Browsing by Subject "genetic correlation"

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  • Weiss, Alexander; Baselmans, Bart M. L.; Hofer, Edith; Yang, Jingyun; Okbay, Aysu; Lind, Penelope A.; Miller, Mike B.; Nolte, Ilja M.; Zhao, Wei; Hagenaars, Saskia P.; Hottenga, Jouke-Jan; Matteson, Lindsay K.; Snieder, Harold; Faul, Jessica D.; Hartman, Catharina A.; Boyle, Patricia A.; Tiemeier, Henning; Mosing, Miriam A.; Pattie, Alison; Davies, Gail; Liewald, David C.; Schmidt, Reinhold; De Jager, Philip L.; Heath, Andrew C.; Jokela, Markus; Starr, John M.; Oldehinkel, Albertine J.; Johannesson, Magnus; Cesarini, David; Hofman, Albert; Harris, Sarah E.; Smith, Jennifer A.; Keltikangas-Järvinen, Liisa; Pulkki-Råback, Laura; Schmidt, Helena; Smith, Jacqui; Iacono, William G.; McGue, Matt; Bennett, David A.; Pedersen, Nancy L.; Magnusson, Patrik K. E.; Deary, Ian J.; Martin, Nicholas G.; Boomsma, Dorret I.; Bartels, Meike; Luciano, Michelle (2016)
    Approximately half of the variation in wellbeing measures overlaps with variation in personality traits. Studies of non-human primate pedigrees and human twins suggest that this is due to common genetic influences. We tested whether personality polygenic scores for the NEO Five-Factor Inventory (NEO-FFI) domains and for item response theory (IRT) derived extraversion and neuroticism scores predict variance in wellbeing measures. Polygenic scores were based on published genome-wide association (GWA) results in over 17,000 individuals for the NEO-FFI and in over 63,000 for the IRT extraversion and neuroticism traits. The NEO-FFI polygenic scores were used to predict life satisfaction in 7 cohorts, positive affect in 12 cohorts, and general wellbeing in 1 cohort (maximal N = 46,508). Meta-analysis of these results showed no significant association between NEO-FFI personality polygenic scores and the wellbeing measures. IRT extraversion and neuroticism polygenic scores were used to predict life satisfaction and positive affect in almost 37,000 individuals from UK Biobank. Significant positive associations (effect sizes
  • Kavlak, Alper T.; Uimari, Pekka (2019)
    Abstract A major proportion of the costs of pork production is related to feed. The feed conversion rate (FCR) or residual feed intake (RFI) is thus commonly included in breeding programmes. Feeding behaviour traits do not directly have economic value but, if correlated with production traits, can be used as auxiliary traits. The aim of this study was to estimate the heritability of feeding behaviour traits and their genetic correlations with production traits in the Finnish Yorkshire pig population. The data were available from 3,235 pigs. Feeding behaviour was measured as the number of visits per day (NVD), time spent in feeding per day (TPD), daily feed intake (DFI), time spent feeding per visit (TPV), feed intake per visit (FPV) and feed intake rate (FR). The test station phase was divided into five periods. Estimates of heritabilities of feeding behaviour traits varied from 0.17 to 0.47. Strong genetic correlations were obtained between behaviour traits in all periods. However, only DFI was strongly correlated with the production traits. Interestingly, a moderate positive genetic correlation was obtained between FR and backfat thickness (0.1?0.5) and between FR and average daily gain (0.3?0.4), depending on the period. Based on the results, there is no additional benefit from including feeding-related traits other than those commonly used (FCR and RFI) in the breeding programme. However, if correlated with animal welfare, the feeding behaviour traits could be valuable in the breeding programme.
