-
Concept of mappingIdentification of genetic variant underlying
disease susceptibility or a trait value = Causal variantEvidence
for the location of the gene
-
Approaches to MappingCandidate gene
studiesAssociationResequencing approaches
Genome-wide studiesLinkage analysis Genome-wide association
studies (Linkage disequilibrium, LD mapping)
-
Linkage mappingLook for marker alleles that are correlated with
the phenotype within a pedigree
Different alleles can be connected with the trait in the
different pedigrees
-
Association mappingMarker alleles are correlated with a trait on
a population level
Can detect association by looking at unrelated individuals from
a population
Does not necessarily imply that markers are linked to (are close
to) genes influencing the trait.
-
Linkage vs. associationEffectFreq. of causal variantVery
difficultLinkage analysisUnlikely to existAssociation studyModified
from D. Altschuler
-
Linkage vs. association Hirschhorn & Daly, Nature Rev.
Genet. 2005
-
Allelic AssociationDirect AssociationAllele of interest is
itself involved in phenotype
Indirect AssociationAllele itself is not involved, but due to LD
with the functional variant
Spurious associationConfounding factors (e.g., population
stratification)
-
Linkage disequilibriumNon random association between alleles at
different loci. Loci are in LD if alleles are present on haplotypes
in different proportions than expected based on allele
frequencies
Two alleles that are in LD are occurring together more often
than would be expected by chance
-
Linkage disequilibriumLocus A: Alleles A & a; freq. PA &
PaLocus B: Alleles B & b; freq. PB & PbPossible
haplotyoesA
BA
ba
Ba
bExpected frequencies: pApB pApb papB papbObserved frequencies:
pAB pAb paB pabD = pAB - pApB 0
-
LD variation across genomeThe extent of LD is highly variable
across the genomeThe determinants of LD are not fully
understood.Factors that are believed to influence LDGenetic
driftPopulation growthAdmixture or migrationSelectionVariable
recombination rates
-
HaplotypeGenotypes
Locus12 4Locus21 3Locus33 2Locus44 1Locus52 3Locus61
2Identification of phase413122232431HaplotypesPHASE
BEAGLE
-
Haplotype-based analysisIncreased ability to identify regions
that are shared identical by descent among affected individuals
Haplotypes may the causative composite allele rather than a
particular nucleotide at a particular SNP
Haplotype analysis is meaningful only if SNPS are in themselves
in LD
-
Monogenic
verses
Complex traits
-
Monogenic traitMutation in single gene is both necessary and
sufficient to produce the phenotype or to cause the disease
The impact of the gene on genetic risk is the same in all
families
Follow clear segregation pattern in families
Typically rare in population
-
Complex traitMultiple genes lead to genetic predisposition to a
phenotype
Pedigree reveals no Mendelian pattern
Any particular gene mutation is neither sufficient nor necessary
to explain the phenotype
Environment has major contribution
We study the relative impact of individual gene on the
phenotype
-
Some examples
-
Quantitative TraitA biological trait that shows continuous
variation rather than falling into distinct categories
Quantitative trait locus (QTL) - Genetic locus that is
associated with variation in such quantitative trait
-
Assessing genetic contributions to complex traitsContinuous
characters (wt, blood pressure)Heritability: Proportion of observed
variance in phenotype explained by genetic factors
Discrete characters (disease)Relative risk ratio: = risk to
relative of an affected individual/risk in general population
encompasses all genetic and environmental effects, not just those
due to any single locus
-
Factors that influence identification of allelic
associationEffect sizeLinkage disequilibriumDisease and marker
allele frequenciesSample Size
Reviewed by Zondervar & Cardon, Nature Rev. Genet. 2004
-
Odds ratio
-
Sample sizeZondervar & Cardon (Nature Rev. Genet. 2004)No.
of cases= no. of controls; D=0.7; power 80%; =0.001
-
Population stratificationConsider two case/control samples,
genotyped at a marker with alleles M and mSample A2 NS2 NSSample
B
-
Population stratificationSample ASample B2 =14.8
P
-
Dealing with population structureGenomic control (Devlin and
Roeder, 1999)Inflate the distribution of the test statistic by .
estimated from data
-
Dealing with population structureStructured association
(Pritchard et al., 2000)Discover structure from set of unlinked
markers, i.e. assign probabilities of ancestry from k populations
to each individual, and then control for it.
