variation in submergence tolerance
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Variation in submergence tolerance
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http://www.a2mediagroup.com/data/images/news/categories/riceplant.jpg
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Linkage mapping (quantitative)
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intolerant tolerant
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Fine-mapping
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Finding the causative variant
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Transgenic test
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Transgenic test
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Coding variantsht
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Fig. 2B
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Single-locus:
AA x BB
AB (F1)
AB x AB
AAABBABB
(F2)
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25% 50% 25%
AA
ABBA
BB
AA ABBA
BB
“Effect of having a B”
1 locus, incomplete dominance
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Two locilong chrom
short chrom
locus 1
locus 2
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Two loci
A A
A A
long chrom
short chrom
locus 1
locus 2
Parent A
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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
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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
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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
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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
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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
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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
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Two loci, incomplete dominance
Fig. 3.17
Notation is different, trait is qualitative; math is the same.
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2-locus interaction
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http://www.projects.roslin.ac.uk/chickmap/organism.html
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Leghorn Junglefowl
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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
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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
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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
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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
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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”
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Other foibles in QTL mapping
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Pathogenic yeast
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Pathogenic yeast
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How did YJM145 gain the ability to grow at body temperature?
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A model quantitative trait
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A model quantitative trait
Lab parent
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A model quantitative trait
Lab parent Pathogenic parent
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A model quantitative trait
Lab parent Pathogenic parent
100 progeny ≥ pathogenic parent
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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
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Did the mapping…
Significant linkage to yeast chrom XIV and chrom XVI.
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Did the fine-mapping…
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Did the fine-mapping…
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Which gene is causative?
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Tested in hybrid diploids
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Lab
Pat
hoge
nic
Lab
Pat
hoge
nic
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Tested in hybrid diploids
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Lab
Pat
hoge
nic
Lab
Pat
hoge
nic
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Tested in hybrid diploids
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Lab
Pat
hoge
nic
Lab
Pat
hoge
nic
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Tested in hybrid diploids
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Different in sequence
Lab
Pat
hoge
nic
Lab
Pat
hoge
nic
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One mutant gene…
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From pathogenic strain
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One mutant gene…
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From pathogenic strain
From lab strain
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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.
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Two mutant genes…
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From pathogenic strain
From lab strain
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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.
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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.
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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…
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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?
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Lab parent Pathogenic parent
NO progeny as extreme as diploid hybrid
Diploid hybrid
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Lab parent Pathogenic parent
NO progeny as extreme as diploid hybrid
Diploid hybrid
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Linked mutations of opposite effect
Path
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Linked mutations of opposite effect
Path
Lab
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Linked mutations of opposite effect
Path
Lab
Very unlikely
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“Multiple linked loci”