A Review of Identification of Pathotypes in the Daylily Rust Pathogen with an Eye Toward Breeding for Disease Resistance
Brian Reeder
Overview of Paper
In the paper entitled Identification
of Pathotypes in the Daylily Rust Pathogen Puccinia
hemerocallidis - James W. Buck (Department of Plant Pathology,
University of Georgia, Griffin, GA 30223, USA - Received: January 23, 2013;
accepted: May 16, 2013. - Journal
of Phytopathology 161 (2013) 784–790 - 2013), the abstract at the beginning of
the paper states...
"Daylily rust, caused by
Puccinia hemerocallidis, has been present in the United States since 2000. In
2003, inoculations with a single isolate of P. hemerocallidis identified
daylily cultivars with high levels of resistance to the fungus. The present
study was carried out to determine if pathotypes of P. hemerocallidis are
present in the southeastern United States. Sixteen isolates of P.
hemerocallidis were each inoculated onto leaf segments from 19 daylily
cultivars and the resulting disease phenotype assessed. A significant effect of
rust isolate on host reaction phenotype was observed for nine of the 19 daylily
cultivars. Five of the nine cultivars displayed reaction phenotypes with
different isolates of P. hemerocallidis that included at least one susceptible
or moderately susceptible and also resistant phenotypes. These results indicate
that different pathotypes of the fungus are present in the southeast United
States. Daylily hybridizers interested in screening for host resistance to P.
hemerocallidis will need to include multiple isolates of the fungus to allow for
this host specialization."
We can see from this statement that we now have good
evidence that there is more than one strain of rust in the US, but there also seems to be more than one gene for resistance to the potential
strains of rust pathogen studied in the paper.
The paper gives an overview of the methods used. The
research is conducted in greenhouses for quarantine of each isolate. Each isolate may or may not be a unique strain of rust. I have received no
data showing any gene typing of each isolate. To my knowledge at this time, the
isolates are determined by unique accession. That is, each isolate came from a
different garden, so that there were 16 accessions from sixteen Georgia gardens
in the study. To the best of my knowledge at this time, all evidence of strain
differences in rust accessions is based on the reactions of the host materials.
So at this time I would stress that the most we can know from the paper is that
it seems highly that there are at least two different strains of rust amongst
the 16 isolates, though there could be more than two.
The same can be said for any hypothesis of ‘resistance
genes’ based on this paper - there seems to be the indication of variation in
resistance amongst the nineteen cultivars used in the research project. Of
those nineteen, nine show different responses to the 16 isolates and of those
nine, six were observed to have a wider divergence in rust presentation with
reactions that were both resistant and susceptible, depending upon the isolate.
As the most common type of apparent resistance variation is expressed as one
rating up or down (i.e., HR to R or R to MR or MR to MS), those cultivars that
show a wider jump between rating variations (i.e., R to S) are notable and may
indicate actual strain differences in the rust pathogen as well as variable
resistance/susceptibility genes in the host (daylily plant). However, as
breeders, we may be more interested in those cultivars that showed the highest
resistance to every isolate, as these may represent individuals with more than
one resistance gene or with a resistance gene offering protection against more
than one rust strain. Both instances could be useful in breeding for
resistance.
These quotes of interest caught my eye in the paper’s Discussion section.
I will quote each here and offer a bit of commentary.
“In conclusion, the present study clearly
shows that pathotypes of P. hemerocallidis that differ in virulence to daylily
cultivars are present in the south east United States. “
This is accurate. We can now make a fairly good case for
there being more than one strain of rust. Further work may reveal much more
about this, if any of the research being done is published or made available to
the hobby in some form.
“The number of resistance genes to P. hemerocallidis present in
Hemerocallis sp. is unknown. Diploid and tetraploid cultivars, with dormant to
evergreen growth habits, were included in this study with no apparent
differences in susceptibility observed. The chrysanthemum – Puccinia horiana
pathosystem is thought to contain at least seven resistance genes (De Backer et
al. 2011). Incorporation of disease resistance into new daylily cultivars would
be a valuable tool for reducing the impact of daylily rust on the ornamental
industry… Development of DNA markers that can detect resistance in diploid and
tetraploid Hemerocallis germplasm could greatly facilitate current breeding
efforts… Daylily hybridizers interested in producing new cultivars resistant to
P. hemerocallidis will need to include multiple isolates of the rust fungus to
allow for this host specialization.”
This well surmises where the hobbyist breeder with an
interest in increasing rust resistance in their gene pool now finds themselves.
We can be relatively certain that there is more than one strain of rust in the
US. We know that there are resistance genes to rust pathogens in other species.
We know that such genetic resistance can be vertical (single dominant major
genes) or horizontal (multiple genes combined).