-
Association analysis approachesCasecontrol studies Markers
frequencies are determined in a group of affected individuals and
compared with allele frequencies in a control population
Family based methods Based on unequal transmission of alleles
from parents to a single affected child in each family.
Associations are summed over many unrelated families
-
Case-Control studies: 2 testGenotypesAlleles2x3 contingency
table2x2 contingency tableTest of independence:2 = (O-E)2/E with 2
or 1 df
-
Family based testsGenotypes from independent family trios where
the child is affected
Use the non-transmitted genotypes or alleles as internal
controls to the transmitted ones
-
Family-based association studies
1 4 transmitted
2 3 non-transmitted??1 23 41 4control
Is an allele transmitted more often than its not transmitted to
affected offspring ?
-
TDT: Transmission Disequilibrium TestG/GG/gG/gNon-transmitted G
gTransmittedG
ga b
c dTDTG = (TG-NTG)2/(TG+NTG)
=(b-c)2/(b+c) ~ 21
-
TDT: Transmission Disequilibrium TestMultiallelic markersETDT
(Sham & Curtis, 1995)Missing parent genotypesTRANSMIT
(Cayton,1999)HaplotypesTDTHAP (Clayton & Jones,
1999)SibsTDT/STDT (Spielman & Ewens, 1998)PedigreesPBAT (Martin
et al, 2000)Quantitative traitsQTDT (Abecasis et al. 2000)
-
Some limitationsSubjects random or structure familyParents not
availableDifficult when there are very many genes individually of
small effectEnvironmental influence may obscure genetic
effectsGenetic heterogeneity underlying disease phenotypeHidden
(unaccounted) relationship
-
Rare alleleSingle family is segregating
AaOffspring group IOffspring group IIBb
-
Complex pedigree & Quantitative traits
-
Complex pedigreeNon-independence among pedigree membersOnly
polygenic relationship is not sufficientAssociation analysis should
account for the point-wise relationship among
individualsIdentical-by-decent probabilities
-
Methods Combined linkage and LD Generalized linear
modelsMixed-model (Yu et al. 2006)Bayesian approach
-
Combined linkage and LDPolygene the whole relationship in
pedigree is used Identical-by-descend coefficients were estimated
for point-wise relationship
Phenotype= Fixed factors + Polygene + HaplotypePhase
determination - GDQTLQTL mapping - DMU
-
QTL for Clinical Mastitis in cattleLA
Chart1
1.744403
2.544403
2.844403
2.944403
3.044403
3.044403
3.044403
2.444403
1.944403
1.944403
1.844403
2.044403
2.244403
2.444403
3.544403
3.144403
2.944403
2.944403
3.844403
7.544403
10.644403
10.944403
11.744403
12.344403
12.944403
13.534403
13.144403
10.144403
12.144403
11.944403
10.944403
10.444403
9.944403
9.944403
10.744403
10.644403
8.944403
5.844403
5.144403
5.444403
6.244403
6.844403
6.844403
5.544403
LA
Morgan
LRT
profile_M1_90h10
3.70E-0210110.132350.14670.62276.43E-033.49E-026.19E-031013.3444032.3444033.70E-021011.61.744403-0.00
0.16351010.49.33E-020.224210.622392.77E-032.04E-026.16E-031013.3444032.9444030.16351010.82.544403-0.00
0.253251010.64.92E-020.321510.614657.81E-041.25E-026.26E-031013.3444032.7444030.261010.52.8444031.44
