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Accuracy of genomic selection for growth and wood quality traits in two control-pollinated progeny trials using exome capture as the genotyping platform in Norway spruce.

https://arctichealth.org/en/permalink/ahliterature299456
Source
BMC Genomics. 2018 Dec 18; 19(1):946
Publication Type
Journal Article
Date
Dec-18-2018
Author
Zhi-Qiang Chen
John Baison
Jin Pan
Bo Karlsson
Bengt Andersson
Johan Westin
María Rosario García-Gil
Harry X Wu
Author Affiliation
Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden.
Source
BMC Genomics. 2018 Dec 18; 19(1):946
Date
Dec-18-2018
Language
English
Publication Type
Journal Article
Keywords
Exome
Genetic markers
Genomics - methods
Genotype
Models, Genetic
Models, Statistical
Norway
Phenotype
Picea - genetics - growth & development
Plant Breeding
Pollination
Selection, Genetic
Wood - chemistry - genetics
Abstract
Genomic selection (GS) can increase genetic gain by reducing the length of breeding cycle in forest trees. Here we genotyped 1370 control-pollinated progeny trees from 128 full-sib families in Norway spruce (Picea abies (L.) Karst.), using exome capture as genotyping platform. We used 116,765 high-quality SNPs to develop genomic prediction models for tree height and wood quality traits. We assessed the impact of different genomic prediction methods, genotype-by-environment interaction (G?×?E), genetic composition, size of the training and validation set, relatedness, and number of SNPs on accuracy and predictive ability (PA) of GS.
Using G matrix slightly altered heritability estimates relative to pedigree-based method. GS accuracies were about 11-14% lower than those based on pedigree-based selection. The efficiency of GS per year varied from 1.71 to 1.78, compared to that of the pedigree-based model if breeding cycle length was halved using GS. Height GS accuracy decreased to more than 30% while using one site as training for GS prediction and using this model to predict the second site, indicating that G?×?E for tree height should be accommodated in model fitting. Using a half-sib family structure instead of full-sib structure led to a significant reduction in GS accuracy and PA. The full-sib family structure needed only 750 markers to reach similar accuracy and PA, as compared to 100,000 markers required for the half-sib family, indicating that maintaining the high relatedness in the model improves accuracy and PA. Using 4000-8000 markers in full-sib family structure was sufficient to obtain GS model accuracy and PA for tree height and wood quality traits, almost equivalent to that obtained with all markers.
The study indicates that GS would be efficient in reducing generation time of breeding cycle in conifer tree breeding program that requires long-term progeny testing. The sufficient number of trees within-family (16 for growth and 12 for wood quality traits) and number of SNPs (8000) are required for GS with full-sib family relationship. GS methods had little impact on GS efficiency for growth and wood quality traits. GS model should incorporate G?×?E effect when a strong G?×?E is detected.
PubMed ID
30563448 View in PubMed
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Accurate Non-parametric Estimation of Recent Effective Population Size from Segments of Identity by Descent.

https://arctichealth.org/en/permalink/ahliterature268195
Source
Am J Hum Genet. 2015 Sep 3;97(3):404-18
Publication Type
Article
Date
Sep-3-2015
Author
Sharon R Browning
Brian L Browning
Source
Am J Hum Genet. 2015 Sep 3;97(3):404-18
Date
Sep-3-2015
Language
English
Publication Type
Article
Keywords
Chromosomes - genetics
Computer simulation
Finland
Genetics, Population - methods
Great Britain
Humans
Linkage Disequilibrium
Models, Genetic
Pedigree
Polymorphism, Single Nucleotide - genetics
Population Density
Software
Abstract
Existing methods for estimating historical effective population size from genetic data have been unable to accurately estimate effective population size during the most recent past. We present a non-parametric method for accurately estimating recent effective population size by using inferred long segments of identity by descent (IBD). We found that inferred segments of IBD contain information about effective population size from around 4 generations to around 50 generations ago for SNP array data and to over 200 generations ago for sequence data. In human populations that we examined, the estimates of effective size were approximately one-third of the census size. We estimate the effective population size of European-ancestry individuals in the UK four generations ago to be eight million and the effective population size of Finland four generations ago to be 0.7 million. Our method is implemented in the open-source IBDNe software package.
Notes
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PubMed ID
26299365 View in PubMed
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Adding cows to the reference population makes a small dairy population competitive.

