Evolution of Plant Secondary Metabolites

Kliebenstein Lab

UC Davis Plant Sciences

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A frequent question is if I have the money to conduct 100 analyses for a QTL project, should I do one measurement on 100 lines or should I do two measurements on 50 lines. In simplistic terms, the main determinant of your power to detect a QTL is the percent of the total measured variation that it controls. Shown below is a simple model where there are two QTL controlling the genetic variation in situations where genetics controls 90, 75, 50 or 25 % of the total variance. The equivalent to Heritability being 90, 75 50 or 25%. Under these situations 100 or 1000 measurements were split into either individual analysis of 100 or 1000 lines versus duplicate measurements of 50 or 500 lines respectively. As shown in the figure below, the replicated measurements of fewer lines always allowed for the QTL to control more of the total variance. Hence, there is a higher likelihood of identifying the QTL using the replicated design on fewer lines. This is most true at the lower heritability situations where replication nearly doubled the experimental variance controlled by the QTL. At all situations, the replicated experimental design is more powerful. However, if your trait is high heritability (e.g. >80%) a non-replicated design is possible however not totally optimal.

The old definition, that I like, is a metabolite that controls the ability of an entire organism to exist. This is in contrast to a primary metabolite that is required for a single cell of that organism to exist. Primary metabolites would be compounds like Amino Acids and Sugars. Secondary metabolites would be compounds like flavonoids, terpenoids and glucosinolates. If it is something that you taste or smell or alters your mood, it is likely that it is a secondary metabolite or related to one. Another good place to get a handle on what these compounds are is to go to your nutritional supplement/aromatherapy aisle at the grocery store. There you’ll see vials labeled bioflavonoids or Rutin or Quercetin—all Plant derived flavonoids. Also, carotene and lycopene are considered plant secondary metabolites. If you like wine, the purple color is a flavonoid as well.

Frequently Asked Questions

A QTL is a quantitative trait locus. Now, what does this really mean. Imagine that you cross a tall plant with a short plant and you look at the height of the progeny/children. These progeny will have a wide range of heights. Height is a quantitative phenotype/trait in that it has a numerical value say six versus five foot tall. Next, lets say the parents have different variants at a specific gene, a locus, and we have the ability to measure this gene. Now we measure the height of the progeny and which copy of the gene they have and see if the progeny with one copy are taller than the other. If the answer is yes, we have a quantitative trait locus (QTL) —a gene or region that controls a quantitative phenotype.

What is a QTL?

What is a secondary metabolite?

How should I partition replicates?

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