0.290251010.16.40E-020.283270.621831.18E-031.41E-026.17E-031013.3444033.2444030.290251010.42.944403-0.00
0.327251013.31.60E-030.408480.621133.24E-059.73E-036.19E-031013.3444030.0444030.326251010.33.0444030.58
0.327751012.85.48E-030.406690.616444.75E-059.93E-036.27E-031013.3444030.5444030.3291010.33.0444030.53
0.34710105.52E-020.302370.620588.68E-041.29E-026.19E-031013.3444033.3444030.3471010.33.044403-0.00
0.371011.51.62E-020.38230.618521.38E-041.01E-026.18E-031013.3444031.8444030.371010.92.4444030.03
0.3751011.71.66E-020.380560.619751.46E-041.01E-026.18E-031013.3444031.6444030.3751011.41.9444030.21
0.376751012.87.03E-030.390730.626527.12E-059.78E-036.09E-031013.3444030.5444030.376751011.41.944403-0.00
0.377651012.16.89E-030.383230.632184.23E-059.46E-035.98E-031013.3444031.2444030.38051011.51.844403-0.00
0.377951012.25.73E-030.394260.625383.43E-059.61E-036.10E-031013.3444031.1444030.389751011.32.0444030.02
0.378251013.12.80E-030.39690.62832.62E-059.59E-036.06E-031013.3444030.2444030.41011.12.2444030.02
0.378551010.12.07E-020.329240.653311.30E-048.88E-035.50E-031013.3444033.2444030.4121010.92.4444031.12
0.378851012.41.16E-020.376370.630611.12E-049.77E-035.99E-031013.3444030.9444030.429251009.83.5444031.06
0.38051012.31.57E-020.371310.628541.56E-049.97E-036.02E-031013.3444031.0444030.4421010.23.1444032.18
0.389751012.81.63E-020.375340.624222.65E-041.05E-026.09E-031013.3444030.5444030.46351010.42.944403-0.00
0.3977510136.11E-030.405960.616545.79E-059.94E-036.28E-031013.3444030.3444030.4871010.42.944403-0.00
0.398251012.95.52E-030.405350.61775.18E-059.90E-036.26E-031013.3444030.4444030.5181009.53.844403-0.00
0.398751012.78.11E-030.402630.616196.66E-051.00E-026.29E-031013.3444030.6444030.58551005.87.544403-0.00
0.399251013.14.42E-030.402730.621384.65E-059.79E-036.18E-031013.3444030.2444030.64351002.710.644403-0.00
0.4121010.74.18E-020.322870.625085.94E-041.18E-026.08E-031013.3444032.6444030.654751002.410.944403-0.00
0.42475-44746.35E-070.408790.623373.17E-099.58E-036.13E-031013.34440300.6631001.611.744403-0.00
0.42525-3992.22.17E-060.408780.623376.74E-099.57E-036.13E-031013.34440300.671100112.344403-0.00
0.42925-5266.21.40E-070.408790.623361.61E-099.58E-036.13E-031013.34440300.6741000.412.944403-0.00
0.442-5266.21.40E-070.408790.623361.61E-099.58E-036.13E-031013.34440300.682999.8113.534403-0.00
0.46351010.33.84E-020.331540.623364.51E-041.12E-026.08E-031013.3444033.0444030.690751000.213.144403-0.00
0.4871010.63.48E-020.338810.623373.92E-041.09E-026.09E-031013.3444032.7444030.704251003.210.144403-0.00
0.5181009.54.54E-020.315710.625145.09E-041.13E-026.05E-031013.3444033.8444030.7171001.212.144403-0.00
0.58551005.47.20E-020.266180.623557.47E-041.24E-026.14E-031013.3444037.9444030.7221001.411.944403-0.00
0.64351006.95.10E-020.301990.628963.89E-041.05E-025.96E-031013.3444036.4444030.7311002.410.9444030.56
0.65425-141371.71E-060.408790.623361.55E-099.57E-036.13E-031013.34440300.7351002.910.444403-0.00
0.6631010.51.78E-020.368020.629418.12E-059.16E-035.85E-031013.3444032.8444030.74751003.49.944403-0.00
