Couple of quick things:

• Linkage drag

• Needs to be minimized in the introgression of QTL, especially from exotic species

• How do we do this?

Tolerance

• The ability to maintain yield in the face of high disease/ symptoms– Not necessarily the same as apparent

resistance• In the end that’s what we need!• More difficult to score for than resistance

Costs of 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

Field

Greenhouse

High nutrient low nutrient

Constitutive defense gene expression

Low defence gene induction

How about R-genes?

• Why are R-genes polymorphic within a species anyway?

• 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 pathogen

• 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-

crossing– 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

http://www.i-med.ac.at/phd/neuroscience/lectors/christoph_schwarzer.html

Rpm1 gene

Able to create two completely isogenic lines differing for just Rpm1

Looked at presence/absence of RPM1

• A 9% fitness cost• Is this a common occurrence?• Rps5 has a similar cost (J.Bergelson pers.

com.)

Rpw8 has a cost in absence of pathogen

• Undral et al 2007 Intraspecific Genetic Variations, Fitness Cost and Benefit of RPW8, A Disease Resistance Locus in Arabidopsis thalianaGenetics176, 2317-2333

• In this paper they just compared transgenic and non-transgenic lines

Wild

Typ

e

Tran

sgen

ic e

xpre

ssin

Rpw

8

Disease pressure No Disease

Some of the transformants looked like this

Why might this occur

• Metabolic costs of expressing another gene– Unlikely– ~30,000 genes in Arabidopsis

• Inappropriate activation of R-genes– Possible– See hybrid necrosis and evidence from Rpw8

R-protiens require other host factors for proper folding

Sangster and Q

ueitsch 2005The HS

P90 chaperone

complex, an em

erging force in plant development and

phenotypic plasticity Current O

pinion in Plant B

iology8;86-92

• 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 phenomenon

• 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

Time

Freq

unec

yFr

equn

ecy

Directional selection(selective sweep)

Balancing selection

Tim

e of

sam

plin

g

• Balancing selection implies different alleles are beneficial in different situations

• Can identify “signatures” of balancing selection– If the two alleles are recently diverged there should be

few polymorphisms in the regions surrounding them– If the two alleles have been maintained separately for

a long time there should be lots of polymorphism in the region surrounding them

Sliding window analysis of silent (synonymous and noncoding) sites in RPS5 flanking regions

Tian D et al. PNAS 2002;99:11525-11530

©2002 by National Academy of Sciences

Do not ask me about this graph!Similar study showed similar results for Rpm1: Stahl et al 1999 Nature 400:667-671

• Surely these must be exceptions• >100 RGAs in Arabidopsis, they can’t all have

a yield penalty!– Rps5, Rpw8 and Rpm1 seem to have significant

costs, – 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 paper”

– 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 isn’t

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 yield?