https://arctichealth.org/en/permalink/ahliterature263440
Source
J Dairy Sci. 2014 Sep;97(9):5822-32
Publication Type
Article
Date
Sep-2014
Author
J R Thomasen
A C Sørensen
M S Lund
B. Guldbrandtsen
Source
J Dairy Sci. 2014 Sep;97(9):5822-32
Date
Sep-2014
Language
English
Publication Type
Article
Keywords
Animals
Breeding - economics - methods
Cattle - genetics - growth & development
Dairying - economics - methods
Denmark
Female
Genomics - methods
Genotype
Male
Models, Genetic
Population Density
Reproducibility of Results
Selection, Genetic
Abstract
Small dairy breeds are challenged by low reliabilities of genomic prediction. Therefore, we evaluated the effect of including cows in the reference population for small dairy cattle populations with a limited number of sires in the reference population. Using detailed simulations, 2 types of scenarios for maintaining and updating the reference population over a period of 15yr were investigated: a turbo scheme exclusively using genotyped young bulls and a hybrid scheme with mixed use of genotyped young bulls and progeny-tested bulls. Two types of modifications were investigated: (1) number of progeny-tested bulls per year was tested at 6 levels: 15, 40, 60, 100, 250, and 500; and (2) each year, 2,000 first-lactation cows were randomly selected from the cow population for genotyping or, alternatively, an additional 2,000 first-lactation cows were randomly selected and typed in the first 2yr. The effects were evaluated in the 2 main breeding schemes. The breeding schemes were chosen to mimic options for the Danish Jersey cattle population. Evaluation criteria were annual monetary genetic gain, rate of inbreeding, reliability of genomic predictions, and variance of response. Inclusion of cows in the reference population increased monetary genetic gain and decreased the rate of inbreeding. The increase in genetic gain was larger for the turbo schemes with shorter generation intervals. The variance of response was generally higher in turbo schemes than in schemes using progeny-tested bulls. However, the risk was reduced by adding cows to the reference population. The annual genetic gain and the reliability of genomic predictions were slightly higher with more cows in the reference population. Inclusion of cows in the reference population is a rapid way to increase reliabilities of genomic predictions and hence increase genetic gain in a small population. An economic evaluation shows that genotyping of cows is a profitable investment.
PubMed ID
24996280 View in PubMed
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[A genetic-epidemiological model of predisposition to ischemic heart disease (1)].

https://arctichealth.org/en/permalink/ahliterature222353
Source
Kardiologiia. 1993;33(10):18-21, 3-4
Publication Type
Article
Date
1993
Author
T A Rozhkova
V A Koshechkin
E I Drigalenko
G S Zhukovskii
E Iu Solov'eva
Source
Kardiologiia. 1993;33(10):18-21, 3-4
Date
1993
Language
Russian
Publication Type
Article
Keywords
Adult
Alleles
Chi-Square Distribution
Disease Susceptibility
Environmental health
Gene Frequency
Genes, Dominant
Genes, Recessive
Genotype
Humans
Male
Middle Aged
Models, Genetic
Moscow - epidemiology
Myocardial Ischemia - diagnosis - epidemiology - genetics
Pedigree
Prevalence
Urban Population - statistics & numerical data
Abstract
A genetic and epidemiological sample of 20-59-year-old males, Moscow residents (n = 3141), was surveyed. The authors obtained data on the prevalence of coronary heart disease from epidemiological criteria and genealogical data on cardiovascular diseases by the "Familial History" questionnaire in the first-degree relatives who were interviewed by using a genetic and mathematical monolocus diallelic model. It was found that out of the 10 possible variants under study a genetic and environmental variant with independent penetrance of 3 genotypes adequately describes the prevalence of coronary heart disease in the families and in the population. This suggest that both genetic and environmental factors have an influence on the prevalence of coronary heart disease and that there is a possible genetic polymorphism of the disease.
PubMed ID
8139164 View in PubMed
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Age-specific genetic and maternal effects in fecundity of preindustrial Finnish women.