0.671751009.11.29E-020.380570.629195.04E-058.90E-035.76E-031013.3444034.2444030.74351003.49.944403-0.00
0.6741008.31.34E-020.372360.63394.77E-058.66E-035.63E-031013.3444035.0444030.77151002.610.744403-0.00
0.6821009.12.18E-020.375630.619449.80E-059.24E-035.92E-031013.3444034.2444030.7971002.710.6444030.10
0.690751010.51.55E-020.357370.643626.36E-058.55E-035.55E-031013.3444032.8444030.810251004.48.944403-0.00
0.693751013.21.86E-030.403110.625331.37E-059.52E-036.08E-031013.3444030.1444030.8271007.55.844403-0.00
0.694251013.21.57E-030.405040.624181.19E-059.56E-036.11E-031013.3444030.1444030.84851008.25.144403-0.00
0.69475-201371.71E-060.408780.623371.74E-099.57E-036.13E-031013.34440300.86551007.95.444403-0.00
0.69525-217534.35E-070.408790.623378.07E-109.58E-036.13E-031013.34440300.881007.16.244403-0.00
0.704251006.52.71E-020.3150.657061.16E-048.13E-035.23E-031013.3444036.8444030.894751006.56.8444030.33
0.7171007.21.25E-020.349220.649953.65E-058.18E-035.36E-031013.3444036.1444030.909751006.56.8444030.48
0.7221010.68.27E-030.385280.629342.82E-059.15E-035.89E-031013.3444032.7444030.9511007.85.544403-0.00
0.7311004.73.08E-020.30030.663771.23E-047.57E-034.96E-031013.3444038.6444031.70
0.73925998.444.35E-020.396760.593962.70E-049.40E-036.00E-031013.34440314.9044038.94
0.740751000.72.89E-020.359220.626561.16E-048.45E-035.51E-031013.34440312.6444033.41
0.74351004.52.52E-020.345970.641839.93E-058.11E-035.33E-031013.3444038.8444031.29
0.77151002.37.32E-020.263810.6236.50E-041.20E-026.15E-031013.34440311.044403-0.00
0.798251005.43.07E-020.339660.627761.77E-049.73E-035.92E-031013.3444037.944403-0.00
0.810251004.46.21E-020.270220.634835.22E-041.11E-025.89E-031013.3444038.944403-0.00
0.8271008.32.49E-020.353260.627281.48E-049.73E-035.98E-031013.3444035.044403-0.00
0.84851007.45.72E-020.273680.640435.88E-041.13E-025.78E-031013.3444035.9444030.20
0.86551008.83.05E-020.351950.620062.51E-041.05E-026.18E-031013.3444034.544403-0.00
0.881006.65.50E-020.29710.623885.27E-041.14E-026.06E-031013.3444036.744403-0.00
0.894251004.83.67E-020.355180.605542.35E-041.06E-026.35E-031013.3444038.5444031.77
0.909751006.26.11E-020.278480.6296.37E-041.18E-025.97E-031013.3444037.144403-0.00
0.9511007.65.74E-020.291790.624376.92E-041.22E-026.07E-031013.3444035.744403-0.00
profile_M1_90h10
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0
LDLA
LA
LD
QTL Profile-Mast-Red-
-
QTL for Clinical Mastitis in cattleLALD
Chart1
1.744403-0.000000032
2.544403-0.000000032
2.8444031.4432015598
2.944403-0.0000000321
3.0444030.58485429
3.0444030.531389156
3.044403-0.0000000321
2.4444030.0272408303
1.9444030.2057662723
1.944403-0.0000095168
1.844403-0.0000265088
2.0444030.0162969604
2.2444030.0185906067
2.4444031.1206260126
3.5444031.0601634282
3.1444032.1779390253
2.944403-0.0001126592
2.944403-0.0000075699
3.844403-0.0000236027
7.544403-0.0000757402
10.644403-0.0000096231
10.944403-0.000000032
11.744403-0.00018067
12.344403-0.0002281395
12.944403-0.0000682414
13.534403-0.0000101858
13.144403-0.0000286556
