Understanding Genetic Combinations in Plant Breeding

By Grubbycup
Published: November 25, 2020 | Last updated: April 20, 2021 09:25:11
Key Takeaways

Many home gardeners will partake in some form of classical breeding as a hobby or to develop plants that are well suited to their own needs. Grubbycup breaks down the various plant-breeding methods.

Natural Selection

Imagine a hypothetical stand of plants growing naturally. The environment will put genetic pressure on the plants. If a plant doesn’t survive the growing conditions long enough to reproduce, then it is selected against. The plants that do survive long enough to reproduce are selected for. Plants that do better and have more successful offspring will out-propagate the others. Over generations, as the successful plants outcompete the less successful plants, the colony will adapt to the environment or naturalize.


Early Plant Breeding

What is most successful in an area is not necessarily the most desirable to humans.

For example, if our hypothetical plant has flowers, then it may be that a plant with red flowers is more desirable to humans than a plant that has white flowers, even if the plant with white flowers is better suited for reproductive success (maybe the pollinators like the white flowers better). Simple forms of plant breeding would involve human intervention, and could involve either removing plants with white flowers, or saving seed from the plants with red flowers. This creates a situation where the plants with red flowers are selected for, and those with white flowers are selected against. Eventually, with enough generations, all (or at least most) of the plants will start producing offspring with red flowers. One benefit to this type of breeding is it’s relatively simple to just keep saving seed from the plants closest to a particular ideal, and the plant line will tend to approach that ideal.


Read also: The Basics of Breeding Your Own Cannabis Strains

Brassica oleracea is a well-known example of this type of selective breeding. In its original form it is known as wild cabbage, but human intervention through breeding has led to a variety of domesticated forms. There are different varieties of Brassica oleracea in much the same way as there are different breeds of dogs, although it is generally better known by its various common names:

  • Brassica oleracea bred for loose leaves is better known as kale.
  • Brassica oleracea bred for large tight headed leaves is better known as cabbage.
  • Brassica oleracea bred for small tight headed leaves is better known as Brussels sprouts.
  • Brassica oleracea bred for large stems is better known as kohlrabi.
  • Brassica oleracea bred for their edible immature flowers has resulted in cauliflower, broccoli, romanesco, and so on.

All of these were bred just by selecting for certain traits over many generations.


A problem with this level of basic plant breeding is unexpected results can occur. If at least some of the underlying mechanisms involved are understood, then a breeding program can be much more efficient and predictable.

Mendelian Genetics

Gregor Mendel is often referred to as the father of modern genetics — he developed the laws of Mendelian inheritance in the 1800s and advanced our understanding of how inheritance works. This type of classical breeding is commonly used to improve the existing population of plants into new varieties.


In our hypothetical red and white flowered plant example, flower color is a trait dictated by the gene for flower color. The value of the gene is dictated by two alleles. Each parent will have two alleles, which may or may not be the same. They will pass on one or the other (random chance) to each of their offspring. When a seed is formed, for every gene, one allele is inherited from the pollen (on the father’s side) and the other from the egg (on the mother’s side). For the flower color gene, let’s call the red allele ‘R’ and the white allele ‘r’.

Illustration demonstrating cross-pollination versus selfing.

True Breeding Traits

If a red-flowering father is true breeding (homozygous) for red flower color, then both of his alleles are the same (in this case coded for red). For simplicity, this can be expressed as RR, one R for each of his two alleles. Since both of his alleles are for red flowers, he will have red flowers, and no matter which allele he passes on to his children, it will be an allele for red flowers (because it will either be an R or the other R). The same is true for homozygous mothers.

If a white-flowering mother is true breeding for white flower color, then both of her alleles are the same, but this time coded for white. For simplicity, this can be expressed as rr. When she produces seeds, she will donate either her first r or her second r, but an r in either case. Again, the same would be true for homozygous fathers.

The parent generation is called the P generation. When two members of the P generation are crossed, the resulting children are members of the F1 generation. The children of the F1 generation are called the F2 generation, their children are the F3 generation, and so on.

Read also: Breeding with Autoflowering Cannabis

If both members of the P generation are true breeding for red flowers, then the offspring will all have red flowers. Any of the possible combinations of alleles will result in every member of the F1 generation getting an R from each of the two parents. The father will give one or the other of his two Rs and the mother will give one or the other of her two Rs, forming offspring that will have two Rs. The same would be true with white flowers. Two parents homozygous for white flowers will make offspring with white flowers.

Where things start to get complicated is when a red-flowered pollen-bearing hypothetical plant and a white-flowered egg-bearing hypothetical plant are crossed together. The father will donate one of his two Rs, and the mother will donate one of her two rs, resulting in children that will all have one of each (Rr). This is the F1 generation (in this case also the hybrid generation). Since the offspring will have one R and one r, they are heterozygous for flower color.

Hybrid F1s

Two Rs form red flowers, and two rs form white flowers. What flower color the plants will have when they have one allele of both will depend on which is dominant. Alleles that win ties (when there is one of each) are called dominant, and those that lose ties are called recessive. So, if red is dominant, then the Rr children will all have red flowers. If white-colored flowers were dominant, then the F1 generation would all have white flowers (there are also some cases where heterozygous alleles have what is called incomplete dominance that can result in things like pink flowers, but that is a more advanced topic). F1 hybrids tend to be similar to each other and can exhibit a robustness that is called hybrid vigor. For this example, assume red flower color is dominant.

Read also: Pollinating in Greenhouses


If two members of the F1 generation (Rr) are crossed (say that three times fast) then each parent will pass one of their two alleles. The four combinations possible in the F2 generation are RR, Rr, rR, and rr. These are commonly expressed as a punnett square.

  • In the case of RR, the child plant will have red flowers.
  • In the case of rR or Rr, the child plant will have red flowers (because of dominance).
  • In the case of rr, the child plant will have white flowers.

In other words, about 75 per cent of the offspring will have red flowers, and about 25 per cent will have white flowers.

Breeding for recessive traits is easier than breeding for dominant traits. In the example, while there are fewer white flowers, they will all be rr (because they didn’t have an R to lose to). For the dominant trait however, RR, Rr, and rR will all have red flowers, and no way to tell them apart. With recessive traits, if they show, they are true breeding. With dominant traits, one has to run trials and use statistics to be able to determine when it is statistically likely to be homogeneous.

Illustration depicting the genetic combinations in plant breeding.


While traditional forms of breeding have involved probability and record keeping to determine and change the alleles in an existing plant population, there are also more direct methods that can create genetically modified organisms (GMOs). By using genetic engineering techniques, the alleles are changed or replaced in the laboratory. Early methods included introducing a mutagen and observing the survivors for promising candidates. Later methods include using a gene gun and carrier viruses to alter (or replace) alleles. One concern with GMOs is they allow the resulting lifeforms to be patented/owned by the generating company that can have legal and social repercussions if they are allowed to become a major source in the public food chain (or health).

Read also: Understanding Genetically Modified Organisms


Many gardeners perform some form of classical breeding if for no other reason than to develop plants that are well suited to their own needs. It can be a fun and engaging hobby, if not one suited for instant gratification. With time and patience (and a little know how) progress can be made in home gardens, which can help with both diversity and disease defense.


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Written by Grubbycup | Indoor Gardener, Owner & Writer of Grow with Grubbycup

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Grubbycup has been an avid indoor gardener for more than 20 years. His articles were first published in the United Kingdom, and since then his gardening advice has been published in French, Spanish, Italian, Polish, Czechoslovakian and German. Follow his gardening adventures at his website

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