https://arctichealth.org/en/permalink/ahliterature156232
Source
Evolution. 2008 Sep;62(9):2297-304
Publication Type
Article
Date
Sep-2008
Author
Jenni E Pettay
Anne Charmantier
Alastair J Wilson
Virpi Lummaa
Author Affiliation
Section of Ecology, Department of Biology, University of Turku, FIN-20014 Turku, Finland. jenni.pettay@utu.fi
Source
Evolution. 2008 Sep;62(9):2297-304
Date
Sep-2008
Language
English
Publication Type
Article
Keywords
Aging - physiology
Female
Fertility - genetics
Finland
Genetic Variation
Humans
Likelihood Functions
Models, Genetic
Quantitative Trait, Heritable
Regression Analysis
Abstract
A population's potential for evolutionary change depends on the amount of genetic variability expressed in traits under selection. Studies attempting to measure this variability typically do so over the life span of individuals, but theory suggests that the amount of additive genetic variance can change during the course of individuals' lives. Here we use pedigree data from historical Finns and a quantitative genetic framework to investigate how female fecundity, throughout an individual's reproductive life, is influenced by "maternal" versus additive genetic effects. We show that although maternal effects explain variation in female fecundity early in life, these effects wane with female age. Moreover, this decline in maternal effects is associated with a concomitant increase in additive genetic variance with age. Our results thus highlight that single over-lifetime estimates of trait heritability may give a misleading view of a trait's potential to respond to changing selection pressures.
PubMed ID
18616570 View in PubMed
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Aggression as a mediator of genetic contributions to the association between negative parent-child relationships and adolescent antisocial behavior.

https://arctichealth.org/en/permalink/ahliterature79587
Source
Eur Child Adolesc Psychiatry. 2007 Mar;16(2):128-37
Publication Type
Article
Date
Mar-2007
Author
Narusyte Jurgita
Andershed Anna-Karin
Neiderhiser Jenae M
Lichtenstein Paul
Author Affiliation
Dept. of Medical Epidemiology and Biostatistics, Karolinska Institutet, Box 281, 171 77 Stockholm, Sweden. jurgita.narusyte@ki.se
Source
Eur Child Adolesc Psychiatry. 2007 Mar;16(2):128-37
Date
Mar-2007
Language
English
Publication Type
Article
Keywords
Adolescent
Aggression
Antisocial Personality Disorder - epidemiology - genetics
Female
Humans
Longitudinal Studies
Male
Models, Genetic
Parent-Child Relations
Risk factors
Sweden - epidemiology
Twins, Dizygotic - genetics
Twins, Monozygotic - genetics
Abstract
Previous research suggests that the association between conflictual parent-child relationships and maladjustment among adolescents is influenced by genetic effects emanating from the adolescents. In this study, we examined whether these effects are mediated by childhood aggression. The data come from the Twin study of CHild and Adolescent Development (TCHAD), a Swedish longitudinal study including 1,314 twin pairs followed from age 13-14 to 16-17. Early adolescent aggression, parental criticism, and delinquency in later adolescence were rated by parents and children at different time points. Multivariate genetic structural equation models were used to estimate genetic and environmental influences on these constructs and on their covariation. The results showed that approximately half of the genetic contribution to the association between parental criticism and delinquency was explained by early adolescent aggression. It suggests that aggression in children evokes negative parenting, which in turn influences adolescent antisocial behavior. The mechanism proposed by these findings is consistent with evocative gene-environment correlation.
PubMed ID
17136502 View in PubMed
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AKT1 fails to replicate as a longevity-associated gene in Danish and German nonagenarians and centenarians.

