Genetics & Breeding

Resistance Genetics: Origin of Resistant Alleles

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

You are currently reading the Origin of Resistant Alleles lesson.

The first Resistance Genetics lesson on Trait Expression described how genes are expressed by providing the cell protein coding instructions. This Resistance Genetics lesson on Genotype and Phenotype focused on the inheritance of genes and explained the occurrence of phenotype variation in families.

This lesson on the origin of resistant alleles describes how and where pesticide resistance in a population begins.

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

Learning Objectives

By the end of this module, each student should be able to:

  • Identify genetic and environmental influences on phenotype,
  • List environmental factors that vary in a growing environment and can influence an organisms’ phenotype,
  • Describe how new alleles can enter a gene pool from mutation or migration,
  • Predict the impact of mutation and migration on the rate of change in a gene pool,
  • Compare the effectiveness of pest resistance management when fitness costs of resistance alleles are or are not a factor.

Introduction

Since pesticide resistance is the phenotype we are centered on in this module, it is important to understand how resistance in populations originates. The emergence and spread of resistance in a population are evolutionary processes, and understanding the evolutionary mechanisms involved can better inform risk assessment and justify management strategies. We most often think of resistance at the individual organism level (Fig. 1).

A green plant with elongated leaves growing in a dry, barren field under a blue sky.
Figure 1. An individual horseweed (Erigeron canadensis) is a member of a population of horseweed in a field. 2022 by Amy Hauver. Reprinted with permission.

Individuals can be observed that survive a treatment of a pesticide. But resistance emerges and evolves in populations where there is genetic variation among the members of the population (Fig. 2). Resistant alleles become prevalent in the gene pool of the population which results in a significant proportion of the population that can express resistance. Because this evolution of resistance happens to populations, we will start with a description of the genetic makeup of populations.

Populations and gene pools

A population is an intermating group of individuals that are the same species. For most populations, intermating requires the adults in the population must be in the same place at the same time. In contrast to families, where the identity of the parents for a group of offspring are known, we will not know the specific parents of members of populations. What we do know is that all the members of a population share the same gene pool. The gene pool is made up of all the genes from all members of a population that are alive at any given time.

A dry field with sparse plants and a distant tree line under a partly cloudy sky.
Figure 2. This population of horseweed is easy to observe in early spring in an eastern Nebraska crop field. The horseweed plants we can see plus the live but not yet germinated seeds in the soil will possess the genes that collectively make up the population gene pool. 2022 by Amy Hauver. Reprinted with permission.

New Alleles and Allele Frequency Changes

Alleles

All living organisms have genes which are made up of DNA. The different variants of a gene are called alleles (Fig. 3). Some alleles can result in differences in observable (phenotypic) traits, such as pesticide resistance.

Alleles in the gene pool of the population may cause changes in the appearance, behavior, or survival of individuals in the population who express those alleles. New alleles can appear in a population as the result of two factors. Mistakes in chromosome replication, one form of mutations, can create DNA sequence changes and new alleles. Migration of a new alleles carried by an individual at the seed stage or carried in pollen can also add a new allele to a population’s gene pool.

Stylized chromosomes labeled Allele B and Allele b with teal and red bands, respectively.
Figure 3. Two of the same chromosomes with the same genes, but different versions or alleles of the B,b gene. Image created using Adobe Illustrator.

Populations can differ by the alleles that are found in the gene pool, and also by the frequencies of each of those alleles. New alleles that arise by mutations are random and thus are likely to have a neutral or even a detrimental impact on the organism’s biology. On rare occasions, a new allele may give an organism a competitive advantage as it lives in its environment – improving the organisms chances of survival. When this advantage in survival results in a greater chance of successful reproduction, new offspring in the population inherit that beneficial allele. The reproductive advantage based on the population members expression of a specific trait is called natural selection. Succeeding generations will have a higher frequency of this beneficial allele in the gene pool. Beneficial alleles enable populations to respond to the environment, and thus populations adapt to the environmental changes through the allele frequency changes as generations advance. This change in the frequency of alleles present in the population is evolution. Population evolution is essential for long term species survival because the environments found on the planet earth are continually changing.

Allele Frequency Calculations

Allele frequencies reveal the distribution of genetic diversity within a specific population, and they are normally represented as a proportion or percentage of the gene variant (allele) in the population. Allele frequency is calculated by the total number of times the allele of interest is observed in a population divided by the total number of copies of all the alleles for that particular gene in the population:

[latex]\text{Frequency of allele } X = \frac{\text{Number of copies of allele } X \text{ in the population}}{\text{Total number of gene copies in the population}}[/latex]

A population geneticist never KNOWS the exact allele frequencies in a population gene pool, but they can estimate this value by sampling the population and determining the genotypes of the individuals in their sample.

