Variation in submergence Linkage mapping (quantitative) tolerance
intolerant tolerant
http://www.a2mediagroup.com/data/images/news/categories/riceplant.jpg
Fine-mapping Finding the causative variant
Transgenic test Transgenic test GIF . k/Haseloff/SITEGRAPHICS/Agrotrans u cam.ac. . lantsci p http://www.
1 Coding variants Single-locus: g p j . e n
e AA x BB g R T F C / 0 1 3 B B / 9 0 1 9 9 s f (F1) d ~ / AB k u . c a . h t a r t s .
s AB x AB e g a p e m o h / / : p t t h AA AB (F2) BA BB
Fig. 2B
1 locus, incomplete dominance
long chrom Two loci
AB short chrom BA
locus 2 AA BB locus 1
“Effect of having a B” 25% 50% 25% AA AB BB BA
long chrom Two loci long chrom Two loci long chrom
short chrom short chrom short chrom
Parent A A A Parent A A A Parent B B B A A A A B B
locus 2 locus 2 locus 2 locus 1 locus 1 locus 1
2 long chrom Two loci long chrom long chrom Two loci long chrom
short chrom short chrom short chrom short chrom
Parent A A A AA/AA x BB/BB Parent B B B Parent A A A AA/AA x BB/BB Parent B B B A A B B A A B B
locus 2 locus 2 locus 2 locus 2 locus 1 locus 1 locus 1 locus 1 AB/AB (F1)
long chrom Two loci long chrom long chrom Two loci long chrom
short chrom short chrom short chrom short chrom
Parent A A A AA/AA x BB/BB Parent B B B Parent A A A AA/AA x BB/BB Parent B B B A A B B A A B B
locus 2 locus 2 locus 2 locus 2 locus 1 locus 1 locus 1 locus 1 AB/AB (F1) AB/AB (F1) Locus1/Locus 2 Locus1/Locus 2 AB/AB x AB/AB
16 possibilities (F2)
Two loci, incomplete dominance Two loci, incomplete dominance
or BA
3 Two loci, incomplete dominance Two loci, incomplete dominance
How many squares of the Punnett square are represented here?
or BA or BA
or BA or BA
Two loci, incomplete dominance Two loci, incomplete dominance
Effect of B at locus 2
Effect of B at locus 2
Two loci, incomplete dominance Two loci, incomplete dominance
*
0 0.5 1.0 1.5 0 0.5 1.0 1.5 Phenotype What is the genotype? Phenotype A. AA/AA B. AB/AA C. BB/AA D. AA/AB
4 Two loci, incomplete dominance Two loci, incomplete dominance * *
0 0.5 1.0 1.5 0 0.5 1.0 1.5 What is the genotype? Phenotype How many F2’s have this genotype? Phenotype A. AA/AB A. 1/16 B. BB/AB B. 2/16 C. AB/AB C. 3/16 D. AA/BB D. 4/16
Two loci, incomplete dominance 2-locus interaction
Leghorn Junglefowl
Notation is different, trait is qualitative; math is the same.
http://www.projects.roslin.ac.uk/chickmap/organism.html
Fig. 3.17
long chrom Two loci long chrom 2-locus interaction
short chrom short chrom
Parent J J J JJ/JJ x LL/LL Parent L L L J J L L
locus 2 locus 2 locus 1 locus 1 JL/JL (F1) Locus1/Locus 2 JL/JL x JL/JL
16 possibilities (F2)
5 2-locus interaction 2-locus interaction
Effect of J at locus 2 Effect of J at locus 2
2-locus interaction 2-locus interaction
For example: locus 1 is polymorphism in a transcription factor gene that affects protein binding affinity, locus 2 is in a binding site
Effect Effect of J at of J at locus 2 locus 2
Effect of variation at locus 2 depends on genotype at Effect of variation at locus 2 depends on genotype at locus 1: non-additive locus 1: non-additive
2-locus interaction
Effect of J at locus 2 Other foibles in QTL mapping
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”
6 Pathogenic yeast Pathogenic yeast
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 A model quantitative trait
100 progeny ≥ pathogenic parent
Lab parent Pathogenic parent Lab parent Pathogenic parent
7 NO progeny as extreme as diploid hybrid NO progeny as extreme as diploid hybrid
NO progeny as extreme as diploid hybrid Did the mapping…
Significant linkage to yeast chrom XIV and chrom XVI.
Lab parent Pathogenic parent Diploid hybrid
Did the fine-mapping… Did the fine-mapping…
Which gene is causative?
8 Tested in hybrid diploids Tested in hybrid diploids Pathogenic Pathogenic Lab Pathogenic Lab Lab Pathogenic Lab
Tested in hybrid diploids Tested in hybrid diploids Pathogenic Pathogenic Lab Pathogenic Lab Different Lab Pathogenic Lab in sequence
One mutant gene… One mutant gene…
From pathogenic strain From pathogenic strain
From lab strain
9 One mutant gene… Two mutant genes…
From pathogenic strain From pathogenic strain
So diploid with this gene from the pathogenic From lab strain strain grows BETTER at From lab strain high T.
Two mutant genes… Three mutant genes
From lab strain From pathogenic strain
Again, diploid with this From pathogenic strain Diploid with this gene gene from the from the pathogenic From lab strain pathogenic strain grows strain grows WORSE BETTER at high T. at high T!
Three mutant genes Three mutant genes
From pathogenic strain From pathogenic strain
From pathogenic strain From pathogenic strain From pathogenic strain From pathogenic strain
10 No common coding alleles across Three mutant genes
From pathogenic strain strains
From pathogenic strain From pathogenic strain
Alleles from the same strain at different genes/loci can have different effects.
No common coding alleles across Three mutant genes in same “locus” strains
And no expression differences of >3-fold…
Three mutant genes in same “locus” Three mutant genes
So why did 0/900 haploid progeny have a phenotype as extreme as the diploid hybrid?
11 NO progeny as extreme as diploid hybrid NO progeny as extreme as diploid hybrid
Lab parent Pathogenic parent Diploid hybrid Lab parent Pathogenic parent Diploid hybrid
Linked mutations of opposite effect Linked mutations of opposite effect
Path Path Lab
Linked mutations of opposite effect
Path Lab
Very unlikely “Multiple linked loci”
12