10.144403-0.0000163377
12.144403-0.0000277397
11.944403-0.0000000319
10.9444030.5649934652
10.444403-0.0002960709
9.944403-0.0000073671
9.944403-0.000440445
10.744403-0.0000316191
10.6444030.1017906115
8.944403-0.0000471483
5.844403-0.0000482385
5.144403-0.000115464
5.444403-0.0000128659
6.244403-0.0000537135
6.8444030.3325767712
6.8444030.4817941532
5.544403-0.0000388472
1.6982511022
8.9376605056
3.4113730654
1.28536918
-0.000000032
-0.0000278023
-0.0000572169
-0.0000372763
0.1964023707
-0.0001490375
-0.0000270704
1.772013477
-0.0000093862
-0.0000000319
LA
LD
Morgan
LRT
profile_M1_90h10
3.70E-0210110.132350.14670.62276.43E-033.49E-026.19E-031013.3444032.3444033.70E-021011.61.744403-0.00
0.16351010.49.33E-020.224210.622392.77E-032.04E-026.16E-031013.3444032.9444030.16351010.82.544403-0.00
0.253251010.64.92E-020.321510.614657.81E-041.25E-026.26E-031013.3444032.7444030.261010.52.8444031.44
0.290251010.16.40E-020.283270.621831.18E-031.41E-026.17E-031013.3444033.2444030.290251010.42.944403-0.00
0.327251013.31.60E-030.408480.621133.24E-059.73E-036.19E-031013.3444030.0444030.326251010.33.0444030.58
0.327751012.85.48E-030.406690.616444.75E-059.93E-036.27E-031013.3444030.5444030.3291010.33.0444030.53
0.34710105.52E-020.302370.620588.68E-041.29E-026.19E-031013.3444033.3444030.3471010.33.044403-0.00
0.371011.51.62E-020.38230.618521.38E-041.01E-026.18E-031013.3444031.8444030.371010.92.4444030.03
0.3751011.71.66E-020.380560.619751.46E-041.01E-026.18E-031013.3444031.6444030.3751011.41.9444030.21
0.376751012.87.03E-030.390730.626527.12E-059.78E-036.09E-031013.3444030.5444030.376751011.41.944403-0.00
0.377651012.16.89E-030.383230.632184.23E-059.46E-035.98E-031013.3444031.2444030.38051011.51.844403-0.00
0.377951012.25.73E-030.394260.625383.43E-059.61E-036.10E-031013.3444031.1444030.389751011.32.0444030.02
0.378251013.12.80E-030.39690.62832.62E-059.59E-036.06E-031013.3444030.2444030.41011.12.2444030.02
0.378551010.12.07E-020.329240.653311.30E-048.88E-035.50E-031013.3444033.2444030.4121010.92.4444031.12
0.378851012.41.16E-020.376370.630611.12E-049.77E-035.99E-031013.3444030.9444030.429251009.83.5444031.06
0.38051012.31.57E-020.371310.628541.56E-049.97E-036.02E-031013.3444031.0444030.4421010.23.1444032.18
0.389751012.81.63E-020.375340.624222.65E-041.05E-026.09E-031013.3444030.5444030.46351010.42.944403-0.00
0.3977510136.11E-030.405960.616545.79E-059.94E-036.28E-031013.3444030.3444030.4871010.42.944403-0.00
0.398251012.95.52E-030.405350.61775.18E-059.90E-036.26E-031013.3444030.4444030.5181009.53.844403-0.00
0.398751012.78.11E-030.402630.616196.66E-051.00E-026.29E-031013.3444030.6444030.58551005.87.544403-0.00
0.399251013.14.42E-030.402730.621384.65E-059.79E-036.18E-031013.3444030.2444030.64351002.710.644403-0.00
0.4121010.74.18E-020.322870.625085.94E-041.18E-026.08E-031013.3444032.6444030.654751002.410.944403-0.00
0.42475-44746.35E-070.408790.623373.17E-099.58E-036.13E-031013.34440300.6631001.611.744403-0.00
0.42525-3992.22.17E-060.408780.623376.74E-099.57E-036.13E-031013.34440300.671100112.344403-0.00
