Plant Breeding Process

The primary responsibility of a plant breeder is to make decisions. They make decisions at every step of the plant breeding process (Fig. 2). There are three main steps in the plant breeding process:

  1. Make crosses between plants that are the germplasm or source of genes to make new genetic combinations;
  2. Evaluate the genetically diverse plants from these crosses for the traits of interest;
  3. Select new genotypes to increase the seed for final comparison with current cultivars.

Each step requires time, land, money, and labor resources. Every breeding program has limited resources. To be successful the plant breeder must know how to best use the resources available at each step.

Plant breeders are continually considering how they can optimize each step of the breeding process to reduce expenses while increasing efficiency and improving results. One of the factors they must consider when making decisions is how to phenotype the traits of interest. Phenotyping is the process of collecting data on a plant’s observable characteristics to understand how traits are expressed based on the genotype-environment interactions. The data collected from phenotyping is analyzed and used to select desirable genotypes (the genetic makeup of individual plants). A few examples of traits a plant breeder might phenotype are plant color, height, nitrogen use efficiency, or drought resistance.

Often, phenotyping is completed through traditional methods such as manually measuring plant height or weighing bags of seed to measure yield. New technologies such as high throughput phenotyping (HTP) can reduce the labor requirement and collect data more efficiently and effectively.  High throughput methods could provide more data collection at important plant growth stages and better inform the plant breeder’s selection decisions.

Figure 2. The flow of decision making in the plant breeding process. Circles represent a group of seed. Boxes represent actions that happen to the seed. These actions result in an increase or decrease of seed. The size of circle reflects the relative magnitude of seed. Arrows connecting them represent the ways in which one action leads to another action or the resulting group of seed.

Image Source: Dr. Blaine Johnson Lecture 01 “The Introduction”, Cross-Pollinated Crop Breeding adapted with permission by C. Mick, 2022.

The first decision a plant breeder must make is determining the trait improvement targets. This can look different depending on whether the breeding program is public (e.g., a university) or private (e.g., agriculture industry). Determining the target product for release gives the breeder a goal to work towards and they will base all other decisions around that goal.

The genetic improvements needed to achieve the identified target product guide the breeder to make their next decision; which germplasm will they use as parents for their future cultivar? Germplasm is the collection of parent genotypes the breeders can grow to make crosses with to start new families of plants. A plant breeder prefers internal germplasm that comes from their own program or other programs in the area that is already adapted to their target growing environment. This germplasm is already elite; the genotypes are high yielding and express many of the desirable traits breeders, farmers and consumers want in the plants and the harvested product. Making crosses between improved/elite parents produces a higher percentage of plants that meet farmers’ expectations. The breeder can then determine which of these meets the goals for high yielding breeding lines.

 Some breeding goals may motivate the plant breeder to use external germplasm that comes from plant breeding programs outside their region. For example, a maize breeding program may have developed a variety that performs well in drought conditions but is looking to improve the disease resistance against southern rust. They might cooperate with another breeding program that has already made advancements in southern rust disease resistance. This allows breeders to introduce variation to their germplasm pools that is not found within their own but keeps their lines high performing. While this germplasm is improved because it has been through a plant breeder’s selection, breeders find it more challenging to identify good breeding lines from the crosses because the parent line may not be adapted to growing in the target environment.

Plant breeders also have the option of using germplasm even further outside their region and sometimes country to meet a breeding goal. This is used less often because these potential parents are the landraces, wild accessions, or related species. Landraces may have unique versions of genes (alleles) from traits such as biotic or abiotic stress resistance. However, these landraces are far less productive than elite varieties. A low percentage of the offspring produced using landraces as parents will have productivity that meets farmers standards. But a rare percentage may have unique levels of tolerance to stress which meets the farmer’s goal.

After the breeder decides on the germplasm source, they will make crosses. This is where the breeders take advantage of the genetic variation that resides in different alleles found in the germplasm by selecting a male plant to pollinate a female plant. Remember, the goal of plant breeding is to make genetic improvements. When more genetic variation occurs among offspring from a cross, the more potential there is for genetic advancements breeders can accomplish with the breeding process. Sexual crosses allow unique gene combinations from the male and female to generate recombination in offspring which creates a continuum of different genotypes and thus phenotypes that present themselves in the progeny. A plant breeder must have a plan to evaluate this variation.

Breeders must have reliable methods for evaluating plant phenotypes so they can identify the best lines resulting from crosses.  Phenotype variation is controlled by both genetic and environmental variation. Some of the traits a breeder must select for in a breeding line are controlled almost entirely by the genotype of the plant. For example, a wheat breeder may have the goal of breeding a new cultivar that has awns (the long extensions of the glume structures that surround the seeds in a head of wheat, Fig. 3A) and the cultivar should also be tall but not too tall which will avoid lodging (falling over before harvest).

Awnless wheat (Fig. 3A left) is the genotype aa and awned (Fig. 3A right) is AA or Aa. Variation in the growing environment will not influence the development of the awned trait. In contrast, variation in height of the wheat plant is controlled by many gene pairs but will also respond to water availability. Plant breeders will measure the height of the same genotype in multiple environments to have confidence they can predict the plant height in a farmer’s field. It is crucial for the plant breeder to know to what extent environmental variation will affect the traits they need to evaluate to meet their new cultivar goals. These are the traits that will demand more of the time and land use resources of the plant breeder’s program.  Therefore, plant breeders are continually searching for proven technologies that have the potential to more efficiently use resources to evaluate phenotypes that are affected by both genetics and the environment.

Figure 3. Wheat traits. (A) Awnless vs awned wheat (the long “hairs” are awns) is genetically controlled such that environmental factors are minimally important. (B) Plant height is highly influenced by environment and must be measured in various environments to create an estimate.

(A) Figure 7 reprinted from “Advanced Backcross Breeding”, by P.S. Baenziger and P. Hain, 2000. (B)  CIMMYT- CESToluca - MEX - 05092018 – 0010 by A. Cortés, CIMMYT, 2020, Flickr. CC BY-NC-SA 2.0.