  • Ruotanen, Päivi (Helsingin yliopisto, 2020)
    Patellar luxation is a typical orthopaedic disorder in small sized dogs. Patella can luxate either medially or laterally, medial luxation being by far more common than the lateral luxation. PL is considered hereditary since certain breeds have great susceptibility to get the condition, and the symptoms may occur at young age. PL is diagnosed by following the so-called Putnam’s scale where the stifle joint is palpated and manipulated. PL is graded from 0=normal…4=permanent luxation. The aim of this study was to estimate the variance components and the heritability of PL, to visualize PL’s genetic trend and to calculate the genetic correlation between left and right stifle and between PL and hip dysplasia (HD) in Japanese Spitz. The PL, HD and pedigree data were provided by the Finnish Kennel Club. Data were modified with both R-program and Microsoft Office Excel. The pedigree check was performed with RelaX2 program and variance component analyses were done with DMU program using the restricted maximum likelihood method. Heritabilities (h2) were from very low to low depending on the model and breed. When the dependent variable was the mean of left and right patellae of an individual the lowest heritability was in the Pomeranian h2=0.03 and highest in the Chihuahua h2=0.18. The genetic correlation of left and right patellae was 1 in all breeds which suggests that they are genetically the same trait. In the Japanese Spitz the genetic correlation between PL and HD was -0.05. The genetic trend of PL was favorable in the Chihuahua and the Japanese Spitz. In the Pomeranian the trend was negative and neutral in the Finnish Spitz. Based on the results, the selection against PL has not been efficient. In future, patellae health should be controlled by using breeding indexes because the heritability of PL is low. Also, improvements in phenotyping could lead to more accurate selection.
  • Hatton, Sean N.; Panizzon, Matthew S.; Vuoksimaa, Eero; Hagler, Donald J.; Fennema-Notestine, Christine; Rinker, Daniel; Eyler, Lisa T.; Franz, Carol E.; Lyons, Michael J.; Neale, Michael C.; Tsuang, Ming T.; Dale, Anders M.; Kremen, William S. (2018)
    Two basic neuroimaging-based characterizations of white matter tracts are the magnitude of water diffusion along the principal tract orientation (axial diffusivity, AD) and water diffusion perpendicular to the principal orientation (radial diffusivity, RD). It is generally accepted that decreases in AD reflect disorganization, damage, or loss of axons, whereas increases in RD are indicative of disruptions to the myelin sheath. Previous reports have detailed the heritability of individual AD and RD measures, but have not examined the extent to which the same or different genetic or environmental factors influence these two phenotypes (except for corpus callosum). We implemented bivariate twin analyses to examine the shared and independent genetic influences on AD and RD. In the Vietnam Era Twin Study of Aging, 393 men (mean age = 61.8 years, SD = 2.6) underwent diffusion-weighted magnetic resonance imaging. We derived fractional anisotropy (FA), mean diffusivity (MD), AD, and RD estimates for 11 major bilateral white matter tracts and the mid-hemispheric corpus callosum, forceps major, and forceps minor. Separately, AD and RD were each highly heritable. In about three-quarters of the tracts, genetic correlations between AD and RD were >.50 (median = .67) and showed both unique and common variance. Genetic variance of FA and MD were predominately explained by RD over AD. These findings are important for informing genetic association studies of axonal coherence/damage and myelination/demyelination. Thus, genetic studies would benefit from examining the shared and unique contributions of AD and RD.
  • UK Biobank Eye Vision Consortium; CREAM Consortium; Plotnikov, Denis; Cui, Jiangtian; Clark, Rosie; Wedenoja, Juho; Pärssinen, Olavi; Guggenheim, Jeremy A. (2021)
    PURPOSE. Emmetropization requires coordinated scaling of the major ocular components, corneal curvature and axial length. This coordination is achieved in part through a shared set of genetic variants that regulate eye size. Poorly coordinated scaling of corneal curvature and axial length results in refractive error. We tested the hypothesis that genetic variants regulating eye size in emmetropic eyes are distinct from those conferring susceptibility to refractive error. METHODS. A genome-wide association study (GWAS) for corneal curvature in 22,180 adult emmetropic individuals was performed as a proxy for a GWAS for eye size. A polygenic score created using lead GWAS variants was tested for association with corneal curvature and axial length in an independent sample: 437 classified as emmetropic and 637 as ametropic. The genetic correlation between eye size and refractive error was calculated using linkage disequilibrium score regression for approximately 1 million genetic variants. RESULTS. The GWAS for corneal curvature in emmetropes identified 32 independent genetic variants (P < 5.0e-08). A polygenic score created using these 32 genetic markers explained 3.5% (P < 0.001) and 2.0% (P = 0.001) of the variance in corneal curvature and axial length, respectively, in the independent sample of emmetropic individuals but was not predictive of these traits in ametropic individuals. The genetic correlation between eye size and refractive error was close to zero (r(g) = 0.00; SE = 0.06; P = 0.95). CONCLUSIONS. These results support the hypothesis that genetic variants regulating eye size in emmetropic eyes do not overlap with those conferring susceptibility to myopia. This suggests that distinct biological pathways regulate normal eye growth and myopia development.
