Energy Efficiency and Process Variation Tolerance of 45 nm Bulk and High-k CMOS Devices
Variation in submergence tolerance .
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Transcript of Variation in submergence tolerance .
Variation in submergence tolerance
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http://www.a2mediagroup.com/data/images/news/categories/riceplant.jpg
Linkage mapping (quantitative)
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intolerant tolerant
Fine-mapping
Finding the causative variant
Transgenic test
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Transgenic test
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Coding variantsht
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Fig. 2B
Single-locus:
AA x BB
AB (F1)
AB x AB
AAABBABB
(F2)
25% 50% 25%
AA
ABBA
BB
AA ABBA
BB
“Effect of having a B”
1 locus, incomplete dominance
Two locilong chrom
short chrom
locus 1
locus 2
Two loci
A A
A A
long chrom
short chrom
locus 1
locus 2
Parent A
Two loci
A A
A A
long chrom
short chrom
locus 1
locus 2
Parent AB B
B B
long chrom
short chrom
locus 1
locus 2
Parent B
Two loci
AA/AA x BB/BBA A
A A
long chrom
short chrom
locus 1
locus 2
Parent AB B
B B
long chrom
short chrom
locus 1
locus 2
Parent B
Two loci
AA/AA x BB/BB
AB/AB (F1)
A A
A A
long chrom
short chrom
locus 1
locus 2
Parent AB B
B B
long chrom
short chrom
locus 1
locus 2
Parent B
Two loci
AA/AA x BB/BB
AB/AB (F1)
A A
A A
long chrom
short chrom
locus 1
locus 2
Parent AB B
B B
long chrom
short chrom
locus 1
locus 2
Parent B
Locus1/Locus 2
Two loci
AA/AA x BB/BB
AB/AB (F1)
A A
A A
long chrom
short chrom
locus 1
locus 2
Parent AB B
B B
long chrom
short chrom
locus 1
locus 2
Parent B
Locus1/Locus 2
AB/AB x AB/AB
(F2)16 possibilities
Two loci, incomplete dominance
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or BA
Two loci, incomplete dominance
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or BA
or BA
Two loci, incomplete dominance
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or BA
or BA
Two loci, incomplete dominanceHow many squares of the Punnett square are represented here?
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Effect of B at locus 2
Two loci, incomplete dominance
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Effect of B at locus 2
Two loci, incomplete dominance
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0 0.5 1.0 1.5
Phenotype
Two loci, incomplete dominance
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0 0.5 1.0 1.5
Phenotype
*
What is the genotype?A. AA/AAB. AB/AAC. BB/AAD. AA/AB
Two loci, incomplete dominance
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0 0.5 1.0 1.5
Phenotype
*
What is the genotype?A. AA/ABB. BB/ABC. AB/ABD. AA/BB
Two loci, incomplete dominance
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0 0.5 1.0 1.5
Phenotype
*
How many F2’s have this genotype?A. 1/16B. 2/16C. 3/16D. 4/16
Two loci, incomplete dominance
Two loci, incomplete dominance
Fig. 3.17
Notation is different, trait is qualitative; math is the same.
2-locus interaction
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http://www.projects.roslin.ac.uk/chickmap/organism.html
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Leghorn Junglefowl
Two loci
JJ/JJ x LL/LL
JL/JL (F1)
J J
J J
long chrom
short chrom
locus 1
locus 2
Parent JL L
L L
long chrom
short chrom
locus 1
locus 2
Parent L
Locus1/Locus 2
JL/JL x JL/JL
(F2)16 possibilities
2-locus interaction
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2-locus interaction
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2-locus interaction
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Effect of J at locus 2
2-locus interaction
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Effect of J at locus 2
Effect of variation at locus 2 depends on genotype at locus 1: non-additive
2-locus interaction
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Effect of J at locus 2
Effect of variation at locus 2 depends on genotype at locus 1: non-additive
For example: locus 1 is polymorphism in a transcription factor gene that affects protein binding affinity, locus 2 is in a binding site
2-locus interaction
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Effect of J at locus 2
Locus 2 is epistatic to locus 1: effects of locus 1 are masked in individuals with JJ or JL,LJ at locus 2
Locus 2 follows a dominance model: JJ and JL,LJ have the same phenotype, LL differs
“The dominant allele of locus 2 does the masking”
Other foibles in QTL mapping
Pathogenic yeast
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Pathogenic yeast
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How did YJM145 gain the ability to grow at body temperature?
A model quantitative trait
A model quantitative trait
Lab parent
A model quantitative trait
Lab parent Pathogenic parent
A model quantitative trait
Lab parent Pathogenic parent
100 progeny ≥ pathogenic parent
NO progeny as extreme as diploid hybrid
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NO progeny as extreme as diploid hybrid
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Lab parent Pathogenic parent
NO progeny as extreme as diploid hybrid
Diploid hybrid
Did the mapping…
Significant linkage to yeast chrom XIV and chrom XVI.
Did the fine-mapping…
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Did the fine-mapping…
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Which gene is causative?
Tested in hybrid diploids
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Lab
Pat
hoge
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Lab
Pat
hoge
nic
Tested in hybrid diploids
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Lab
Pat
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Lab
Pat
hoge
nic
Tested in hybrid diploids
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Lab
Pat
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Lab
Pat
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Tested in hybrid diploids
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Different in sequence
Lab
Pat
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Lab
Pat
hoge
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One mutant gene…
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From pathogenic strain
One mutant gene…
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From pathogenic strain
From lab strain
One mutant gene…
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From pathogenic strain
From lab strain
So diploid with this gene from the pathogenic strain grows BETTER at high T.
Two mutant genes…
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From pathogenic strain
From lab strain
Two mutant genes…
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From pathogenic strain
From lab strain
Again, diploid with this gene from the pathogenic strain grows BETTER at high T.
Three mutant genes
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From lab strain
Diploid with this gene from the pathogenic strain grows WORSE at high T!
From pathogenic strain
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Three mutant genes
From pathogenic strainFrom pathogenic strain
From pathogenic strain
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Three mutant genes
From pathogenic strainFrom pathogenic strain
From pathogenic strain
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Three mutant genes
From pathogenic strainFrom pathogenic strain
From pathogenic strain
Alleles from the same strain at
different genes/loci can have different
effects.
No common coding alleles across strains
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No common coding alleles across strains
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And no expression differences of >3-fold…
Three mutant genes in same “locus”
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Three mutant genes in same “locus”
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Three mutant genes
So why did 0/900 haploid progeny have a phenotype as extreme as the diploid
hybrid?
Lab parent Pathogenic parent
NO progeny as extreme as diploid hybrid
Diploid hybrid
Lab parent Pathogenic parent
NO progeny as extreme as diploid hybrid
Diploid hybrid
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Linked mutations of opposite effect
Path
Linked mutations of opposite effect
Path
Lab
Linked mutations of opposite effect
Path
Lab
Very unlikely
“Multiple linked loci”