We have seen fourteen years of data, both scientific
research and anecdotal observations, which allows us to surmise that there are
genes for resistance in the daylily gene pool and we can make use of any such
genes in our own field selection programs for rust resistance. Identification
of resistance/susceptibility genes with laboratory methods is not currently
available to the hobbyist breeder. There is no way to know if such testing will
ever be made available or if it will be kept as a proprietary intellectual property.
In the mean time, the hobbyist simply needs to do what we have always done, and
breed best to best using what data we can find, what research is made available
and our own observations.
Discussion of Practical Applications
So how do we hobbyist breeders apply the information gained
through Dr. Buck’s paper? What is actually applicable to us? For me, the most
important take-away is something I had previously taken for granted anyhow -
there is not just one ‘rust’ pathogen. We will
generally note variations in response in any given cultivar based potentially
upon both environmental factors and/or strain interactions. Of special interest
are those cultivars that show high resistance in many locations and over many
years. It is possible that, if multiple genes for resistance occur in the
daylily (which seems likely), then there are individuals that, quite by chance,
already have more than one gene for resistance combined into their genotype.
Such individuals would be highly useful in any effort to breed for resistance.
Even if a new, more virulent strain of pathogen arises that defeats the
resistance of any of these long term resistant individuals, they are still
useful breeders for the resistance they convey to other strains of the
pathogen. In short, such cultivars may be useful for a gene-pyramiding project.
Joan Senior
Discussion of Most Resistant Cultivars
For brevity, in considering the cultivars in the study, I
will focus on those six cultivars that showed the highest and most consistent
resistance with no susceptibility ratings in Dr. Buck’s paper - Hush
Little Baby, Joan Senior, Prairie Blue Eyes, Going Bananas, Stella De Oro and
Mardi Gras Parade.
It is by chance that I grow and have grown all six of these
cultivars for a long period of time, some as long as thirty + years. It is also
by chance that I had identified each of these cultivars as showing strong
resistance to rust in my own field observations and so have been using them in
breeding for several years already. I am already into the second generation
with some of these cultivar’s descendants and I am seeing, what suggests to me,
heritability of that high resistance. I believe any of these cultivars can
offer a base upon which to add more resistance genes through outcrossing to
other cultivars that also show high resistance. It is a place to start.
Now I know the arguments. These are all plain, old, cheap
cultivars, so why would anyone want to use them? Stella De Oro, after all, is
universally disparaged and seen as a near blight by refined daylily personages.
However, my own breeding tests show that ideas of “old” or “plain” are more in
the mind of the person thinking the thought. By combining modern faces and
advanced phenotypes onto these older cultivars, new advances can be seen that
were not possible back in the day when the cultivars were being
bred from. By dipping the best of now back into the best of before,
advances are possible and this also allows us to keep identifying potentially
resistant new daylilies to make intensified gene combinations by breeding them back onto older, more
proven cultivars. Both advanced faces and plant
traits can be selected for in one program, after all.
Stella De Oro
Uses in Breeding Programs and Methods
We would typically suggest that individuals showing broad
resistance, much as the six I detailed above, might have ‘vertical’ resistance,
while a plant showing less complete resistance may show ‘horizontal’
resistance, but things may not always be so cut and dry. There can be instances
where vertical resistance may give resistance to only one specific strain, or
there may be instances where a single gene infers resistance to multiple
strains. Conversely, horizontal resistance, being quantitative, can fall anywhere
on a spectrum, depending on the concentration of genes in any given individual.
In instances where many resistance genes are combined into one individual, we
may see resistance to multiple strains. In some instances, this can be
perceived as ‘vertical’ resistance, especially where the resistance is very
complete.
Gene Pyramiding is a concept in genomics that involves
stacking multiple genes for resistance into one genome. While pyramiding is in
many ways similar to the concept of horizontal resistance, in that there are
multiple genes concentrating greater resistance, the difference is that in
pyramiding we are making a conscious effort to add as many resistance factors
as we can, possibly also tolerance and slow progression of sporulation traits,
into one individual to increase field performance against the rust pathogen(s).
Some might suggest that a path would be to inbreed each of
these six cultivars from the research paper and to thus concentrate their own
resistance genes into homozygous lines, and this would certainly be interesting
from a research standpoint, but from a hobby standpoint, I think this is one of
our least productive routes for many reasons.
Another potential route is to cross the six cultivars from
the paper to create lines of concentrated rust resistance. While this is
feasible, and certainly could be interesting, I think it has two major
drawbacks. The first is that none of the six cultivars offer anything terribly
modern from the point of view of the flower. The second is that we do not know
how many resistance genes may or may not be contained within all six of those
cultivars. So strictly relying on those six cultivars, and only those six
cultivars, is much too limiting for most modern breeding programs.