  • Tikkanen, Minna (Helsingfors universitet, 2014)
    Genetic and phenotypic parameters and relationships for fertility traits, body type traits and production were estimated. The data analyzed included 21,450 Ayrshires. Animals were reared in 2,647 herds, born from 1994 to 2005 and were progeny of 1652 sires. Analyzed fertility traits were days from first service to last insemination and number of inseminations to conception for heifers, and days from calving to first insemination for first parity cows. Production traits were first lactation milk and lifetime milk and body type traits were stature, body depth, chest width, angularity, top line, rump width and rump angle. Variance components and the heritability estimates were calculated by restricted maximum likelihood (REML) method using the DMU software. The heritability estimates of first lactation milk yield and lifetime milk yield were 0.28 and 0.08, re-spectively. The heritabilities for fertility traits in virgin heifers and first lactation cows were low (0.02 – 0.03). Heritability estimates for the type traits varied from 0.10 to 0.43. The largest heritability was found for stature (0.43) and rump width (0.27). The highest positive genetic correlations were angularity with first lactation milk (0.41) and lifetime milk (0.45), and the highest negative genetic correlation was between top line and first lactation milk (-0.33). Chest width and rump angle had a positive genetic correlation to days from calving to first insemination. The significant genetic correlations were heifer fertility with body depth, rump width and rump angle. Estimated correlations between heifer fertility traits and lifetime milk yield were positive and moderate. First parity cow fertility was not related to production traits. Fertility traits and lifetime milk have a low heritability. Progress can be made relatively fast in body traits and first lactation milk by breeding, because of the moderate heritabilities. Selection for some body type traits may cause improvement in production but deterioration in fertility. Declined heifer fertility is associated with high lifetime production. However is not reasonable to put emphasis on poor heifer fertility in selection.
  • Int Myasthenia Gravis Genomics Con; Chia, Ruth; Saez-Atienzar, Sara; Murphy, Natalie; Tienari, Pentti J.; Traynor, Bryan J. (2022)
    Myasthenia gravis is a chronic autoimmune disease characterized by autoantibody-mediated interference of signal transmission across the neuromuscular junction. We performed a genome-wide association study (GWAS) involving 1,873 patients diagnosed with acetylcholine receptor antibody-positive myasthenia gravis and 36,370 healthy individuals to identify disease-associated genetic risk loci. Replication of the discovered loci was attempted in an independent cohort from the UK Biobank. We also performed a transcriptome-wide association study (TWAS) using expression data from skeletal muscle, whole blood, and tibial nerve to test the effects of disease-associated polymorphisms on gene expression. We discovered two signals in the genes encoding acetylcholine receptor subunits that are the most common antigenic target of the autoantibodies: a GWAS signal within the cholinergic receptor nicotinic alpha 1 subunit (CHRNA1) gene and a TWAS association with the cholinergic receptor nicotinic beta 1 subunit (CHRNB1) gene in normal skeletal muscle. Two other loci were discovered on 10p14 and 11q21, and the previous association signals at PTPN22, HLA-DQA1/HLA-B, and TNFRSF11A were confirmed. Subgroup analyses demonstrate that early-and late-onset cases have different genetic risk factors. Genetic correlation analysis confirmed a genetic link between myasthenia gravis and other autoimmune diseases, such as hypothyroidism, rheumatoid arthritis, multiple sclerosis, and type 1 diabetes. Finally, we applied Priority Index analysis to identify potentially druggable genes/proteins and pathways. This study provides insight into the genetic architecture underlying myasthenia gravis and demonstrates that genetic factors within the loci encoding acetylcholine receptor subunits contribute to its pathogenesis.
  • Häkli, Katja (Helsingfors universitet, 2013)
    The objective of this study was to estimate genetic parameters of minks Aleutian Disease (AD) infections and investigate the genetic relationships between Aleutian Disease infection and fertility traits. The research data was obtained from the Finnish Fur Breeders Association. The data had information from one mink farm in years 2006-2010. The data contained 27 753 one year old female minks. Only those females who had more than three kits were tested. There were 18 478 tested minks of which 9.2 % had AD. The pedigree data had 41 573 animals. In this study AD infection, pregnancy and felicity were binary traits. AD inf. 1 = sick, 2 = healthy. If female had kit(s) or aborted or lost her kit(s) after birth, pregnancy (PREG) = 2, otherwise = 1. If female lost her kits after birth, felicity (FEL) = 1. If litter size were at least one, FEL = 2. The heritability estimates and variance components (REML) were calculated using multi trait animal model and DMU-software. Heritability estimates for the studied traits were low: 0.07 for AD infection, 0.07 for PREG, 0.04 for FEL and 0.08 for litter size. The heritability estimate for AD was smaller than the common litter variance for the trait. Genetic correlations between AD inf. and FEL, and AD inf. and litter size were positive. The genetic correlations between AD inf. and FEL were 0.447 ± 0.132 and between AD inf. and litter size 0.290 ± 0.108. The results suggest that resistance for AD inf. has genetic variation. Although the heritability estimate for the trait was low, it can be affected by selection. Genetic correlations between AD inf. and fertility traits were favourable. Selection for larger litter size could increase mink resistance for AD infection.
