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Blog S1E4 - Genotyping Galore: Crafting Crops From Genetic Blueprints

Breed, Sow, Grow: Adventures and Challenges in Plant Breeding

Here we are again, dear friends of plant science and plant breeding! After exploring phenotype and phenotyping in the last post, today we look into genotyping. Genotyping is a powerful tool that holds the key to truly game-changing plant breeding and shaping the future of agriculture. Together, we'll learn what's behind genotyping and dive into its applications, importance, and the challenges it brings. So grab your lab coat and get ready to read more about the very core of plant genetics.

The genetic blueprint of plants

We already know that the phenotype is the appearance of the plant (or any organism), i.e. all the characteristics of a plant, which in the broadest sense includes all external and internal structures and functions. It is determined by the genotype (G), the environment (E) in which the plant grows, and the interaction of both (GxE). The genotype, in turn, is the sum of all genes of a plant, the genetic makeup. It represents the genetic blueprint.

Genotyping is the process of identifying the specific variations in the genetic makeup - also called alleles - of individual plants. It helps us to read and understand the plant's blueprint so that we can improve plants based on DNA (or deoxyribonucleic acid, a series of molecules that contain the genetic instructions for the development, function, growth, and reproduction of all known living organisms). How does it work? By genotyping, we analyze an individual's DNA sequence and compare it to a reference sequence - which is a well-characterized genome from the same species - or to the DNA of another plant. By studying these differences, scientists can gain insight into the plant's traits and breeding potential.

Studying the variations

Genotyping focuses on the variations in DNA between individual plants and within whole populations. These are called “genetic polymorphisms”. Scientists study these variations to understand traits, improve crops, and ensure plant diversity. It's like looking at different blueprints for our house, one where the kitchen and living room are next to each other and the other where there is no living room. In plant breeding, polymorphisms are invaluable natural biomarkers - naturally occurring characteristics by which physiological processes, diseases, etc. can be identified. They help us to track the inheritance of certain genes, determine their exact position, and learn which genes are behind a phenotypic expression. They lead us to the genes responsible for desirable plant traits, be it disease resistance, high yield, or nutrient content. Probably the most common type of genetic variation are single nucleotide polymorphisms or SNPs (pronounced "snips").

Genotyping in action

But what do scientists and plant breeders do when they want to determine the genetic variations present? The first step is to take a tissue sample, usually leaves, for DNA extraction. As this involves such small amounts of DNA and our current equipment is unable to read it, the extracted DNA is copied using PCR (polymerase chain reaction) to facilitate the analysis. DNA sequencing is the process of finding out the exact sequence of the DNA molecules. We are now able to identify genetic variations and patterns within our plant population and create genetic profiles and maps. Such genetic maps show the positions and distances between genes or markers on the chromosomes. With that information, we can determine which genetic variations correlate with certain traits - this is called trait association. In breeding programs, this information is used as a guide to select and cross plants with desired traits and develop new better-adapted varieties.

It should also be mentioned that there are a variety of DNA sequencing methods. These sequencing methods vary in the amount of DNA that can be sequenced within a given time frame, read length, accuracy, cost, and data analysis approaches. 

Why perform plant genotyping?

Plant genotyping can be useful in various aspects:

  • Plant improvement: Identifying plants with desirable traits such as disease resistance and higher yields.
  • Efficient breeding: Speeding up breeding by selecting genetically advantageous plants, reducing time and resources.
  • Understanding population structures: Disassembling the genetic diversity within and between different plant groups and thus reconstructing the genetic family trees and origin stories.
  • Adaptation to climate change: Identifying climate-resilient genes for plants that respond better to environmental changes.
  • Reconstructing pedigree: Dissecting genetic diversity within and between different plant groups to reconstruct genetic relationships (pedigree).
  • Optimizing agricultural practices: Genetic markers help farmers make informed decisions to maximize yield and quality.
  • Nature conservation and biodiversity: Studying genetic diversity supports nature conservation and prevents the loss of important genetic resources.


Although genotyping is an indispensable tool, it is not without its challenges. Complex genomes, lack of data, cost, and the need for reference sequences can present hurdles. However, scientists are continuously developing innovative solutions to overcome these limitations and realize the full potential of genotyping.

Plant genotyping is leading the way in plant breeding to ensure an improved and climate-adapted agricultural future. It bridges the gap between phenotype and genetic origin of trait expressions, allowing us to breed plants that thrive in diverse conditions and meet the ever-increasing demands of climate change. Whenever you see a lush field of crops, remember that dedicated scientists from a wide range of disciplines are shaping the future of agriculture.


Stay tuned for our next episode, "Data Drama: Breeding's Behind-the-Scenes"!

If you missed any of our previous episodes, read them here:
S1E1 - Breeding Brilliance: Unveiling the Crop Superheroes
S1E2 - Genius Genes: Unlocking Genetic Diversity
S1E3 - Phenomenal Phenotyping: The Science of Collecting Data


Do you want to know how Computomics can support plant breeding for the future?
Check out our Climate-Smart Breeding page or contact us!

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