I believe the most productive route is for each breeder who
has the interest to use some of these six cultivars and to combine them with their own favorite cultivars,
seedlings, and interests in form, color or pattern, especially those alternate
cultivars that have also been shown to have or are known to have some
resistance themselves. In other words, these six cultivars would possibly have
applications both in pyramiding with other resistant lines as well as being
useful in salvage projects to bring desired flower traits into more resistant
genetic backgrounds.
First, let us look at using any of these cultivars in
salvage projects. I believe that it is this type of breeding where the most
interest is likely to be found in the daylily world, as a number of remarkable
and popular cultivars show various levels of susceptibility.
The desire to salvage the good traits into a more desirable background setting
is standard fair in ornamental plant breeding and daylily breeders have been
doing this type of thing as long as daylilies have been bred.
In short, a salvage project is a cross of highly resistant x
less resistant/more susceptible. This cross is done to bring the expression of
resistance together with desired flower traits in the F1 and/or later
generations. Generally, a field test of F1 offspring will reveal some with
higher resistance. Select toward resistance where possible. The F1 can then be
interbred, backcrossed to the more resistant parent or outcrossed to another
resistant cultivar or seedling. Selection is toward resistance in at least the
second generation (F2, Bc1, etc.), if not the first (F1). From this technique,
plants of usable resistance can be secured for further breeding work and in
some instances, resistance may be increased even in the F1. Salvage projects
may become a very important aspect of daylily breeding for spreading resistance
genes further through the gene pool, but it is not the most important method
for increasing resistance within individuals.
The most important form of breeding for increasing
resistance genes within given individuals is to stack multiple genes for
resistance together through the pyramiding of genes. We do this by breeding
resistant individuals carrying different genes (or suspected different genes,
in the hobby setting) together. We are seeking to combine the different genes
from each parent into the offspring for broader-based, multigenic resistance to the given
pathogen in future generations. We may expect to see some progress in the F1,
selecting those that field trial with the most resistance or we may see little
to no increase in the F1 and seek more expression in the F2 and later
generations. Much will depend on the nature of the genes involved.
Regardless, we have many options once we have our F1. In my
own situation, I prefer to field trial such seedlings for resistance levels. I
then select for acceptable expressions of field resistance. I may repeat this
for one or more years before I ever begin breeding. Once I begin breeding such
F1 plants, I might go in any of many directions. I can backcross to either
parent to concentrate that particular form of resistance, making a BC1
generation. This can often be a wise thing to do in both directions. Another
thing I can do is to interbreed the F1 to make an F2. This is the best way to
find the new recombination of both forms of rust resistance in one plant.
Whether we need to breed to full homozygosity for any/all of the resistance genes
will depend on their penetrance and their nature (dominant/recessive). Finally,
the F1 can be outcrossed to other lines, cultivars or seedlings, in an effort
to combine the resistance of both parents with another type of resistance. This
later example tends to only work well when dealing with highly penetrant
dominant genes, typically.
As you can see, there are many directions and
possibilities for our F1 seedlings. Our main aim is to combine the genes for
resistance from both parents into the offspring. Once we have a plant or plants
(whether as an F1 expression of dominant genes or in the F2) that show the
targeted combination of traits we are looking for, we can then move forward. We
may choose to work within the line to concentrate traits or we may seek to
further build our pyramid by going out to a different lineage, also showing
resistance, in the hopes of adding yet another genetically distinct set of
genes for resistance.
Pyramiding of genes can go on indefinitely, so long as there
are new genes to add. When an older, proven cultivar seems to ‘fail’, it may
well be that it has encountered a new strain of rust that it does not have
resistance for, so such cultivars should not be discarded, but used in
pyramiding with new resistance genes to the new strain of rust to keep building
a broad base of genetic resistance. The cultivar reacting to a new strain of
rust that has been resistant for many years, through many tests and in many
locations in the past has not suddenly ‘lost’ its resistance. It still has
resistance to the rust pathogen strains it was previously tested against and
those genes can and should still be put to use.
Over time, we can assume that
any and all genetic resistance will fail as new strains of the pathogen emerge.
The speed at which this will occur is anyone’s guess, but with time, that
failure is inevitable. Rather than see this as a problem, through pyramiding of
resistance genes, we can continue to build on past successes and resistant
bloodlines. In this way, we incorporate a broader range of resistance so that
plants can safely overcome the challenges of many strains of rust.
An excellent
place to start will be to make some use of those cultivars that have been
tested in research projects (such as that detailed in the Buck paper) and field
trials, as well as those with a number of anecdotal reports and personal
experiences. Some of the six cultivars with the highest scores in the Buck
paper should find a place in any and all diploid breeding programs. As well,
tetraploid conversions exist of several of these six cultivars.
We will look
more in-depth at some of these six cultivars in a coming blog post.
Hush Little Baby
