Overview

Overuse and reliance on pesticides to control agricultural pests has caused pest populations to evolve due to the application of artificial selection. Individuals with a higher tolerance for pesticides survive to reproduce – increasing resistant individuals that will eventually outnumber the ones that are controllable.

Resistance Genetics is a set of 4 lessons that teach about the genetic basis of pesticide resistance. These lessons can be used together or as separate lessons.

1. Trait Expression – the lesson you are reading now
2. Genotypic Inheritance and Connection to Phenotype
3. Origin of Resistant Alleles
4. Selecting Genes for Resistance – Evolution of Resistance to Pesticides in Populations

You are currently reading the Trait Expression lesson. In Trait Expression, we discuss the role of genetics in the development of pesticide resistance.

Authors

• Amy Hauver, University of Nebraska-Lincoln
• Jacob Nikodym, University of Nebraska-Lincoln
• Callie Braley, University of Nebraska-Lincoln
• Don Lee, University of Nebraska-Lincoln

Published November 2025

Introduction

Take a moment and observe Figure 1. What do you see? If a farmer was walking through this field, what would they think? The living plants in the picture are the weed kochia (Bassia scoparia). Looking closely, they would see many dead kochia plants in this field because it was treated with an ALS herbicide. But most of the surviving kochia plants in this field grew from seeds that were distributed the year before by a single plant as it tumbled and turned with the prevailing wind. If the farmer had applied ALS herbicide the year before to kill kochia and other weeds, the success of this weed control method would motivate them to repeat it this year. The farmer may have been pleased with the ALS weed control last year, but likely not this year.

Why is this occurring? The farmer is observing the results of biological history that they have been a part of developing. The kochia plant, growing in the field the year before, possessed a gene that mutated to create a new version or allele. When this mutant allele was expressed, it encoded a protein that interacts in a different way with the ALS herbicide. This different interaction allowed this plant to survive the herbicide treatment and continue its life cycle. By the time it died at the end of the growing season, it had successfully produced hundreds of seeds. After it was no longer alive, its seeds tumbled with it as the wind moved it across the field and distributed its seeds. Many or most of the seeds inherited the herbicide resistance allele and they too were able to resist the farmer’s herbicide application.

Traits

Understanding why the ALS herbicide resistance trait was expressed in some of the families of kochia plants in our farmer’s field, but not in others, requires us to understand trait expression. Trait expression, sometimes referred to as the central dogma, is the process by which the instructions in DNA are read in the cell to build a functional protein. The mystery of why unique characteristics or traits in animals and plants could appear across generations was solved when early molecular geneticists discovered the identity of genes. Genes are specific sequences of DNA nucleotides that are part of a chromosome. These geneticists determined that genetic information flows from a DNA sequence to an amino acid sequence, creating proteins that accomplish specific functions inside cells. The function of these proteins controls the traits we observe in organisms.

Genes are passed from one generation to another. The most obvious examples of gene inheritance occur when a single gene controls variation in a trait. Very simple patterns of gene inheritance can be observed with traits such as flower color in plants or wing color in insects. In other instances, there can be a range in the expression of a trait. In Figure 2, the three plants have all been exposed to the same herbicide treatment, but they express a range of resistance to the treatment.

Trait Expression and Traits

The process by which the DNA instructions are read by the cell to encode a functional protein is called trait expression. Trait expression is the flow of genetic information from DNA to RNA to protein.

Video – Introduction to Resistance Genetics

Watch this short video to help you picture the connections between genes, trait expression and traits.

Trait Expression has Two Center Stages – Transcription and Translation

 

Genes are part of the huge macromolecule called the chromosome. Hundreds or even thousands of genes can be part of the same chromosome. Because of their size, chromosomes remain in the nucleus during the trait expression process. The building of proteins happens in the cytoplasm of the cell. Thus, trait expression requires a two-step information transfer process. The first step in the transfer of genetic information is transcription.

During transcription, the DNA nucleotide sequence of the gene is read to build an RNA message (messenger RNA or mRNA) with a corresponding nucleotide sequence (Fig. 3). In this step, DNA making up the chromosome is unwound, and a specific gene is targeted for expression. Transcription enzymes read the DNA and assemble mRNA – which is then moved outside the nucleus for translation.

