OK Giovanni; we're now getting closer to your research question, which I understand. If you cannot measure fruit yield because of the limitations of the lab environment, presumably you can measure a surrogate for yield (at the phenotypic level) in terms of growth rate (either destructively, automatic phenotyping through imagery or physical measurement of leaf dimensions, shoot extension growth, or similar). That would then allow you to study the impact of the viral disease on growth as a measure of plant fitness (to the disease agent).

At the molecular level, you need to monitor processes associated with growth, of which photosynthesis is an obvious one, or the relative ratio of photosynthesis to respiration, in case the virus response induces increased respiration. Maybe chlorophyll fluorescence characteristics would be useful to consider, though even for these, many genes are involved (see our recent paper Czyczyło-Mysza et al. Molecular Breeding 32:189–210 (2013). If you had to choose a single gene whose expression to monitor (though I would choose a few to monitor fitness), you might just as well put them all in a hat and pull one out blindfold! There is unlikely to be a single gene that will work for your experiments - they will be genotype-dependent, light-dependent, nutrient dependent, maybe tissue-dependent, phenology-dependent and who knows what else!

So, as you have already mentioned photosynthesis and respiration, I would add fluorescence characteristics to your list of options to consider; though still many genes in my view.

I hope that's some help.

Steve

This is a question that can be ansvered with Yes. There are genes that are more related to plant fitness than others. However, there are many! By example, if You move a tropical plant to the arctic, it will die because it dont have genes that build the plant to make it survive the harsh climate. Or it could be under situations of drought, wetness, high temperature, low temperature, light stress, salinity and so on. At a total new environment or a dramatic climatic change the plant need genes that make it survive that environment. Of course most plants (I dont dare to say all!) can survive within a changing climate to some extent. But, the phenotype will change dependent on the growing conditions that will vary between seasons and years. Horticulturist, like me,are optimist and they tend to move plants to grow somewhere they never should have been! The result is often a disaster!.

Thanks Rolf. My question is more specific.

For example, in a quantitative real time-PCR assay, which genes could be considered as markers of plant fitness?

Possibly, genes related to photosynthesis. Photosynthetic efficiency (expression analysis of key genes through qRT-PCR) should be a good indicator whether a plant(s) species or cultivar is adapted well under certain environmental condition(s).

Zakir, any specific suggestion by you?

Giovanni, I think you can look for RbcL, PsbA, PsbD, Lhcb ... genes. Following link might be helpful.

http://www.life.illinois.edu/delucia/Publications/Bilgin%20metagenomic.pdf

and

Planta (2004) 219: 23–31

DOI 10.1007/s00425-003-1201-6

Sorry to be rather negative, but my view is that as Rolf said above there are many genes that are related to fitness, but not in a simple way. Take a simple example with no genes: any trait affects fitness through its interaction with the environment. Under drought conditions, even something as simple and direct as shoot biomass early in the season may be negatively correlated with fitness (e.g. through depletion of soil water, or reduced root:shoot ratio...), while under ample water supply will increase fitness..

I do not think that there is any universal gene marker for fitness. Only for specific responses that may have different effects on fitness depending on the environment or background genotype. Of course any lethal mutation is tightly linked to fitness, or any character affecting seed production, pollination, seed dispersal, health, etc. There are too many genes that affect fitness, so it is impossible to predict overall fitness from the expression of a few genes.

Giovanni,

I guess some etymology would help here: Fitness comes from "fit". But you fit to something or you are fit to something. Which I mean is that the concept of Fitness includes in itself the Environment, so it doesn't really make sense to look for a Fitness gene. Instead, what plant geneticists look at is genes that improve plant fitness to a specific set of conditions (drought, low temperatures, strong winds, high UV radiation, day length....). And even this is a partial approach because very often these conditions do not come alone but coexist or appear close together and the plant reaches a compromise between to extreme solutions, as very often more than a solution is possible depending on the extent and intensity of the problem. So finally what determines Fitness to a specific set of conditions is, first, the complete set of conditions (drought plus heat or drought in winter? Long or short? Mild or intense?), and second a vital strategy that gives the context to these conditions (a pioneer species or a secondary species? stress tolerant, avoidant o the plant escapes the stress?). What shows more Fitness? A pioneer plant that invades a forest gap or the species that comes later and dominates the gap after some years? Both may show a high degree of fitness to their specific role, and the genes involved, to return to your question, will be different.

Just to end as some have mentioned photosynthesis: when late in the seventies of the last century some researchers looked at what had been improved in wheat cultivars after several decades of selection that century, they were surprised by the fact that photosynthesis per unit leaf area had decreased in the more productive cultivars, but total plant photosynthesis had increased as they had more and bigger leaves. Which gene would you look at before and after knowing that?

