What kinds of “tools” are available to me?

Sequencing has become extremely affordable and accessible. I work with you and third-party analytical labs to collect and send samples, coordinate appropriate analyses, and receive data. Common services include total RNA extraction from whole plant tissues, mRNA sequencing for full transcriptomic profiling, RT-qPCR for expression profiling of individual target genes, metabolomic profiling, screening for markers involved in epigenetic modification, and more. This data can be coupled with physiological data such as nutrient analyses, yield, biomass, disease scoring, etc. for a powerful understanding of why you see the performance results you see in the field.

What is a transcriptomic analysis or profile?

Transcriptomic analysis is a process of looking at the expression levels of all known genes of an organism in specific tissue at specific times. A transcriptomic profile summarizes the major and minor effects of a treatment or condition on the expression levels of all of the known genes for that species. When a gene is “expressed”, that gene is copied from the DNA into a mobile version of that gene (mRNA or messenger RNA) to be sent for translation in another part of the cell or throughout the plant. Translation of mRNA makes the protein that has a certain function, mRNA is basically a mobile recipe for that protein. For many genes, more copies of that mRNA results in more of that protein, and possibly an increased level of function of that process, and vice versa. “Up-regulation” indicates genes that are being expressed at higher levels in a treatment group compared to a control group, and “down-regulation” indicates genes that are being expressed at lower levels in a treatment group compared to a control group. Check out the blog posts on Gene Expression and Transcriptomic analysis for more information.

Is this a form of gene modification?

No. The plant is expressing/suppressing these genes whether we look at them or not. We are not changing the DNA sequence, inserting or removing genes, or in any way modifying the plant genome sequence. We are simply reading the “language” of plant gene expression to gain a deeper and more detailed understanding of how a treatment or condition is affecting a plant.

How can this kind of data be used?

Transcriptomic data can be conclusive, or it can lead to follow up research. If you are seeking publication in a peer-reviewed journal, validation work is often required of transcriptomic data. If your goal is to start somewhere in understanding candidate mechanisms of your project, transcriptomic analysis can be a great tool to find the major effects of a treatment on plants, if they exist. Transcriptomic data can also be used to rule out candidate mechanisms for faster product development.

This data is also a powerful tool for finding potential similarities of responses amongst different crop species. For example, if a gene pathway’s expression levels in corn are significantly impacted, and similar pathways exist in soybeans, your product could potentially affect those same genes in soybeans. However, it's important to note that some genes may be species-specific, meaning that your product may not have the same effect across all species.

How long does a project usually take?

This is dependent on your research project’s individual goals. Some projects are conducted through short term greenhouse trials on fast growing plants like Arabidopsis, and may be finished within a couple of months. Most projects that utilize field trials are dependent upon the seasonality of the crop, and will require 1-4 months of data analysis and interpretation following the sampling.

However, if speed is a factor for your project, there may be ways to get the answers you need in a shorter time frame.