Conventional breeding

As mentioned in my previous blog of the DNA series, conventional breeding (CB), which is a method of plant modification, has been used for thousands of years, far before we knew about DNA. Even if we did not understand how characteristics were inherited from one generation to the next, we knew that they were being passed down, and we used it in our favor to domesticate plants and animals. Until the date of this publication (November 2025), conventional breeding has been widely used, and there are more products on the market derived from this than we could ever imagine!

Before using conventional breeding, a developer must have clear goals, taking into consideration the necessity of the farmers and consumers. The most common desired traits in CB are increased yield, resistance to disease and pests, improved quality, resistance to abiotic stress, photosensitivity, synchronous maturity, and elimination of toxic substances, which are focused on farmers necessities. Because this is a well-established technique, breeders have standardized techniques for each crop based on its breeding characteristics.

Genotype vs. phenotype

The first step when developing CB crops is selecting parents with desirable traits based on the plant’s phenotype. Genotype refers to the genes and phenotype refers to the physical traits that result from the genotype. As an example, we can imagine a plant with a purple flower. This plant has a genotype that codes for purple flowers, and the flower phenotype colour is described as being purple. However, not all genotypes will develop phenotypes, and phenotypes are influenced by the environment (epigenetics[1]). This can be the case of plant growth and development, yield, and fruit/vegetable size. In the figure, we can see that from one genotype, we can have different phenotypes, caused by changes in the environment.

One clear example of this is the study by Segal and Hur (2022), who evaluated different variables and their changes between identical twins (with the same DNA, and therefore the same genotype) who were separated and raised apart. In this case, the most prominent physical change was their height. Despite the clear difference between humans and plants, this works the same way for plants, environment and external factors can result in different phenotypes.

Another interesting biological fact is how the genetics of the parents can affect the probability of their characteristics showing up in their offspring. To explain we will dive into the simplest way we pass along genes. For each gene that is passed onto the next generation, the individual offspring inherits two alleles, one from each parent. The alleles can be represented by letters, uppercase ‘A’ and lowercase ‘a’. ‘A’ is a dominant allele, and ‘a’ is a recessive allele. The presence of a dominant trait amongst alleles results in the expression of dominant genotype as the phenotype. If we have a dominant homozygosis (AA), or heterozygosis (Aa) the dominant allele trait is the one to show up. For the recessive trait to appear in the offspring, it must be a recessive homozygosis of a’s (aa) That might be a little confusing, so let’s understand it better in the figure below.

Using Gregore Mendel’s experiment on pea flower colour of either purple or white; purple is the dominant colour trait when it is AA or Aa, but if the plant has aa alleles, the flower will be white. In this example, both parentals are heterozygous Aa. Then, the probability for the offspring to have a white flower is 25%, and the probability for the offspring to have a purple flower is 75%.

OK, but does that mean that if I have four offsprings, I will have three with purple flowers and one with white flowers? No. For each offspring, the probability is the same, so there could be dozens of generations without the white flower trait showing up, for example. See why cross breeding is so complex and may take a lot of time?

How is conventional breeding developed?

Now, let’s use the example below to better understand how CB works. We have two plants, and both have desired traits, but they also have undesirable traits. What a developer will do is cross them until the genetic combination gives them an offspring with both desirable traits. In the case of the figure below, it would be a corn with good kernel size, and resistant to disease X.

To make sure the desirable characteristics are not just on ideal conditions, the breeders put the selected offspring through a rigorous assessment process, mimicking the environment where those will be cultivated, to analyze how this variety will perform as a plantation crop. There are different ways of doing conventional breeding, but the most common is as described in the example above.

Conventional breeding has been used in combination with mutagenesis (next topic of this series) to shorten the time it takes to get new positive mutations[2]. In Canada, canola has been developed with CB, and others such as mustard, wheat, rice, yellow mustard, and sorghum have been developed, mainly for herbicide tolerance, with a combination of CB and classic mutagenesis. Other traits like high amylose starch in wheat were also developed using CB and classic mutagenesis in the country.

Another way conventional breeding has evolved is by using visual markers, which are called marker-assisted selection (MAS). This technology uses identifiable DNA sequences that are linked with the gene of the desirable trait, so breeders know which plants to breed, instead of waiting for the plant to fully develop in the field. In this way, breeders can evaluate the plants earlier, saving them a good amount of time (and money).

Regulation of conventional breeding

Conventional cross breeding between non-genetically modified parents is not regulated. This technique is not regulated because it is so close to what occurs in nature: plants cross, and the offspring with the most fitting characteristics are selected by the environment (natural selection – previous blog), with no addition of DNA from a non-related species. Using mutagenesis with CB is also not regulated because one of the important drivers of evolution is mutation, which occurs naturally. One of the random mutations an organism can go through in nature is the knockout of a gene, which can be an exclusion of the entire gene, or just one base pair that makes the resulting protein non-functional. This is also what gene editing tools are capable of.

Gene editing techniques such as CRISPR-Cas9 (future blog) are fighting to fit into the conventional breeding category so they don’t have to go through all the regulatory processes that usual genetically modified (GMs) varieties go through. The regulatory process of usual GMs is time-consuming and expensive. About 7 million more USD is spent on regulatory activities and authorization when compared to conventional breeding techniques, and about 9 more years for regulated crops when compared to conventional ones.

Now, just to mess with your understanding of this, there are some conventional breeding that are currently being regulated. Those are the ones where the crossing parents are GM varieties, and the objective is for the offspring to show stacked traits. This is the case of some varieties of canola, cotton, maize, and soybean in Canada. There are 309 GM crop varieties coming from CB around the world from 8 different crops (alfalfa, canola, cotton, eucalyptus, maize, safflower, and soybean). That would account for an additional amount of ~ 2.1 billion USD spent only on the regulation process of those GM CB varieties.

Conclusions

Conventional breeding is indeed a technique that works; it has been used for thousands of years and is still used to this day. It has evolved since our ancestors’ use of it. Now we have established protocols that work for each crop. We have knowledge of the importance of mutation for new traits, so we started using it to speed up the process, and we have MAS, which makes it possible to identify the presence of the desired characteristics in the early stages of the offspring plant. With all those evolutions in CB techniques, it still plays a major role in the development of new varieties. Conventional breeding is also widely used with GM plant parents, to obtain varieties with stacked GM traits, such as herbicide tolerance, insect resistance, and antibiotic resistance, among others.

The main obstacle for CB is the time it takes to get new varieties with the desired traits. Since the nature of crossing is very random, it could take generations for the combination of the desired traits to show up in the offspring. Since mutation is very random and could not occur for many generations, breeders could spend dozens of years trying to isolate the desirable traits. Because of that, CB has been used with mutagenesis, which is also not regulated. Regulatory wise, new breeding technologies such as gene editing are fighting to fit in as conventional breeding so they do not have to go through the regulation process of GM crops.

In the next blog of this series, we’ll explore mutation breeding in more detail: how mutations occur naturally, how humans harness them to improve crops, and why this process has become a cornerstone of modern plant breeding. Stay tuned!