Calculating allele frequencies

Consider this small sample of 20 Colorado potato beetles (CPB) from a population (Fig. 4). Each insect has two copies of a gene (T) that controls resistance to an insecticide.

A grid of beetles labeled "Tᴿ" and "Tˢ," with totals "Tᴿ = 14" and "Tˢ = 26" displayed to the side.
Figure 4. Allele frequency for a resistant allele (TR) from a population sample. Created using Adobe Illustrator.

Assume we have a method to determine the genotype of each beetle at a gene pair known to control resistance to an insecticide. If we determine the genotype of each beetle, we can count up the number of resistant copies present (TR= 14) and the number of susceptible copies present (TS = 26). The number of copies of each allele is divided by the total number of allele copies in the sample to get the allele frequency.

Frequency of allele TR = [latex]\frac{14}{40} = 0.35 = 35\%[/latex]

Frequency of allele TS = [latex]\frac{26}{40} = 0.65 = 65\%[/latex]

 

The frequencies of all alleles of a gene must add up to 1.0, or 100%

These calculations show the genetic diversity of this insect population for the resistant allele. The analysis reveals the status of the gene pool in this Colorado Potato Beetle population. Our analysis detected two alleles at the T gene pair and the frequency of each allele. This sampling and analysis can be repeated on different populations of CPB to compare the gene pools of each population.

Video - Calculating Allele Frequencies

Describes how allele frequencies for population genetics are calculated for pesticide resistant insects.

Forces that Change the Gene Pool (part 1)

Group of red and black bugs illustrating a gene pool concept with text on the left.
Figure 5. Example of a population that forms a a gene pool. Interbreeding individuals in a population form what is referred to as a gene pool. Notice that the insects are all the same species, which is part of the requirement for forming a population of individuals. The ability to interbreed means that there is no physical or genetic basis by which the insects are separated, which allows them to be a part of a single gene pool. Image created using Adobe Illustrator.

Knowing how alleles control pesticide resistance and how these alleles originate can guide management tactics that are deployed to manage resistance development. Alleles controlling traits such as fungicide, herbicide, or insecticide resistance can result from new mutations within the population or exist from standing variation among individuals in a population. Changes in allele frequencies over time are influenced by four forces. Biologists who study the genetic makeup of populations and predict genetic change are motivated to understand how these forces could impact a particular population and a particular gene from the gene pool (Fig. 5).

  1. Random mutations can change the protein coding information in the DNA. The mutation might change the structure of the protein or change the copy number of the protein.
  2. The frequency of alleles beneficial to a population can be increased through selection.
  3. Alleles can be introduced into the populations through gene flow resulting from migrating individuals carrying new alleles between populations or carrying different frequencies of alleles that are already in the gene pool.
  4. Genetic drift changes the frequency of alleles in a population as a result of chance events that occur over time. These chance events are not influenced by the traits expressed by the population members.

Allele Frequency Changes: Mutation and Selection

This video details the impact of mutations and selection on allele frequencies for various pesticide resistant populations.

Force #1: Mutations

A new mutation can originate from the effects of environmental factors, such as ultraviolet radiation from the sun, a chemical which can change DNA structure (a mutagen). Mutations arise as mistakes in DNA replication during cell division. A mistake in replication creates a permanent change in the nucleotide sequence of DNA caused by an insertion, deletion, or substitution of nucleotides. A mutation may occur once and increase in frequency in the population (Fig. 6). There can also be multiple, independent new mutations occurring in the same gene. New alleles can always occur in a population from mutations. Mutations are rare; therefore, mutation rates are initially low so mutation would have a very small impact on increasing the frequency of any specific allele in a gene pool. However, once a mutation is present, there are other forces that can change the frequency of resistance alleles more rapidly in a gene pool.

Series showing mutation in plant cells through four stages with increasing pink highlights.
Figure 6. The original population (A) and its expressed phenotypes (B) has a single allele that is the same throughout the population. A mutation occurs randomly in the population, causing a new allele to develop (C) that spreads through the population (D). Created using Adobe Illustrator.

