There was correlation in rice study but it seems not very tight. However, if you have a lot of different species, there will be more tight correlation between genetic diversity and secondary metabolites, which usually called "Chemotaxonomy".

If there indeed is a correlation between distribution diversity and biochemical diversity then one also needs to consider their dispersal history that could have lead to such a correlation, isn't it? So far as studying the expressibility of the gene goes, I am not sure what you intending to address exactly. If certain parameters of the habitat are influencing the gene's expression it would be interesting to elucidate how these are modifying gene expression, either directly or indirectly.

Dear Paromik,

As others have commented there is often a link with secondary metabolite accumulation and diversity within populations. There are numerous chemical diversity studies that show clearly that the type of secondary metabolites that accumulate in populations can act as definitive markers of plant populations. Often however is is not the levels of individual chemicals but rather diffentiation within the diversity of the chemicals themselves. In particular secondary modifications of the base aglycone with sugars, acyl groups and even more complex chemical moieties are found to be the basis for the chemical diversity observed and used that in turn are useful as markers.

Without doubt there will also be level differences in the key metabolite classes and these might be considered to reflect the plants response to the differing environments that make up the niches the population is found to occupy. However a degree of caution should be exercised as it is likely that these levels may also reflect seasonal differences in environmental conditions that should be figured into any comparative analysis.

Linking the patterns of gene expression to levels of secondary metabolites is a reasonable thing to look at. Again caution should be exercised as it is not always the case that the levels of metabolite that accumulate directly correlate to the levels of steady state transcript found for key genes that act in the synthesis of the metabolites in question. Prior knowledge or evidence should always be sought that the accumulation of particular metabolites are transcriptionally controlled. More often than we like to admit the link between transcript accumulation and the explicit assumption that this also links to protein and thefore protein activity levels and metabolite levels does not bear up to scrutiny. Also it is important to remember that we work with dynamic systems with the time frames for alteration in pools of lmetabolites in the millisecond to second time frame, while transcriptional regulation acts in minutes at the short end of the time frame to days or even weeks. The significance of this is that in most analyses we might conduct we only ever look at a snap shot in time and that correlations of transcript abundance to metabolite levels may be misleading at best.

In my previous work looking at the regulation of secondary metabolites that contribute to flower colour we can certainly use transcript abundance for key genes encoding either transcription factors or structural genes to study diffentiation accumulation patterns in various chemo/ecotypes. However if you are interested in tool for classification of population diversity I would opt for more stable metrics such as QTLs or SNP based markers that reflect the chemical and population diversity but are not as prone to change in the volatile manner that transcripts enevitably will.

I hope that you find this useful

Regards

Chris

See if there is secondary metabolite being produced in one genotype at a very high rate than other i.e. the expression levels are different, that is never reflected by the genetic diversity...simply because genetic diversity will only reflect which base pair sequence is sitting there in one genotype or absent in other. So i really feel that you can never get any kind of reliable correlation between genetic diversity data and your any biochemical or other such assay, because again genetic diversity represents the nucleotide differences rather than the expression levels. Secondly as i quoted earlier in one of your query that when we are talking about genetic diversity we are mostly talking about any differences among the germplasm irrespect of whether it is coding region or non-coding regions of DNA (especially in eukaryotes). But the correlation in terms of association among certain markers and some traits can be found by concept of association mapping in all species and nested association mapping in only plants and some animals, because it exploits the recombination events which have occured over years in a species (more in organism with faster rate of reproduction) and provide us association among only those markers and traits that are really linked tightly. So these correlation/associations are only reliable. So, never link expression rate/yield of metabolites with correlations and gentic diversity.

The question is beautifully explicated and interesting, but still the regulation is inquired in two mechanistically farthest possible level of gene expression machinery. The explanation lies in the answers of following set of questions: What is known about the genetic diversity of population at gene level or nucleotide level?; What is known about the metabolism of secondary metabolites and changes in metabolites, enzyme activities in the pathways?; Are there any known condition leading to changes in the transcripts corresponding to secondary metabolic pathway and linked primary metabolic pathways in the genetically diverse populations?; Are there any changes in transcript levels of the above said genes correspond to enzyme quantity?; Are the changes in the transcript correspond to change in the corresponding enzyme quantity with or without the change in enzyme quantity?; We must design the experiments in order to look for the changes where pathway through the flux is fluctuating?; And then look for the cause and effect in the context of biochemistry? And, I think outstanding knowledge of statistics is needed to draw the metabolic network or conclusions.

I am suggesting for following references: (Bender and Fink, 1998; de Meaux et al., 2005; Rodriguez-Avila et al., 2011; Spiering et al., 2011; Sulpice et al., 2010; Wu et al., 2008; Yang et al., 2012)

Vicki Funk at the Smithsonian (who is a Research Gate member) was the first person to produce a phylogenetic analysis using secondary compounds as characters. So, she would know the accumulated literature on that topic best.

i truly think we can associate diversity of secondary metabolites production with genes sequences. i have been working with maize cultivars producing different levels of benzoxazinoids and with the genome sequences and the sequencs since then on many cultivars of maize or close relatives. we will be able soon i think to select high producer alleles with the optimal genetic backgroung. Integrated QTL reasearch and allelic detection of best variant will definitely help answering your question; of course end product and metabolome should alsways be check to confirm the gain in the production of seconday metabolites. by hte way if you want to get rid of specific secondary product the same can be done by counter-selection!

On a University of Reading field course in SE Spain, an undergraduate project looked at the essential oils in Rosemary (Rosmarinus officinalis) from some eight different habitats and places. All had the same oils, but some spots on tlc plates were hardly visible whilst very dark and flooding in others. We jokingly said that if you wanted rosemary for after-shave, collect by the beach, but for cooking with your lamb collect from the mountain. This needs material collecting and repeating under controlled conditions as oil production changes so much for plants under stress.

Mostly plants are cross pollinated and that results in variation or genetic diversity. this has direct implication on gene expression and diversity in terms of quality or quantity of secondary metabolites produced. The production of secondary metabolites is complex and regulated by several genes hence there are possibility of variation due to this genetic recombination. this is even observed in self pollinated crops like lupin