  • Debes, Paul; Piavchenko, Nikolai; Ruokolainen, Annukka; Ovaskainen, Outi; Moustakas-Verho, Jacqueline E.; Parre, Noora; Aykanat, Tutku; Erkinaro, Jaakko; Primmer, Craig R. (2021)
    Sexual maturation timing is a life-history trait central to the balance between mortality and reproduction. Maturation may be triggered when an underlying compound trait, called liability, exceeds a threshold. In many different species and especially fishes, this liability is approximated by growth and body condition. However, environmental vs. genetic contributions either directly or via growth and body condition to maturation timing remain unclear. Uncertainty exists also because the maturation process can reverse this causality and itself affect growth and body condition. In addition, disentangling the contributions of polygenic and major loci can be important. In many fishes, males mature before females, enabling the study of associations between male maturation and maturation-unbiased female liability traits. Using 40 Atlantic salmon families, longitudinal common-garden experimentation, and quantitative genetic analyses, we disentangled environmental from polygenic and major locus (vgll3) effects on male maturation, and sex-specific growth and condition. We detected polygenic heritabilities for maturation, growth, and body condition, and vgll3 effects on maturation and body condition but not on growth. Longitudinal patterns for sex-specific phenotypic liability, and for genetic variances and correlations between sexes suggested that early growth and condition indeed positively affected maturation initiation. However, towards spawning time, causality appeared reversed for males whereby maturation affected growth negatively and condition positively via both the environmental and genetic effects. Altogether, the results indicate that growth and condition are useful traits to study liability for maturation initiation, but only until maturation alters their expression, and that vgll3 contributes to maturation initiation via condition.
  • Lehto, Emilia (Helsingfors universitet, 2012)
    The aim of this study was to investigate the genetic relationships between conformation and performance traits in Finnish Warmblood riding horse population. The research material included the RHQT (riding horse quality test) results from the years 1996-2010 and the pedigree data for the horses. The RHQT results were received from the Finnish Breeders Association and the pedigree data was received from the Finnish trotting and breeding association’s horse register. The RHQT results consisted of 640 horses and the pedigree data consisted of 4 458 horses. The REML estimates of (co)variance components were calculated by VCE6 using multi trait model. Altogether there were six trait groups, which consisted of 27 different traits. Because of the large number of traits, the analyses were done in smaller subsets with two trait groups at the same time. The heritability estimates for the studied traits were quite high and the standard errors were small. The genetic correlations within each trait group were strong and positive. Thus it could be concluded that same genes or groups of genes affect all the traits within the trait group. The other explanation for this could be that in reality the judges have evaluated the same traits as different traits. The genetic correlations between conformation traits and all gait traits and dressage traits indicate that conformation can be used indirectly in the breeding of gait and dressage traits. Furthermore, it could be concluded that the genetic relationships between conformation and show-jumping traits are quite low. The genetic correlations between gait traits and show-jumping traits were low. The genetic correlations between gait traits and dressage traits were positive and strong. These strong and positive correlations indicate that the judged traits are actually same or very similar. From the results of this study can be concluded that all three different tests for show-jumping traits are actually measuring the same traits. Because of this one test would be adequate to produce the information of horses quality, capacity and breeding value. Moreover it can be concluded that there are genetic relationships between conformation and performance in Finnish Warmblood riding horse population. These discovered relationships can be used when breeding traits that have low heritabilities, such as the mechanic of movement in the walk or rideability. Furthermore, these results can be used to improve the judging methods in RHQT and other performance tests.
