224. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Rheumatoid arthritis (RA) is a complex autoimmune disease targeting synovial joints. Traditionally, RA is divided into seropositive (SP) and seronegative (SN) disease forms, the latter consisting of an array of unrelated diseases with joint involvement. Recently, we described a severe form of SN-RA that associates with characteristic joint destruction. Here, we sought biological characteristics to differentiate this rare but aggressive anti-citrullinated peptide antibody-negative destructive RA (CND-RA) from early seropositive (SP-RA) and seronegative rheumatoid arthritis (SN-RA). We also aimed to study cytotoxic CD8+ lymphocytes in autoimmune arthritis. CND-RA, SP-RA and SN-RA were compared to healthy controls to reveal differences in T-cell receptor beta (TCR beta) repertoire, cytokine levels and autoantibody repertoires. Whole-exome sequencing (WES) followed by single-cell RNA-sequencing (sc-RNA-seq) was performed to study somatic mutations in a clonally expanded CD8+ lymphocyte population in an index patient. A unique TCR beta signature was detected in CND-RA patients. In addition, CND-RA patients expressed higher levels of the bone destruction-associated TNFSF14 cytokine. Blood IgG repertoire from CND-RA patients recognized fewer endogenous proteins than SP-RA patients repertoires. Using WES, we detected a stable mutation profile in the clonally expanded CD8+ T-cell population characterized by cytotoxic gene expression signature discovered by sc-RNA-sequencing. Our results identify CND-RA as an independent RA subset and reveal a CND-RA specific TCR signature in the CD8+ lymphocytes. Improved classification of seronegative RA patients underlines the heterogeneity of RA and also, facilitates development of improved therapeutic options for the treatment resistant patients.
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| 44. |
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| 45. |
- Lindgren, Gabriella, et al.
(författare)
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A genome-wide scan for candidate lethal variants in Thoroughbred horses
- 2020
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Domestic animal populations are often characterised by high rates of inbreeding and low effective population sizes due to selective breeding practices. These practices can result in otherwise rare recessive deleterious alleles drifting to high frequencies, resulting in reduced fertility rates. This study aimed to identify potential recessive lethal haplotypes in the Thoroughbred horse breed, a closed population that has been selectively bred for racing performance. In this study, we identified a haplotype in the LY49B gene that shows strong evidence of being homozygous lethal, despite having high frequencies of heterozygotes in Thoroughbreds and other domestic horse breeds. Variant analysis of whole-genome sequence data identified two SNPs in the 3 ' UTR of the LY49B gene that may result in loss of function. Analysis of transcriptomic data from equine embryonic tissue revealed that LY49B is expressed in the trophoblast during placentation stage of development. These findings suggest that LY49B may have an essential, but as yet unknown function in the implantation stage of equine development. Further investigation of this region may allow for the development of a genetic test to improve fertility rates in horse populations. Identification of other lethal variants could assist in improving natural levels of fertility in horse populations.
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| 46. |
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| 47. |
- Marco, Maugeri, 1983, et al.
(författare)
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Linkage between endosomal escape of LNP-mRNA and loading into EVs for transport to other cells
- 2019
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- RNA-based therapeutics hold great promise for treating diseases and lipid nanoparticles (LNPs) represent the most advanced platform for RNA delivery. However, the fate of the LNP-mRNA after endosome-engulfing and escape from the autophagy-lysosomal pathway remains unclear. To investigate this, mRNA (encoding human erythropoietin) was delivered to cells using LNPs, which shows, for the first time, a link between LNP-mRNA endocytosis and its packaging into extracellular vesicles (endo-EVs: secreted after the endocytosis of LNP-mRNA). Endosomal escape of LNP-mRNA is dependent on the molar ratios between ionizable lipids and mRNA nucleotides. Our results show that fractions of ionizable lipids and mRNA (1:1 molar ratio of hEPO mRNA nucleotides:ionizable lipids) of endocytosed LNPs were detected in endo-EVs. Importantly, these EVs can protect the exogenous mRNA during in vivo delivery to produce human protein in mice, detected in plasma and organs. Compared to LNPs, endo-EVs cause lower expression of inflammatory cytokines.
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| 48. |
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| 49. |
- Mikko, Sofia
(författare)
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A Nonsense Variant in the ST14 Gene in Akhal-Teke Horses with Naked Foal Syndrome
- 2017
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Ingår i: G3. - : Oxford University Press (OUP). - 2160-1836. ; 7, s. 1315-1321
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Tidskriftsartikel (refereegranskat)abstract
- Naked foal syndrome (NFS) is a genodermatosis in the Akhal-Teke horse breed. We provide the first scientific description of this phenotype. Affected horses had almost no hair and showed a mild ichthyosis. So far, all known NFS affected horses died between a few weeks and 3 years of age. It is not clear whether a specific pathology caused the premature deaths. NFS is inherited as a monogenic autosomal recessive trait. We mapped the disease causing genetic variant to two segments on chromosomes 7 and 27 in the equine genome. Whole genome sequencing of two affected horses, two obligate carriers, and 75 control horses from other breeds revealed a single non-synonymous genetic variant on the chromosome 7 segment that was perfectly associated with NFS. The affected horses were homozygous for ST14:c.388G>T, a nonsense variant that truncates more than 80% of the open reading frame of the ST14 gene (p.Glu130*). The variant leads to partial nonsense mediated decay of the mutant transcript. Genetic variants in the ST14 gene are responsible for autosomal recessive congenital ichthyosis 11 in humans. Thus, the identified equine ST14:c.388G>T variant is an excellent candidate causative variant for NFS and the affected horses represent a large animal model for a known human genodermatosis. Our findings will enable genetic testing to avoid the non-intentional breeding of NFS affected foals.
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| 50. |
- Mikko, Sofia
(författare)
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Aktuell genetisk forskning på häst
- 2009
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Ingår i: Medlemstidning för Mälardalens Varmblodsklubb. ; , s. s. 24-
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Tidskriftsartikel (populärvet., debatt m.m.)
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