Crop breeding

What are phenotyping and genotyping?

You most likely know that all living things have DNA. This ladder-like, complex, molecule found in each cell carries the genetic information to control growth and functioning of that organism. DNA is like an “instruction manual” that gives every living plant and animal its own unique traits.

Each trait is controlled by one or more genes in the DNA. For example, in humans, eye color, height and even whether you have a tendency to get freckles, are controlled by genes. In plants, their height, leaf area, yield, etc., are controlled by DNA. Even traits like disease resistance, drought tolerance, or flower color can be controlled by one or more genes in the DNA.

Man in barley field with tablet collecting data
Research manager Scott Fisk, Oregon State University, collecting field data on their current barley crop. This is called phenotyping Credit: CSSA staff

In order to find the gene(s) within a cell that control a trait, breeders collect data from the field, greenhouse and the lab. We collect physical, measurable data about specific plants. For example, we may score a trait such a disease resistance on a 1 to 9 scale (least to most resistant), or measure plant height with a yardstick. This is referred to as phenotype. The entire process is called phenotyping and the data collected is very important to crop breeders.

We take as many measurements of the trait as possible. We look at sometimes hundreds of plants in a field or greenhouse. We input this data into our tablets, or even notebooks. It is important to measure these traits in other field locations. We also study our plants over multiple years to see how weather and climate can affect them.

On a cellular level inside each plant, the DNA is made up of chromosomes. Let’s say that within the DNA “instruction manual” these chromosomes are very specific diagrams or lists that cells can follow.  Before DNA ‘sequencing’ became more widely available, breeders would draw a “linkage map” that helped predict where on the DNA each trait was located. The linkage map contains an outline of the chromosomes, and is helpful to determine the “nearest stopping point” to the trait we are looking for.

Many plants now have entire genetic maps done, or better yet, have all their DNA sequenced. It’s a big deal to have a plant’s DNA sequenced, and can help breeders in selecting new crop varieties to develop. No matter how these chromosome maps are made – either through linkage maps or sequencing, this step is called genotyping.

Crop breeders often are working to find plants with new traits. This could be resistance to one particular pest, like rust resistance. Or, we can be looking for ways to increase yield, which is a very important trait! So, we are breeding for improved phenotypes – and we can look at genotypes to predict outcomes of our breeding work.

woman in white lab coat with blue gloves inserting a tube into a centrifuge
Christine Bradish inserting a tube of extracted DNA into a centrifuge; later she will study the DNA to help predict yield of a natural plant chemical called sclareol. Credit: SV Fisk

In the lab, we extract DNA from the plants and compare them at the molecular level. If we are looking for disease resistance, for example, we would extract DNA from plants that are both susceptible and resistant to the disease, i.e., a “1” and “9” on our phenotyping scale. Then we are able to compare the DNA of these two plants.

corn cob with dna strand with corresponding traits
Each trait of an organism will correspond with one or more locations in the DNA. This genetic code is called genotype, whereas the traits are called phenotypes. Credit: ASA/CSSA staff.

We use statistics to compare the physical “phenotype” data from the field to the genetic “genotype” data in the lab in order to find where on the chromosome (think a specific part on a diagram in an instruction manual) the trait for disease resistance is. If a plant has the gene/genes for disease resistance, then the plant itself will be more resistant to disease.

In the same way, if a plant has more genes related to good yield, that plant will have a better yield than one with less DNA for yield.

The plants susceptible to the traits we are researching will be different on the genetic level from the plants without the traits. Then we can choose to grow only those plants with superior traits, and eliminate plants with inferior traits.  This saves time, space needed to grow plants in the field, and phenotyping effort (bottom line $$$).

Genetics can help us predict which plants will be the healthiest, and therefore produce the most yield. This valuable information allows breeders to know which varieties growers should select, and helps them choose the healthiest plants in the future.

Answered by Christine Bradish, AVOCA. To read more, or watch a video of Dr. Bradish in action, visit this page!

About us: This blog is sponsored and written by members of the American Society of Agronomy and Crop Science Society of America. Our members are researchers and trained, certified, professionals in the areas of growing our world’s food supply while protecting our environment. We work at universities, government research facilities, and private businesses across the United States and the world.

Categories: Crop breeding

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