Sliding window analysis of silent (synonymous and noncoding) sites in RPS5 flanking regions. Window size is 250 silent sites with a 25-site increment. Abscissa is base position relative to DJ in aligned sequences. (A) Observed nucleotide diversity between RPS5+ and RPS5− alleles and average divergence between A. thaliana and A. lyrata sequences, with Jukes-Cantor correction (39). (B) Results of a coalescent model with selection and recombination (3, 10). For each sliding window, plotted is the ratio of average pairwise difference between allelic classes (observed or predicted under balancing selection) to average pairwise difference expected under the standard neutral model (see Materials and Methods for details). Results for two scaled recombination rates are shown for balancing selection (BS) predictions: ρ = 6 × 10−4, our best estimate of this parameter, and ρ = 6 × 10−5, a 10-fold lower rate. Both expected curves assume an equilibrium frequency of the two allelic classes, P = 0.5; The scaled mutation rate (β) between RPS5+ and RPS5− is fitted for each curve to bring the predictions close to data at the site under selection (assumed to be the DJ).
2-1-10.ppt - PowerPoint Presentation
Couple of quick things:
• Linkage drag
• Needs to be minimized in the introgression of
QTL, especially from exotic species
• How do we do this?
• The ability to maintain yield in the face of
high disease/ symptoms
– Not necessarily the same as apparent
• In the end that’s what we need!
• More difficult to score for than resistance
• Why is defence inducible?
– Why not induce basal defences constitutively?
Induced resistance can be costly
• costly to over do it
– Analogous to autoimmune disease
• Costly not to do anything though
Fitness Costs of Mutations Affecting the Systemic
Acquired Resistance Pathway in Arabidopsis thaliana
Heidel et al 2004 Genetics 168, 2197-2206
High nutrient low nutrient
How about R-genes?
• Why are R-genes polymorphic within a
• Avr genes are polymorphic
• But why doesn’t each plant keep a full
complement of R-genes?
– Presumed advantage in the presence of the
corresponding Avr gene
– How about in its absence?
Maintaining R-genes may be costly
• In the absence of the corresponding
• Tian, D., Traw, M.B., Chen, J.Q., Kreitman, M., and Bergelson, J.
(2003). Fitness costs of R-gene-mediated resistance in Arabidopsis
thaliana. Nature 423, 74-77.
How to compare plants
with/without a resistance gene
• Need isogenic lines
• Could create NILs by conventional back-
– But the plants would differ for a large locus
containing many genes
– Difficult to attribute change in phenotype to
any single gene
How to compare plants
with/without a resistance gene
• Can transform a susceptible line.
– But the insertion of a transgene may itself
have an effect
Used a Cre/lox system
Able to create two completely isogenic lines differing for just Rpm1
• A 9% fitness cost
• Is this a common occurrence?
• Rps5 has a similar cost (J.Bergelson pers.
Rpw8 has a cost in absence of
• Undral et al 2007 Intraspecific Genetic Variations, Fitness Cost
and Benefit of RPW8, A Disease Resistance Locus in Arabidopsis
• In this paper they just compared transgenic and non-transgenic
Disease pressure No Disease
Why might this occur
• Metabolic costs of expressing another
– ~30,000 genes in Arabidopsis
• Inappropriate activation of R-genes
– See hybrid necrosis and evidence from Rpw8
R-protiens require other host
factors for proper folding
• In hybrid necrosis it appears that the
introduction of functional R-genes into a
novel genetic background may lead to
mis-regulation of their activity.
• Maybe this type of thing occurs often with
the R genes in their natural background
but at much lower levels.
Other evidence for this
• There are two reasons we might see
polymorphism in a natural population
– One allele might be rising in a pop and the
other falling and we have caught the
population “in transition”
– Or it’s a stable situation-balancing selection
• Balancing selection implies different
alleles are beneficial in different situations
• Can identify “signatures” of balancing
– If the two alleles are recently diverged there
should be few polymorphisms in the regions
– If the two alleles have been maintained
separately for a long time there should be lots
of polymorphism in the region surrounding
• Surely these must be exceptions
• >100 RGAs in Arabidopsis, they can’t all
have a yield penalty!
– Rps5, Rpw8 and Rpm1 seem to have
– but other studies on RPS2 and RPP5 do not
give similar results. No fitness cost of the R-
genes in absence of disease
• Korves and Bergelson2004 A Novel Cost of R Gene Resistance in the
Presence of Disease Am Nat 163: 489–504
• Caveat , it’s a little more complicated than this!
Bergelson pers. com.
• “the key here is that the costs are required for
long-lived polymorphisms. Rpm1, for example,
looks to be an ancient balanced polymorphism
and therefore we expect costs.”
• “There are lots of R genes that are not balanced
polymorphisms, but instead have relatively
young alleles. You can see a range of
evolutionary trees by looking at our Plant Cell
– Bakkera et al 2006 A Genome-Wide Survey of R Gene Polymorphisms in Arabidopsis[The
Plant Cell 18:1803-1818 (2006)
Are all R-genes polymorphic anyway?
• If there is no fitness cost they would likely go to
fixation in the population
• If they are fixed, how would we detect them?
• Possibly many (most?) RGAs are like this, I
don’t think it’s really been investigated.
• Would need the genomic sequence of multiple
genomes of different lines.
• Difficult to investigate as it’s tricky to tell what is
functionally important polymorphism and what
Costs of Quantitative Risistance
• Genetics of Brassica rapa. 3. Costs of Disease
Resistance to Three Fungal Pathogens Mitchell-Olds
and Bradley 1996 Evolution, 50, 1859-1865
• Recurrently selected for quantitative levels
of disease Recurrently selected for
quantitative levels of disease resistance
• Again, there are several other studies that
do not show this effect.
• This is an area requiring further work
• When you select for higher yield might you
be creating lines with lower resistance?
• When you select for increased resistance
might you be creating lines with lower