The mRNAs travel from the nucleus to the ribosomes, where they are read by this protein building machinery, and the information encoded in the mRNA is used to build the amino acid sequence that forms the protein (Fig. 3).

Transcription

During transcription, the DNA sequence of a specific gene is read by the enzyme RNA polymerase, which builds a complimentary messenger RNA (mRNA) strand. One distinction in this process is that thymine nucleotides in the DNA will be converted to uracil nucleotides in the complimentary mRNA (Fig. 4). These new mRNA strands are smaller and more mobile than DNA and are easily transported outside of the nucleus. The result of transcription is that the mRNA will be read to determine the specific amino acid sequence of a protein in the process of translation (Fig. 5).

Video – Trait Expression: Transcription

Trait expression is the process by which genes becomes proteins and it occurs in two parts, Transcription and translation. This video describes the process of transcription.

Translation

Translation is the process of reading the sequence encoded in the nucleotides of the mRNA to build the amino acid sequence of the protein. The synthesis of the proteins is directed by the newly transcribed mRNA and is completed with the help of a ribosome (Fig. 6).

Once the mRNA moves outside of the nucleus into the cytoplasm of the plant cell, ribosomes attach to mRNA and translation begins (Fig. 7).

During translation, the ribosomes read the information in a mRNA sequence in groups of three. These groups of three mRNA nucleotides are called codons.

One codon, methionine (Met), always acts as a start codon to signal the beginning of protein construction (Fig. 8). It signals where the ribosome should bind to start translation. There are also three stop codons that tell the ribosome when a protein is complete. Every codon between the START and STOP codons specify which amino acid the ribosome should add next from the amino acid pool.

This genetic code for matching amino acids to codons is redundant. There are 64 possible codons in the triplet code, but only 20 amino acids need to be encoded. Each amino acid is coded by one to six different codons.

In summary, here is the translation process

• Getting started: Ribosomes assemble around the mRNA and bind to the start codon to initiate translation.
• Extending the chain: Ribosome read the mRNA, building the protein one amino acid at a time. An incomplete protein is called a polypeptide chain. As the ribosome reads the codons, it adds the corresponding amino acid to the growing protein chain.
• Termination: This is when the finished polypeptide chain is released at the stop codon of the mRNA sequence. After being released, the chain folds into the 3D shape of a proteins and is moved to the place in the cell where the protein can perform its function.

Video – Trait Expression: Translation

This video describes the process of translation.

DNA Replication and Mutations

Why does DNA replication occur?

When plants and animals grow, they get bigger by adding more cells to their multicellular body. This requires a cell division process called mitosis. Before a cell divides, its DNA is copied (replicated). This is a fundamental process occurring in all living organisms.

The process of DNA replication is performed by the enzyme DNA polymerase. During DNA replication, DNA polymerase reads the DNA sequence from the existing nucleotides and builds a complementary DNA strand. For this to happen, other enzymes work together to unwind the DNA into two strands, where both strands of the double helix act as templates for the formation of new DNA molecules (Fig. 9).

DNA replication and mutations

A mutation is a change in the DNA sequence that makes up a gene. Mutations can arise if a mistake happens during replication. The rate of mutation is very low because the DNA replication process is accurate. But because an organism has so many cycles of replication as they build and replace cells during their lifetime, it is common for multicellular plants and animals to acquire mutations in some of their genes from these random mistakes made during replication. Mutations in DNA create new alleles, or different versions of that particular gene. Mutations can be harmless, detrimental, or beneficial for the organism. What is important about mutations is that they can create new genetic variation among members of a population, and this genetic variation may provide a selective advantage to individuals that make up a population.

Let us return to our farmer’s field that was the home for a kochia weed population (Fig. 1). Imagine this: A mutation occurs during the replication of a new cell in a kochia plant as the cell is developing into a seed embryo. This mutant allele is now found in almost every cell of the new plant as it grows. By chance, the mutation was in the gene that encodes the protein targeted by the herbicide used by the farmer. This small change in the mutant allele still encoded a protein that had the structure to perform its normal function in the plant, but now it no longer had a structure that promoted interaction with the herbicide. The result is that the herbicide will no longer have its intended impact on the plant, and the plant will be resistant to that herbicide. This is an example of a mutation that would have a beneficial impact for the plant. The scenario just described was the series of chances that led to a kochia plant surviving herbicide treatment. However, there are other possible consequences of random mutations (Fig. 10).