0.42925-5266.21.40E-070.408790.623361.61E-099.58E-036.13E-031013.34440300.6741000.412.944403-0.00
0.442-5266.21.40E-070.408790.623361.61E-099.58E-036.13E-031013.34440300.682999.8113.534403-0.00
0.46351010.33.84E-020.331540.623364.51E-041.12E-026.08E-031013.3444033.0444030.690751000.213.144403-0.00
0.4871010.63.48E-020.338810.623373.92E-041.09E-026.09E-031013.3444032.7444030.704251003.210.144403-0.00
0.5181009.54.54E-020.315710.625145.09E-041.13E-026.05E-031013.3444033.8444030.7171001.212.144403-0.00
0.58551005.47.20E-020.266180.623557.47E-041.24E-026.14E-031013.3444037.9444030.7221001.411.944403-0.00
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0.73925998.444.35E-020.396760.593962.70E-049.40E-036.00E-031013.34440314.9044038.94
0.740751000.72.89E-020.359220.626561.16E-048.45E-035.51E-031013.34440312.6444033.41
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0.77151002.37.32E-020.263810.6236.50E-041.20E-026.15E-031013.34440311.044403-0.00
0.798251005.43.07E-020.339660.627761.77E-049.73E-035.92E-031013.3444037.944403-0.00
0.810251004.46.21E-020.270220.634835.22E-041.11E-025.89E-031013.3444038.944403-0.00
0.8271008.32.49E-020.353260.627281.48E-049.73E-035.98E-031013.3444035.044403-0.00
0.84851007.45.72E-020.273680.640435.88E-041.13E-025.78E-031013.3444035.9444030.20
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0.909751006.26.11E-020.278480.6296.37E-041.18E-025.97E-031013.3444037.144403-0.00
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profile_M1_90h10
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LDLA
LA
LD
QTL Profile-Mast-Red-
-
QTL for Clinical Mastitis in cattleLALD/LALD
Chart1
2.3444031.744403-0.000000032
2.9444032.544403-0.000000032
2.7444032.8444031.4432015598
3.2444032.944403-0.0000000321
0.0444033.0444030.58485429
0.5444033.0444030.531389156
3.3444033.044403-0.0000000321
1.8444032.4444030.0272408303
1.6444031.9444030.2057662723
0.5444031.944403-0.0000095168
1.2444031.844403-0.0000265088
1.1444032.0444030.0162969604
0.2444032.2444030.0185906067
3.2444032.4444031.1206260126
0.9444033.5444031.0601634282
1.0444033.1444032.1779390253
0.5444032.944403-0.0001126592
0.3444032.944403-0.0000075699
0.4444033.844403-0.0000236027
0.6444037.544403-0.0000757402
0.24440310.644403-0.0000096231
2.64440310.944403-0.000000032
011.744403-0.00018067
012.344403-0.0002281395
012.944403-0.0000682414
013.534403-0.0000101858
3.04440313.144403-0.0000286556
2.74440310.144403-0.0000163377
3.84440312.144403-0.0000277397
7.94440311.944403-0.0000000319
6.44440310.9444030.5649934652
010.444403-0.0002960709
2.8444039.944403-0.0000073671
4.2444039.944403-0.000440445
5.04440310.744403-0.0000316191
4.24440310.6444030.1017906115
2.8444038.944403-0.0000471483
0.1444035.844403-0.0000482385
0.1444035.144403-0.000115464
05.444403-0.0000128659
06.244403-0.0000537135
6.8444036.8444030.3325767712
6.1444036.8444030.4817941532
2.7444035.544403-0.0000388472
8.6444031.6982511022
14.9044038.9376605056
12.6444033.4113730654
8.8444031.28536918
11.044403-0.000000032
