7 Agronomic questions to answer with Transcriptomic Analysis

Transcriptomic analysis is one of several sets of tools in molecular biology that allow us to see how a plant is responding to its environment or to products that we apply. With biologicals, often it is difficult to know what to look for in terms of plant responses, especially when we see effects (like increased growth or improved stress resistance) that have many factors that contribute to their physiological manifestations. It’s easy to assume that the biological product must be increasing photosynthesis, or increasing nutrient uptake. However, there are many factors that could be giving the plant a boost in its growth or stress mitigation. Transcriptomic analysis gives a first set of possible explanations. Here are a few questions we can use gene expression analysis to answer:

1.      What kind of response is my product inducing in the plant?

Transcriptomic analysis can show us what pathways the plant is turning on or shutting down in response to what we put on it. Is your product stressing the plant? We can see this reflected in stress-response genes. Is your product increasing chlorophyll or reducing its degradation? We can see this effect reflected in its gene expression profile. There are more analyses that could be used to further characterize and demonstrate specific mode(s) of action, but gene expression analysis can give us a really targeted place to start, as well as rule out what the MoA likely is not.

2.      How long does the response last?

In timed studies, we can see how long the response lasts. Does the response last for only 2 days, so multiple treatments would be helpful? Do multiple treatments amplify the response, or does the response basically plateau at a certain point, and thus, additional treatments are wasted? Does the response last for the entire season? We can see if gene expression patterns that are elicited are maintained, how long they are maintained, or if they slowly return to a baseline.

3.      Are there off-target effects?

Aside from phytotoxicity screens or longer yield studies, it can be difficult to know if a product is having off-target effects that don’t necessarily show physical signs. For example, is a product actually inducing stress responses that, while it may be helpful in abiotic stress remediation, may also cause a yield drag when conditions are optimal? We can see if the plant is stressed, and if it is inducing genes that put the brakes on growth to allow the gas pedal on stress response.

4.      Is the response localized or systemic? (i.e., does foliar or in-furrow application make a difference?)

We can easily see if a plant’s responses to a product are localized to where the product is applied, or if the responses are systemic or maybe even different depending on the tissue. By looking at different tissues (leaves, roots, stems, flowers, etc.), we can compare expression profiles and see if the response of product applied only to roots or only to leaves affects other tissues, and if these effects are the same.

5.      What is the best growth stage to apply the product?

Plant growth and development is regulated by its gene expression patterns. Some genes are more or less responsive, depending on the growth stage of the plant. If, for example, we want to induce gene expression of growth-related genes to increase biomass and photosynthetic tissue to increase yields hopefully, then if we wait until reproduction (like flowering or tassel), the plant has already shifted its “focus” to reproduction, so these genes may not be quite as responsive at that point, or even increased expression may not actually affect their growth. This would indicate that an earlier application timepoint would be more likely to produce the results we want.

6.      What’s the best rate to apply?

Sometimes changes in biological rates produce subtle changes in plant gene expression profiles that are difficult to see real-time in the field, but do result in end-of-season yield changes. Differences in induced expression profiles are clearly seen if rate-based effects are present. Similarly, it is clear to see if rates are too high, and inducing stress or growth-limiting responses, or if rates are too low, and the expression changes aren’t robust enough to affect physiology.

7.      Does applying with other products affect the efficacy of my product?

Many products will be tank-mixed with other products to reduce trips in a field. Does applying other products along with your product affect the plant’s response to your product? This can also be tested with transcriptomic analysis.

If you’d like to integrate transcriptomic analysis into your biological product development, I’d love to work with you. Visit here to book a free consultation.