Mutations can have one of two outcomes on the protein: the change in DNA sequence can have no effect on the protein (silent mutation) or it can affect the protein by changing its structure and function (point mutation or frame shift mutation). This change in protein structure caused by the mutation of the DNA can have different impacts on the plant depending on the environment it is growing in.

There are three major effects that a mutation has on the final protein (Fig. 11):

• Neutral effect: there is no obvious impact on the phenotype of the plant and is seemingly unchanged.
• Positive effect: impact of the mutation on the plant has a beneficial effect.
• Negative effect: impact on the plant is detrimental and could potentially kill the plant.

These outcomes are dependent on the environment in which the plant lives. If a mutation occurs that aids the weed’s ability to resist a usually harmful pesticide like an ALS herbicide and the grower does not apply any ALS herbicide to their fields, then the impact of this mutation is not visible and is neutral. Once the grower applies an ALS herbicide, however, the mutation’s impact on the plant changes from a neutral one to a beneficial one.

If the mutation in the gene encoding the ALS herbicide target protein results in the protein losing its beneficial function in the plant, this mutation will have a negative effect on the plant. Whether the plant encounters the ALS herbicide or not, this mutant allele would have a selective disadvantage for the plant. The plant may not be able live long enough to complete its life cycle, and this mutant allele will not be passed on to future generations.

What different kinds of mutations lead to these changes in the effect of mutation? ALS inhibiting herbicides work by binding to an ALS enzyme that is key in the production of amino acids. Research that includes the sequencing of DNA from different kochia (Bassia scoparia) plants that were resistant to ALS inhibitors, such as Classic, revealed that the mutations changed a single amino acid in the ALS enzyme. This small change in the protein resulted in a change in target site sensitivity to the herbicide’s presence.

Frameshift mutations are mutations that can result in the addition or deletion of nucleotides in a gene. Because these mutations will affect the codon originally containing that mutation and all subsequent codons in the gene, they likely have a major impact on the protein encoded by the mutant allele.

Point mutations result from changes in a single nucleotide in the DNA sequence. There are three types of point mutations and each can have a different effect on the final protein. We’ll discuss this in terms of ALS inhibitor herbicide resistance in kochia (Fig. 11):

1. Silent mutation: the mutation changes a single nucleotide in the DNA sequence and has no effect on the final protein, so it also has no effect on the structure of the ALS enzyme and the kochia maintains its target site sensitivity and remains susceptible.
2. Missense mutation: the mutation in the kochia changes a single nucleotide in the DNA sequence, which results in changes in the amino acid – altering the structure of the enzyme enough that the ALS herbicide can no longer bind to it, creating herbicide resistance. This specific missense mutation can either have a negative, neutral, or positive effect, depending on how the protein functions and whether the ALS inhibiting herbicide is being applied.
3. Nonsense mutation: If there is single nucleotide mutation that changes a codon that would normally code for an amino acid into a stop codon, it halts the construction of the protein. If a plant cannot survive without this enzyme, the mutation has a detrimental effect on the survival of the kochia plant. Because the plant will not survive, this mutation will not be maintained in the plant population.

Video – Mutations

A summary of two types of genetic mutation (frameshift and point mutation) and how the mutation can impact trait expression. Mutations are learned through the lens of pesticide resistance.

Quiz

Conclusion

Mutations are a natural and sometimes beneficial part of life. There is no organism on the planet that has a perfect, error free system for replicating their DNA. So while mutations are rare, if an organism is abundant, the chances are some individuals in a population will have mutations occur and they will possess mutant alleles. This motivates us to look a little more closely into the consequence mutations at the molecular level and how they impact trait expression and can impact the development of pesticide resistance.

Acknowledgements

The materials for these lessons were developed with support from the United States Department of Agriculture National Institute of Food and Agriculture National Needs Fellowship Program, Award No. 2016-38420-25297. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the U.S. Department of Agriculture.