Giovanni,

To add to the fitness debate, you need to decide clearly your research question before you start considering fitness. What do you mean by fitness? Why do you choose what you choose as a measure of fitness? Are you talking about yield of a crop plant or survival of some ephemeral species in a particular ecosystem, or something else? Once you have clearly identified and stated your research question, then you can start to consider what fitness means in relation to answering that question.

Inevitably, whatever you decide as your research question concerning fitness, there will be a large number of genes associated with that measure of fitness. You only have to look at the diversity of QTLs for a particular trait from experiment to experiment and from genetic background to genetic background to realise that there are many genes involved.

Nevertheless, there is evidence for crop plants that some genes are more generally expressed across a range of environments than others. A recent paper on metabolomics with Peter Langridge's group on wheat (Hill et al. Plant Physiology 162: 1266-1281, 2013) showed that key genes affect the expression of clusters of metabolites in response to a particular environment. So, there are plenty of genes for you to select from there!

However, the "holy grail" of a gene for drought resistance, for example, is unlikely to exist ..... because everyone has a different research question they are trying to answer!

Best of luck searching for your "holy grail"!

Steve

Dear all,

I agree with your consideration. However, as you know, all phenotypic traits result from interactions between genotype and environment, but in scientific experiment the researcher may try to reduce as much as possible the environmental effect if he wants to study gene expression.

Therefore, for example, let me be more specific.

Imagine a number of tomato plants grown in lab under highly controlled conditions. Some plants are inoculated with a virus, and the rest are mock-inoculated. Viral disease is measured as symptom severity and virus titre, for example, and affects several biometric parameters, which can be considered as fitness measures. A number of genes involved in the plant-virus interaction are studied in terms of expression normalized by one or a few reference genes (housekeepers), that notoriously do not vary upon that viral infection. As I mentioned, perhaps one of the more comprehensive fitness measure is yield, since it is the final step of plant cycle. However, in lab yield cannot be obtained, or cannot be properly obtained. Therefore, in order to reinforce data mentioned above, I would like to measure fitness in terms of expression of some key genes. To me, genes related to photosynthesis or respiration could be appropriate, because I guess that in a given controlled environment, one stress condition affecting negatively the fitness might reduce photosinthesis or increase respiration.

This is my rough hypothesis for which I ask your opinion.

OK Giovanni; we're now getting closer to your research question, which I understand. If you cannot measure fruit yield because of the limitations of the lab environment, presumably you can measure a surrogate for yield (at the phenotypic level) in terms of growth rate (either destructively, automatic phenotyping through imagery or physical measurement of leaf dimensions, shoot extension growth, or similar). That would then allow you to study the impact of the viral disease on growth as a measure of plant fitness (to the disease agent).

At the molecular level, you need to monitor processes associated with growth, of which photosynthesis is an obvious one, or the relative ratio of photosynthesis to respiration, in case the virus response induces increased respiration. Maybe chlorophyll fluorescence characteristics would be useful to consider, though even for these, many genes are involved (see our recent paper Czyczyło-Mysza et al. Molecular Breeding 32:189–210 (2013). If you had to choose a single gene whose expression to monitor (though I would choose a few to monitor fitness), you might just as well put them all in a hat and pull one out blindfold! There is unlikely to be a single gene that will work for your experiments - they will be genotype-dependent, light-dependent, nutrient dependent, maybe tissue-dependent, phenology-dependent and who knows what else!

So, as you have already mentioned photosynthesis and respiration, I would add fluorescence characteristics to your list of options to consider; though still many genes in my view.

I hope that's some help.

Steve

All right Steve! Chlorophyll fluorescence characteristics, and photosyntesis:respiration ratio sound good. Excellent suggestions. Many thanks.

You're welcome!

I have followed the discussion with interest. The ideas of Steve is very good, but since You consider yield as the ultimate sign of plant fitness, it could also be an idea to register flower initiation and development (number of flowers per bud?)- if You keep the plants that long! That would give You a possibility to calculate a potential yield. However, as stated by many there are several genes involved also here.

One of the problems of defining fitness is the time scale you are working on, as plants are very adaptive to their environment. Looking at parameters of growth and biochemical mechanisms associated with this would be monitoring immediate responses of fitness to a changed environment (disease challenge, for example).

However, reproductive development is more downstream of fitness, as defined in terms of growth, so inevitably more factors (genes) will be involved in determining fitness for later stages of plant development, so more complexity when deciding what to monitor.

It then comes down to establishing what your research question is. If your research question is the fitness of yield to disease, then in the case of tomato, maybe flower abortion and/or abscission are actual GOOD to improve fitness, as they avoid limited resources being wasted on initiating fruit that will never develop.

It's a complex picture!

Steve

Well the term "fitness" in plant biology is still a controversial because of many reasons/traits. some can be easily estimated while some not!

For example: Biomass which is easy to estimated but the genes/factors that are involve in giving biomass is not that straight forward to estimate! Off course nothing is impossible! Just dig into it :)

good luck