7.944403-0.0000278023
8.944403-0.0000572169
5.044403-0.0000372763
5.9444030.1964023707
4.544403-0.0001490375
6.744403-0.0000270704
8.5444031.772013477
7.144403-0.0000093862
5.744403-0.0000000319
LDLA
LA
LD
Morgan
LRT
profile_M1_90h10
3.70E-0210110.132350.14670.62276.43E-033.49E-026.19E-031013.3444032.3444033.70E-021011.61.744403-0.00
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0.371011.51.62E-020.38230.618521.38E-041.01E-026.18E-031013.3444031.8444030.371010.92.4444030.03
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0.38051012.31.57E-020.371310.628541.56E-049.97E-036.02E-031013.3444031.0444030.4421010.23.1444032.18
0.389751012.81.63E-020.375340.624222.65E-041.05E-026.09E-031013.3444030.5444030.46351010.42.944403-0.00
0.3977510136.11E-030.405960.616545.79E-059.94E-036.28E-031013.3444030.3444030.4871010.42.944403-0.00
0.398251012.95.52E-030.405350.61775.18E-059.90E-036.26E-031013.3444030.4444030.5181009.53.844403-0.00
0.398751012.78.11E-030.402630.616196.66E-051.00E-026.29E-031013.3444030.6444030.58551005.87.544403-0.00
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0.4871010.63.48E-020.338810.623373.92E-041.09E-026.09E-031013.3444032.7444030.704251003.210.144403-0.00
0.5181009.54.54E-020.315710.625145.09E-041.13E-026.05E-031013.3444033.8444030.7171001.212.144403-0.00
0.58551005.47.20E-020.266180.623557.47E-041.24E-026.14E-031013.3444037.9444030.7221001.411.944403-0.00
0.64351006.95.10E-020.301990.628963.89E-041.05E-025.96E-031013.3444036.4444030.7311002.410.9444030.56
0.65425-141371.71E-060.408790.623361.55E-099.57E-036.13E-031013.34440300.7351002.910.444403-0.00
0.6631010.51.78E-020.368020.629418.12E-059.16E-035.85E-031013.3444032.8444030.74751003.49.944403-0.00
0.671751009.11.29E-020.380570.629195.04E-058.90E-035.76E-031013.3444034.2444030.74351003.49.944403-0.00
0.6741008.31.34E-020.372360.63394.77E-058.66E-035.63E-031013.3444035.0444030.77151002.610.744403-0.00
0.6821009.12.18E-020.375630.619449.80E-059.24E-035.92E-031013.3444034.2444030.7971002.710.6444030.10
0.690751010.51.55E-020.357370.643626.36E-058.55E-035.55E-031013.3444032.8444030.810251004.48.944403-0.00
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0.73925998.444.35E-020.396760.593962.70E-049.40E-036.00E-031013.34440314.9044038.94
0.740751000.72.89E-020.359220.626561.16E-048.45E-035.51E-031013.34440312.6444033.41
0.74351004.52.52E-020.345970.641839.93E-058.11E-035.33E-031013.3444038.8444031.29
0.77151002.37.32E-020.263810.6236.50E-041.20E-026.15E-031013.34440311.044403-0.00
0.798251005.43.07E-020.339660.627761.77E-049.73E-035.92E-031013.3444037.944403-0.00
0.810251004.46.21E-020.270220.634835.22E-041.11E-025.89E-031013.3444038.944403-0.00
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0.909751006.26.11E-020.278480.6296.37E-041.18E-025.97E-031013.3444037.144403-0.00
0.9511007.65.74E-020.291790.624376.92E-041.22E-026.07E-031013.3444035.744403-0.00
profile_M1_90h10
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LDLA
LA
LD
QTL Profile-Mast-Red-
-