https://arctichealth.org/en/permalink/ahliterature121208
Source
Eur J Hum Genet. 2013 May;21(5):574-7
Publication Type
Article
Date
May-2013
Author
Marianne Nygaard
Mette Soerensen
Friederike Flachsbart
Jonas Mengel-From
Qihua Tan
Stefan Schreiber
Almut Nebel
Kaare Christensen
Lene Christiansen
Author Affiliation
Epidemiology, Institute of Public Health, University of Southern Denmark, Odense C, Denmark. mnygaard@health.sdu.dk
Source
Eur J Hum Genet. 2013 May;21(5):574-7
Date
May-2013
Language
English
Publication Type
Article
Keywords
Aged, 80 and over
Denmark
Female
Genotype
Germany
Humans
Longevity - genetics
Male
Models, Genetic
Polymorphism, Single Nucleotide - genetics
Proto-Oncogene Proteins c-akt - genetics
Abstract
In addition to APOE and FOXO3, AKT1 has recently been suggested as a third consistent longevity gene, with variants in AKT1 found to be associated with human lifespan in two previous studies. Here, we evaluated AKT1 as a longevity-associated gene across populations by attempting to replicate the previously identified variant rs3803304 as well as by analyzing six additional AKT1 single-nucleotide polymorphisms, thus capturing more of the common variation in the gene. The study population was 2996 long-lived individuals (nonagenarians and centenarians) and 1840 younger controls of Danish and German ancestry. None of the seven SNPs tested were significantly associated with longevity in either a case-control or a longitudinal setting, although a supportive nominal indication of a disadvantageous effect of rs3803304 was found in a restricted group of Danish centenarian men. Overall, our results do not support AKT1 as a universal longevity-associated gene.
Notes
Cites: Nature. 2010 Mar 25;464(7288):504-1220336132
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PubMed ID
22929028 View in PubMed
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Alcohol, tobacco and caffeine use: spouse similarity processes.

https://arctichealth.org/en/permalink/ahliterature82321
Source
Behav Genet. 2006 Mar;36(2):201-15
Publication Type
Article
Date
Mar-2006
Author
Reynolds Chandra A
Barlow Tracy
Pedersen Nancy L
Author Affiliation
University of California, Riverside, USA. chandra.reynolds@ucr.edu
Source
Behav Genet. 2006 Mar;36(2):201-15
Date
Mar-2006
Language
English
Publication Type
Article
Keywords
Adult
Aged
Alcohol Drinking - epidemiology - genetics - psychology
Caffeine
Cross-Sectional Studies
Diseases in Twins - epidemiology - genetics - psychology
Female
Humans
Male
Middle Aged
Models, Genetic
Phenotype
Smoking - epidemiology - genetics - psychology
Social Environment
Spouses - psychology - statistics & numerical data
Statistics
Substance-Related Disorders - epidemiology - genetics - psychology
Sweden
Abstract
Spouse similarity research has been largely descriptive yet is of theoretical and empirical importance to understanding individual differences in substance use. The present study considers phenotypic assortment versus social homogamy processes for alcohol, tobacco, and caffeine consumption traits using an extended twin-spouse design. Whereas both assortment processes were supported for quantity of alcohol consumed, phenotypic assortment was supported for quantity of tobacco and caffeine consumed, and social homogamy for tobacco use status. Moderate heritable influences were found for all traits though no shared environmental influences were found beyond those due to social background influences, i.e. those pertaining to social homogamy. Swedish government policies in effect at the time of marriage selection may explain the presence of social homogamy for quantity of alcohol versus quantity of tobacco and caffeine consumed. Social homogamy may be more important for some substance use traits such as alcohol consumption and tobacco use status but not others.
PubMed ID
16645902 View in PubMed
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Allelic association with SNPs: metrics, populations, and the linkage disequilibrium map.