Force #2: Selection

When individuals with a specific genotype have more reproductive success than population members with a different genotype, allele frequencies will change from the force of selection (Fig. 7). Mutations can be harmless, detrimental to the organism, or beneficial for the organism. In the case of pesticide resistance, a mutation might create a new version of the protein that increases the insect, weed, or pathogen's ability to detoxify a harmful pesticide or increase the copies of the protein targeted by the pesticide that is encoded by the gene. In environmental conditions where that pesticide is present, organisms with the mutant allele are more likely to have reproductive success. These beneficial alleles have a selective advantage and the resistance allele will increase in frequency.

Three-part diagram showing a selection process with leaf-like shapes changing from green to highlighted pink.
Figure 7. The original population (A) and its expressed phenotypes (B) has two distinct alleles present in the population. In this population's specific environmental conditions, organisms with the alternate allele (pink) have a selective advantage over the original (blue) allele (C). This alternate allele will be selected for and will increase in frequency in the population. Image created using Adobe Illustrator.

Standing variation

Standing variation is the collection of different alleles present in the gene pool of a population. Some mutations create alleles that have no selection advantage for members of the population in the current environment, but they also cause no disadvantage. The protein encoded by this new allele may have some amino acid changes, but the protein can perform its intended function. Population geneticists would describe these alleles as having no fitness cost. Alleles with no fitness cost can be retained and allow genetic variation to accumulate in some populations. This contributes to the standing variation or natural genetic diversity of a population. Populations that are large and have occupied an ecosystem for a long time would be expected to have more standing variation (genetic diversity). Standing variation can contain pesticide resistance alleles prior to any changes in selective pressure (prior to pesticide application). When the pesticide is applied, these alleles become advantageous and are selected for at a higher frequency in the population. The frequency of resistance alleles, if they are present in the standing variation, is usually very low. However, with repeated cycles of selection pressure (i.e., pesticide applications) across multiple generations, the frequencies can increase dramatically and result in a highly resistant population.

Flowchart showing progression of genetic resistance from an ancestral population to high-frequency resistance mutations over time.
Figure 8. Standing variation chart. Sequence of events that occur in a population with standing variation to increase the frequency of resistance alleles. This population has standing variation, so pesticide applied in the environment causes selection pressure. Imaged created using Adobe Illustrator.

In Figure 8, the population has a range of existing genetic diversity that has accumulated over time and that also includes alleles for pesticide resistance. When the pesticide is introduced, the environment is changed, and selection occurs for individuals with this rare resistant allele. As the selection pressure continues from one generation to the next, these resistance alleles become more prevalent under pesticide selection as the members of the population who are resistant survive and have more offspring than those that are susceptible. This increases the frequencies of the resistance alleles in the population in a relatively short period of time (a few to several generations).

Graph of evolutionary increase in pesticide resistance over time, from an ancestral population to high-frequency resistance mutations.
Figure 9. Scenario of emergence of resistance in a population that has no standing variation. Time is required for new mutant alleles to occur by chance. Image created using Adobe Illustrator.

In Figure 9, the population has no resistance alleles in the gene pool when the pesticide is first introduced into the environment. The pesticide would be effective on all members of the population unless an individual were to escape a lethal dose. The population persists because of these escapes. For resistance to develop, a resistance allele would need to be introduced into the population through mutation or some other factor. In the absence of standing variation, if resistance is able to develop in the population it would occur at a much slower rate than populations with extensive standing variation.

Forces that Change the Gene Pool (part 2)

Allele Frequency Changes: Migration and Drift

The following video describes how gene flow and genetic drift impact allele frequencies.

Force #3 Migration

A plant with small yellowish-white flowers in a rural field.
Figure 10. Horseweed plant. Horseweed produces seeds with accessories that promote dispersal via wind, influencing the migration of alleles to new populations. 2022 by Amy Hauver. Reprinted with permission.

Gene flow is the movement of genes between different populations. Members of one population that migrate to another must mate with members of their new population to change the gene pool of their new population. If the migrating individuals have different alleles or a different frequency of the alleles in their new population, this can cause gene frequency changes in the gene pool. Adults are the most mobile stage of animals. Movement in plants at the seed or pollen stage is common. In weeds, this can be pollen or seed blown by the wind or seed dispersed from dead plants that move, or seeds with special structures that promote their transport by sticking to animals or movement with soil or water (Fig. 10 and 11). For some insects, movement via flight can be an important source of gene migration. In fungi, spores are spread through the air and water, resulting in the transfer of genes between populations.

Expansive dry field with a diagonal strip of green shrubs.
Figure 11. A trail of healthy kochia plants. The pattern of kochia plant growth in the field was present after a single herbicide-resistant plant shed its seed as it tumbled across the field in the wind. Wiersma, A. (2021). Colorado State University. Photo reprinted with permission.