  • Riihimäki, Anna (Helsingin yliopisto, 2019)
    The target of pork production is to produce lean meat efficiently in a sustainable way taking into account environment and ethical aspects. The most important production traits in pigs are average daily gain, feed efficiency and leanness. A lot of research is conducted related to production traits in comparison to feeding behavior traits. The objective of this study was to estimate heritability of feeding behavior traits and their genetic correlations with production traits in Finnish Landrace population. The data included feeding records of 4059 Landrace pigs measured automatically in Figen’s test station. The pigs had started their test period during 2010 - 2016. The measured traits were the number of visits per day (NVD), time spent in feeding per day (TPD), daily feed intake (DFI), time spent feeding per visit (TPV), feed intake per visit (FPV), feeding rate (FR), average daily gain (ADG), back fat thickness (BF) and feed conversion ratio (FCR). Feeding behavior traits were divided into 5 periods. Heritability estimates of feeding behavior traits were moderate. The heritability estimates were 0,22-0,29 for NVD, 0,33-0,47 for TPD, 0,16-0,25 for DFI, 0,22-0,31 for TPV, 0,28-0,36 for FPV, 0,35-0,38 for FR, 0,27 for ADG, 0,22 for BF, and 0,24 for FCR. Compared to other published results heritabilities of TPD and FR were similar. However, heritabilities of other feeding behavior traits were quite low compared to published results. In addition, heritability of BF was unexpectedly low. The genetic correlations of feeding behavior traits were similar at different test periods. The highest positive genetic correlations were between traits TPV – FPV, FPV – FR, and NVD – TPD. The highest negative genetic correlations were between traits NVD – FPV, TPD – FR, and NVD – TPV. Genetic correlations between feeding behavior traits and production traits were low. Only between DFI – ADG, DFI – FCR, and FPV – FCR the genetic correlations were significant (and positive). In conclusion, heritabilities of feeding behavior traits were moderate. Because the only strong genetic correlation between feeding behavior and production traits was obtained between DFI and ADG, including feeding behavior traits in breeding programs is not necessary. However, feeding behavior data are easy to collect from the electronic feeders and the observations are reliable, thus daily feeding records can be used for monitoring animal’s health and welfare.
  • Class, Barbara; Kluen, Edward; Brommer, Jon E. (2019)
    Indirect sexual selection arises when reproductive individuals choose their mates based on heritable ornaments that are genetically correlated to fitness. Evidence for genetic associations between ornamental colouration and fitness remains scarce. In this study, we investigate the quantitative genetic relationship between different aspects of tail structural colouration (brightness, hue and UV chroma) and performance (cell-mediated immunity, body mass and wing length) in blue tit (Cyanistes caeruleus) nestlings. In line with previous studies, we find low heritability for structural colouration and moderate heritability for performance measures. Multivariate animal models show positive genetic correlations between the three measures of performance, indicating quantitative genetic variation for overall performance, and tail brightness and UV chroma, two genetically independent colour measures, are genetically correlated with performance (positively and negatively, respectively). Our results suggest that mate choice based on independent aspects of tail colouration can have fitness payoffs in blue tits and provide support for the indirect benefits hypothesis. However, low heritability of tail structural colouration implies that indirect sexual selection on mate choice for this ornament will be a weak evolutionary force.
  • Middeldorp, C. M.; de Moor, M. H. M.; McGrath, L. M.; Gordon, S. D.; Blackwood, D. H.; Costa, P. T.; Terracciano, A.; Krueger, R. F.; de Geus, E. J. C.; Nyholt, D. R.; Tanaka, T.; Esko, T.; Madden, P. A. F.; Derringer, J.; Amin, N.; Willemsen, G.; Hottenga, J-J; Distel, M. A.; Uda, M.; Sanna, S.; Spinhoven, P.; Hartman, C. A.; Ripke, S.; Sullivan, P. F.; Realo, A.; Allik, J.; Heath, A. C.; Pergadia, M. L.; Agrawal, A.; Lin, P.; Grucza, R. A.; Widen, E.; Cousminer, D. L.; Eriksson, J. G.; Palotie, A.; Barnett, J. H.; Lee, P. H.; Luciano, M.; Tenesa, A.; Davies, G.; Lopez, L. M.; Hansell, N. K.; Medland, S. E.; Ferrucci, L.; Schlessinger, D.; Montgomery, G. W.; Wright, M. J.; Aulchenko, Y. S.; Janssens, A. C. J. W.; Oostra, B. A.; Metspalu, A.; Abecasis, G. R.; Deary, I. J.; Räikkönen, Katri; Bierut, L. J.; Martin, N. G.; Wray, N. R.; van Duijn, C. M.; Smoller, J. W.; Penninx, B. W. J. H.; Boomsma, D. I. (2011)