Simulation100 half-sib families (Dairy cattle pedigree)2000
progeny5 chromosomes 100 cM (each)SNP 5000 15 QTL (1QTL-10%, 4QTL-5
%, 10QTL2%)50% of the genetic varianceHeritability 30%
-
Generalized linear modelsPhenotype= Sire-family +
genotypeSoftware
TASSELhttp://www2.maizegenetics.net/index.php?page=bioinformatics/tassel
-
Generalized linear models
Chart2
0.1835
0.2636
3.3594
1.3907
0.8949
0.3712
0.0882
4.0439
0.8869
0.6752
0.5823
0.8031
1.8517
0.5377
0.6115
0.22
1.6107
1.9395
0.619
0.7986
0.7547
0.4278
0.3316
0.18
0.3717
0.634
1.3364
0.9603
1.8086
0.2673
2.3059
0.2027
1.3108
4.3415
0.52
2.4894
1.3029
2.4428
0.0904
0.6761
0.1139
0.7447
0.6525
0.2554
0.2585
2.2808
0.0945
0.3285
0.4672
0.1376
1.1145
0.0274
0.6086
0.4685
0.3832
0.8612
0.5131
0.0484
0.4784
0.6376
1.5405
2.8763
0.003
4.4918
1.8993
0.9302
0.4412
0.2141
0.2422
4.9983
0.5126
1.867
1.3569
0.0364
2.9332
1.8811
0.0761
3.4407
0.539
0.965
0.7968
0.1367
5.276
0.5838
0.0889
2.9957
0.8132
1.6643
6.088
0.5927
1.0552
4.2731
4.4297
4.4438
1.4274
5.735
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3.507
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0.2778
4.4835
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5.5326
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2.9911
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0.1502
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3.787
1.5422
6.4463
3.0693
3.635
0.501
18.2455
2.1251
4.2093
14.7655
1.824
18.6477
1.7942
14.6718
32.1298
4.5349
0.508
9.0343
32.0644
31.6787
5.1224
8.8595
0.6955
11.0301
9.9566
16.0237
5.6114
9.8432
39.6404
12.5848
18.9746
0.544
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3.0306
23.6879
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14.0837
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41.6533
29.5023
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19.0266
106.7306
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35.1584
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4.9472
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2.8997
1.4008
5.5412
9.7033
17.2022
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0.5553
4.5468
6.3909
3.5692
1.2424
3.8961
3.1044
2.3213
1.057
0.895
1.098
0.2042
0.5901
1.2198
0.6945
2.0249
1.6028
1.5551
2.3086
3.0942
1.9218
0.224
0.4076
1.3798
0.4555
1.4062
2.5417
2.0746
3.2549
3.5973
1.5093
1.2301
3.2485
5.6718
1.1778
1.556
0.9168
1.8398
0.7031
0.3696
3.4078
8.1506
0.7028
0.1285
1.4838
0.2904
1.8968
1.3495
2.3725
5.1781
0.9481
1.1718
0.2679
8.1884
3.8764
1.2691
6.3645
0.1586
1.4305
1.0326
0.4524
0.2748
1.9776
5.0127
1.235
0.7182
1.653
0.1442
2.3866
3.463
3.5524
1.0191
1.9888
2.6553
0.9704
0.0646
2.5706
0.5995
0.7454
0.0458
0.0926
1.7003
0.02
0.2658
1.6579
0.5439
0.1251
1.8378
0.4512
1.7886
0.0994
2.3716
0.5947
4.4607
2.5092
1.4008
0.456
0.0824
0.8297
1.1615
5.1376
0.224
0.5261
1.3178
0.411
1.077
0.2504
2.8298
0.0942
0.7863
0.3932
1.1047
0.7532
0.44
0.1333
3.8575
0.5892
0.868
0.8949
0.6765
3.1234
2.9714
1.2476
2.6731
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