Red Flags Series: Forgetting Redundancy
What is the Red Flag series?
In this series, we will explore common red flags that often occur in agronomic research, with a particular focus on biologicals research. Lack of familiarity with genomics, plant biochemistry, or unique aspects of biologicals and their mechanisms can cause false assumptions and incorrect conclusions. This series aims to identify and explain common mistakes that lead to frustration with biologicals research that does not align with their performance in the field. By reading this series, you will gain insight into the key questions you should ask yourself as you develop your agronomic R&D or questions you can ask to better understand the depth of understanding that a commercial product manufacturer may or may not have, despite how convincing their label might be.
Red Flag no. 1: Forgetting to consider Redundancy
Plants possess remarkable abilities to survive and cope with challenges. One significant challenge is when genes fail to express due to either internal or external factors, express at the wrong time, or develop mutations that impede their proper functioning. However, plants have elegantly built-in redundancies in their genomes, which provide a functional buffer. In case one system fails, backup systems can take over. Like the multiple safety measures taken for a plane to take off, plant genomes also have backup systems that ensure they have a better chance of dealing with problems that arise.
Gene Isoforms
One form of redundancy in plant genomes is when there are multiple versions of a gene present, sometimes called an “isoform”. Isoforms can be found when a gene’s name is something like “gene1.1” and “gene1.2”. In this case, the gene “gene1” has two isoforms. This is usually when two genes are nearly exactly the same in their sequence, with only a small change between the two versions.
An analogy for this might be very slightly different recipes of the same dish. Maybe you make cupcakes with pink icing, and one batch has one drop more red food coloring in the icing, so the icing is barely one shade darker. They are still cupcakes with pink icing and only the tiniest difference between them. The difference between isoforms doesn’t change the function of the gene, but they have identifiably different sequences.
There is an entire field of study that looks at when, where, and why certain gene isoforms might be given preference over others. Sometimes, there doesn’t seem to be a preference, and sometimes, all the isoforms are used similarly. Some genes have only two isoforms, while others may have ten or more. As sequencing technologies become more accurate, it has become easier to identify gene isoforms in the genomes of crop plants, and new ones are constantly being discovered.
Functional Redundancy
Another form of redundancy is when multiple genes do the same thing. Many functions have multiple genes that can carry out that function. Sometimes, the lack of expression of a certain gene does not mean that the function isn’t still occurring through a different gene. It is a common incorrect conclusion to assume that if a certain gene is not expressing, or if it is expressing at lower amounts, then that must mean the function is not occurring or is occurring at a lower rate. This might be true, but it depends entirely on the gene and the system context that the gene operates within. It is absolutely critical to have a contextual understanding of gene systems to do accurate and valuable genomic research. Misunderstanding this data will lead to field results that do not align with molecular research conclusions.
Systems Redundancy
An essential aspect of plant signal pathways is their complexity, involving numerous interactions and steps. A physiological response, like increased growth, has thousands of mechanisms that have to happen to get the end result. There are redundancies within systems to ensure that a physiological response can still occur, even if there are issues. Some systems have more redundancies than others. A system with very little redundancy, such as photosystem II of photosynthesis, is an excellent target for herbicides. If this system is interrupted, the entire system fails, and the plant will die - making it an effective herbicide. However, some plants have ways around this photosystem, making them resilient to the effects of an herbicide that targets Photosystem II.
Many plant systems, though, have more avenues to accomplish the same physiological response. When using genomic data to predict physiological responses or field performance, understanding the system is crucial for accuracy.
Takeaway Points
Gene isoforms exist and should be considered when evaluating results from transcriptomic data.
Functional redundancy means multiple genes can function in the same way, and the activity of all of the genes should be considered before making physiological predictions.
Systems redundancy is particularly important in biologicals research. Biologicals often influence multiple systems and multiple steps in systems, so an understanding of the many different ways that a physiological response may occur is crucial for accurate research conclusions.
Questions about redundancy to ask:
Are there multiple isoforms of these affected genes? Do they behave differently in the plant?
Are there other genes that can carry out this function in the plant? Were they also affected by the product/condition?
What are the steps of this system mechanism in the plant? Are there multiple ways to accomplish this mechanism? Are these other mechanisms affected by the product/condition?
Ignoring or being unaware of redundancies in plant genomes will lead to inaccurate or misunderstood results in your agronomic research. Work with me to avoid this red flag and make contextually accurate, biologically relevant research conclusions in your R&D. Visit here to book a free 20-minute consultation with me to work together.