Because of gene flow, the evolutionary forces that are imposed on one population can be transferred to another population and rapidly influence the gene pool of that population. Gene flow can reveal problems in the management tactics of neighbors. Farmers might avoid imposing selection pressure for herbicides or insecticides, but if their neighbors are selecting for resistance, resistance alleles may arrive from across the fence and road.

While less likely than movement between populations, it is also possible for resistance alleles to move from one species to another. Resistance alleles, present in one species, may move into other, related species through intermating. Hybridization between a ‘donor’ species that has the resistance allele and a target species can result in an interspecies hybrid. If the interspecies hybrid is fertile and can make viable pollen or eggs, the hybrid can cross back to the related target species and transfer resistance alleles into that target species. Cross-species herbicide resistance gene transfer has been documented in a number of weed species, such as Palmer amaranth and spiny amaranth.

Force #4 Drift

Genetic drift results in changes in the frequency of alleles in a population (Fig. 12). It is a result of chance events that happen to members of a population that impact the survival or reproductive success of certain genotypes. These chance events have nothing to do with the particular traits expressed or selection pressure.

For example, sporadic rainfall during a very dry year may allow some members of a weed population to complete their lifecycle while other members of the population just a few hundred feet away die. If the surviving members of the population happen to have a higher frequency of an allele controlling flower color, the frequency of those alleles will increase in the population resulting in more members with this flower color in the future.

Diagram showing "Drift impact" for different group sizes over time with circles and arrows.
Figure 12. Genetic drift over time. Genetic drift will have a bigger evolutionary impact on smaller populations because of the limited genetic diversity within those populations compared to larger populations. Chance events are much more likely to have a significant effect on allele frequency if the populations are small. Image created using Adobe Illustrator.

Applying Concepts to Assess Risk of Resistance

Figure 13 is a risk assessment chart that combines estimates of an organisms reproduction/mating system, potential dispersal (gene flow), and effective population size (effects of genetic variation and potential for genetic drift) to place pathogens into different categories for resistance development potential.

Table showing pathogen genetic diversity, dispersal methods, and effective population size with color-coded ratings.
Figure 13. 3-point risk assessment chart for resistance in insects, weeds, and pathogens. Image created using Adobe Illustrator.

First looking at the reproduction/mating system, there are different levels of genetic diversity that can be used to estimate the evolutionary potential:

  • At the lowest risk (1) is asexual reproduction mating system, which has a low genetic diversity with inbreeding and no opportunity to outcross.
  • The next classification (2) is sexual reproduction mating systems that has a high genetic diversity with opportunity to outcross and create new combinations of alleles.
  • The highest risk (3) has the greatest evolutionary potential and has a mixed reproductive mating system that creates an “epidemic” genetic structure. An epidemic genetic structure is the combination of the low risk asexual reproduction and medium risk sexual reproduction, which creates a greater risk of evolutionary potential.

Next looking at potential gene flow, there are different levels of dispersal that are used to estimate the distance of possible gene flow:

  • At the lowest risk (1) is soil borne pests that have a difficult time dispersing. These pests can move up to 5 meters in total dispersal. For pathogens, this means soil borne organisms like nematodes.
  • The next classification (2) is moderate dispersal, like waterborne pathogens and low distance dispersal of pests spread via animals. For weeds, this can mean Palmer amaranth, which can be spread up to 300 meters.
  • The highest risk (3) for the greatest distance of dispersal of resistance genes is pests that are airborne. These pests are easily dispersed and includes weeds like kochia that tumbles through fields and horseweed that migrate via wind, insects like the beetle corn rootworm and the moth European corn borer that can fly great distances, and pathogens like the fungus stem rust that create spores that can travel high distances.

The final part of this three-point risk assessment chart is the effective population size. In the scenario of the risk of pesticide resistance, the effective population size is the number of breeding individuals in the population of interest that would experience selection pressure caused by the application of a pesticide. The risk is high with a large population of breeding individuals and lower with a smaller population. This results from the likelihood of greater standing variation present in a large population with a greater chance of resistance alleles being present. Smaller populations are slower to adapt because of their limited variation and their increased potential for losing beneficial alleles due to genetic drift.

  • Small effective population of breeding individuals and lower risk (1),
  • Medium effective population of breeding individuals and moderate risk (2),
  • Large effective population of breeding individuals and higher risk of resistance development (3).

Quiz

Allele frequencies in various populations.
Population TR allele frequency TS allele frequency
Population W .35 .65
Population X .04 .96
Population Y 1.0 0
Population Z 0 1.0

Use this table to answer the questions below.

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.

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