use of breeding populations to detect and use qtl
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Use of breeding populations to detect and use QTL. Jean-Luc Jannink Iowa State University 2006 American Oat Workers Conference Fargo, ND24 July 2006. Breeding Populations. Translation. Experimental Populations. Bi-parental cross. - PowerPoint PPT PresentationTRANSCRIPT
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Use of breeding populations to detect and use QTL
Jean-Luc JanninkIowa State University
2006 American Oat Workers ConferenceFargo, ND 24 July 2006
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TranslationExperimentalPopulations
BreedingPopulations
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NI = 200
0
0.5
1
1.5
2
2.5
1 2 3 4 6 10 20 50Number of Effective Factors
Relative EfficiencyMarkers AlonePheno + Markers
Bi-parental cross
From Schön et al., yield, plant height, and grain moisture
all over here
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Community Effort Needed• The number of “effective factors” influencing a
“highly quantitative” trait (e.g., grain yield): probably >50.
• Number of individuals needed to identify such small-effect QTL: probably ~ 1000.
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http://www.barleycap.org
Total:960 Lines / Year
3000 SNP / Line
Objective: Capitalize on phenotyping in breeding programs
96 Lines
96 Lines
96 Lines
96 Lines
96 Lines
96 Lines
96 Lines
96 Lines
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NI = 800
0
0.5
1
1.5
2
2.5
1 2 3 4 6 10 20 50Number of Effective Factors
Relative EfficiencyMarkers AlonePheno + Markers
Barley CAP
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QTL Detection in Breeding Populations
• P = E + G
• P = E + M + u
€
cov(ui,u j ) = 2θ ijσ u2
•
€
P = Xβ + Mα + Zu + e•
€
ˆ g i = M i ˆ α + ˆ u i•€
u ~ N(0, Aσ u2)
€
ˆ u i = 12
ˆ u s + ˆ u d( )
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Requirement of Linkage Disequilibrium
• A specific typed marker allele always comes together with the same causal QTL allele
• This is Linkage Disequilibrium• Under what conditions does this occur?
€
P = Xβ + Mα + Zu + e• usually
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MutationOriginal Population State
AB
aB
aB
aB aB
ABAB
AB AB
aB
aB
aB aB
ABAB
Ab
A mutation arises
The b allele now always occurs in the presence of the A allele
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Subpopulation structure / admixture
Population 1
B A a
B
aB
a B
Ba
B A
A BA B
Population 2
A b
A b
Ab
bA
b A
b A b
A A b
If the populations come together, the b allele again always occurs in the presence of the A allele
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StructureSpring barley &
2 vs. 6 row
Winter barley
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Analysis Given Structure
• Each individual has a probability of belonging to each subpopulation: Q
• Each subpopulation has its own mean, vk
• But only one effect is associated with each allele,
€
P = Xβ + Qv + Mα + Zu + e•
€
P = Xβ + Mα + Zu + e•
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QTL x E?DryWet
QTL x E x Structure?
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NI = 800
0
0.5
1
1.5
2
2.5
1 2 3 4 6 10 20 50Number of Effective Factors
Relative EfficiencyMarkers AlonePheno + Markers
Barley CAP
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Possible UseMake
Crosses
F2F3
F3F4
F1F2
F4 Spc Plt
Head Row
PLT
ALTYr1
Yr2
Yr3
Yr4
Yr5
MakeCrosses
F2F3
F3F4
F1F2
F4 Spc PltALT
Yr1
Yr2Yr3
GenotypeSelect on m
Increase in NZ
Contributephenotypegenotype
data to THT
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Key Question
• What level of LD exists in the “American Oat Population?”
• To detect causal polymorphisms, they need to be in high LD (r2 > 0.5) with typed polymorphisms.
• If (r2 > 0.5) extends over several cM, we will need fewer markers
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LD in European barley
“There were in total 53 marker pairs with distance < 1 cM, of which 32 had a significant correlation (P < 0.01), while 19 pairs were not significantly correlated (P > 0.01) and thus in LE.”
N.B. r2>0.06 => P < 0.01, whereas r2>0.50 needed…
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Linkage Disequilibrium
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LD in North American Oat
• O’Donoughue et al. 1994 “Relationships among North American Oat Cultivars Based on Restriction Fragment Length Polymorphisms”
• 83 cultivars (both spring and winter)• 48 probes• 205 polymorphic bands
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Extended data from Sorrells
• 56 Probes• 239 Polymorphic bands (alleles)• 28441 allele pairs
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Distribution of r2
1
10
100
1000
10000
100000
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
r2
Number of Allele Pairs
NoStruct9SubPop
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Linkage Disequilibrium
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Extended data from Sorrells
• 56 Probes• 40 Probes with position on KxO (Wight
2003)• 21 Probes with a single position on KxO• 8 Probe pairs with single location on
same linkage group
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LD in North American Oat
0
0.05
0.1
0.15
0.2
0.25
0 0.1 0.2 0.3 0.4 0.5Recombination Frequency
r2
8 Probe Pairs223 Probe Pairs
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Questions for DArT markers
• Likely to be biased toward transcribed / untranscribed genomic regions?
• What minor allele frequencies does the discovery process allow?
• Will they mark only a single location in the hexaploid genome?
• We should probably be able to use the discovery / diversity panel for an LD study
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Conclusion
• I think LD-based MAS has promise– integrated discovery and use of QTL– capitalizes on phenotyping by breeders
• I think we are already setting up the DArT marker discovery process so as to get a first estimate of feasibility in oat.
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LD decay over time