https://arctichealth.org/en/permalink/ahliterature195078
Source
Hum Mutat. 2001 Apr;17(4):255-62
Publication Type
Article
Date
Apr-2001
Author
A. Collins
S. Ennis
P. Taillon-Miller
P Y Kwok
N E Morton
Author Affiliation
Human Genetics Research Division, University of Southampton, Southampton, UK.
Source
Hum Mutat. 2001 Apr;17(4):255-62
Date
Apr-2001
Language
English
Publication Type
Article
Keywords
Alleles
Chromosome Mapping
Finland
Gene Frequency - genetics
HLA Antigens - genetics
Haplotypes - genetics
Histocompatibility Antigens Class I - genetics
Humans
Likelihood Functions
Linkage Disequilibrium - genetics
Membrane Proteins
Models, Genetic
Molecular Sequence Data
Polymorphism, Single Nucleotide - genetics
Recombination, Genetic - genetics
X Chromosome - genetics
Abstract
Comparison of different metrics, using three large samples of haplotypes from different populations, demonstrates that rho is the most efficient measure of association between pairs of single nucleotide polymorphisms (SNPs). Pairwise data can be modeled, using composite likelihood, to describe the decline in linkage disequilibrium with distance (the Malecot model). The evidence from more isolated populations (Finland, Sardinia) suggests that linkage disequilibrium extends to 427-893 kb but, even in samples representative of large heterogeneous populations, such as CEPH, the extent is 385 kb or greater. This suggests that isolated populations are not essential for linkage disequilibrium mapping of common diseases with SNPs. The in parameter of the Malecot model (recombination and time), evaluated at each SNP, indicates regions of the genome with extensive and less extensive disequilibrium (low and high values of in respectively). When plotted against the physical map, the regions with extensive and less extensive linkage disequilibrium may correspond to recombination cold and hot spots. This is discussed in relation to the Xq25 cytogenetic band and the HFE gene region.
PubMed ID
11295822 View in PubMed
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An AFLP clock for the absolute dating of shallow-time evolutionary history based on the intraspecific divergence of southwestern European alpine plant species.

https://arctichealth.org/en/permalink/ahliterature90263
Source
Mol Ecol. 2009 Feb;18(4):697-708
Publication Type
Article
Date
Feb-2009
Author
Kropf Matthias
Comes Hans Peter
Kadereit Joachim W
Author Affiliation
Institut für Botanik, Department of Integrative Biology and Biodiversity Research, University of Natural Resources and Applied Life Sciences, A-1180 Vienna, Austria. matthias.kropf@boku.ac.at
Source
Mol Ecol. 2009 Feb;18(4):697-708
Date
Feb-2009
Language
English
Publication Type
Article
Keywords
Amplified Fragment Length Polymorphism Analysis
Brassicaceae - genetics
Caryophyllaceae - genetics
DNA, Plant - genetics
Ecosystem
Europe
Evolution, Molecular
Genetics, Population
Gentiana - genetics
Models, Genetic
Mutation
Phylogeny
Plants - genetics
Regression Analysis
Sequence Analysis, DNA
Species Specificity
Abstract
The dating of recent events in the history of organisms needs divergence rates based on molecular fingerprint markers. Here, we used amplified fragment length polymorphisms (AFLPs) of three distantly related alpine plant species co-occurring in the Spanish Sierra Nevada, the Pyrenees and the southwestern Alps/Massif Central to establish divergence rates. Within each of these species (Gentiana alpina, Kernera saxatilis and Silene rupestris), we found that the degree of AFLP divergence (D(N72)) between mountain phylogroups was significantly correlated with their time of divergence (as inferred from palaeoclimatic/palynological data), indicating constant AFLP divergence rates. As these rates did not differ significantly among species, a regression analysis based on the pooled data was utilized to generate a general AFLP rate. The application of this latter rate to AFLP data from other herbaceous plant species (Minuartia biflora: Schönswetter et al. 2006; Nigella degenii: Comes et al. 2008) resulted in a plausible timing of the recolonization of the Svalbard Islands and the separation of populations from the Alps and Scandinavia (Minuartia), and of island population separation in the Aegean Archipelago (Nigella). Furthermore, the AFLP mutation rate obtained in our study is of the same magnitude as AFLP mutation rates published previously. The temporal limits of our AFLP rate, which is based on intraspecific vicariance events at shallow (i.e. late glacial/Early Holocene) time scales, remains to be tested.
PubMed ID
19175503 View in PubMed
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527 records – page 1 of 53.