Plant genotype – the genetic identity

“Who am I?” is one of life’s most defining questions. The latest molecular science advancement these days may have the answer to this.

You may have heard about the term ‘genotype’. It's mostly about genes. Not the kind you wear, but the one found deep in your cells.

All living things: humans, plants, and animals have DNA, which is short for DeoxyRibose Nucleic Acid. Their DNA contains their hereditary information. Inside the DNA molecule are sections called genes. Each gene instructs the cell to produce proteins which determines a trait or characteristic, such as the color of a human’s eye or a color of flower in plants.

A living organism’s complete set of genetic instructions or all of its genes is called a ‘genome’. A genome has all of the information needed to build an entire organism and for that living organism to grow and stay alive. Advancements in science and technology in today’s world has led to the understanding of how an organism’s body works. It takes only a few days to determine all the functions of its genes and at a fractional cost as compared to the earlier times. For example, the first plant genome of Arabidopsis thaliana (L.) Heynh. took 10 years to finish and cost approximately US$ 100 million. Using the current generation of DNA sequencing technologies, A. thaliana genome can now be sequenced with a USB device on a regular laptop at a cost of under US$ 1000.

With this post, we go on a quest to disseminate information on many elements of plant genetic studies in an easy-to-understand way for everyone out there. Let us begin by learning the fundamentals of genetics:

What is a plant genotype?

The genotype is an organism's genetic makeup, or its genetic blueprint. A genotype contains the precise genes necessary to run an organism, much as the code behind a software program holds the information essential to run the program.

There is a great deal of DNA that we all share of course, that’s why we are all humans, but there is also a great deal of variation in sequences between individuals. Plants of the same species share the same story! Most plant species inherit two genes for every trait from the parental plants – one copy from the male parent and the other from the female parent. These genes come in pairs like your socks. But unlike your socks, the genes in a pair are not always identical. One might be a striped sock and the other might be plain white. These different copies, or versions, of a gene are called ‘alleles’. Different combinations of alleles will make different ‘phenotypes’ (visual appearances of a plant). Each pair of alleles represents the genotype of a specific gene.

An example of plant genotype

Let’s look at an example: In the summer, my brother and I went to visit our cousins who live in the countryside. During this fun-filled period, we were asked to pick pea pods from the garden, open the pods and collect the peas.

'Oh my!' exclaimed my brother. 'Look at these yellow peas.'

'Some of mine are green,’ I said. 'How can that be? The pods came from the same vine.'

What explains these findings?

We discovered that the majority of the peas were yellow, implying that yellow is the dominant, or more frequent, color of peas. We use an uppercase letter to indicate a dominant allele. In this situation, we chose uppercase Y to symbolize the yellow pea gene and lowercase y to represent the green pea gene since green was a rare pea color or recessive allele.

Is genotype similar to a phenotype?

One should not confuse genotype with the similar sounding phenotype. When we describe how an organism, or living thing, looks like, we are describing its phenotype. Phenotype is the physical characteristics of an organism, everything you can observe from how they look to how they act.

You can remember that phenotype is all about the physical as phenotype and physical both start with ''ph”.

Phenotypes were first observed by the Austrian monk Gregor Mendel in his remarkable experiments with pea plants. He observed seven different phenotypes in his pea plants, namely:

  1. Pod color (yellow or green)
  2. Pod shape (inflated or constricted)
  3. Seed shape (round or wrinkled)
  4. Seed color (yellow or green)
  5. Flower color (purple or white)
  6. Flower position (axil or terminal)
  7. Stem length (long or short)
Image credit: "Mendel's experiments: Figure 3," by Robert Bear et al., OpenStax, CC BY 4.0

Mendel crossed different pea plants and observed the differing phenotypes of the offspring. Using this data he concluded that some traits were dominant and others were recessive traits. You can also observe his findings in the picture above.

Genotyping - the technology for genetic research

The process that identifies the differences in DNA sequences of an organism using various biological tests is called genotyping.
Genotyping techniques include:

  1. Restriction Fragment Length Polymorphism Identification (RFLPI);
  2. Random Amplified Polymorphic Detection of genomic DNA (RAPD);
  3. Amplified Fragment Length Polymorphism (AFLP);
  4. Polymerase Chain Reaction (PCR); and
  5. DNA sequencing.
  6. In plants, Genotyping by Sequencing (GBS) is a powerful tool to accelerate plant breeding processes.

In the coming articles, we will go through each genotyping approach in depth.

Application of plant genotyping

The study of heredity and genes is the rapidly developing field of molecular biology. It plays an important role in understanding all aspects of biology and the modern advances in crop improvement, different aspects of agriculture, and the pharmaceutical industry. Understanding the function of plant genes and the mechanisms that control them helps scientists to select for genes and traits that have a favorable impact on how plants grow, such as higher yield or high temperature tolerance. Plant breeders then utilize this information to improve the crops we grow.

Formerly, scientists solely relied on observational methods to choose plants with superior phenotypic features such as height, shape, and so on. However, plant selection in the present era is highly reliant on molecular biology techniques, such as genotyping. A recent study from the John Innes Centre UK confirms the importance of molecular biology techniques. For instance, they discovered that the cold temperatures experienced by a broccoli plant in autumn and winter had an influence on the flowering time. This is vital for crop planning and scheduling. It eventually led them to develop a new innovative short life cycle broccoli that would allow broccoli production in the UK all year round, reducing imports, waste, and dependency on overseas production.

For more interesting articles diving into the fascinating sphere of plant science, keep checking this space!

By Priyanka Biala | 29-March-2022

About the author

Priyanka is based in Toronto, Canada, with her partner and two adorable kids (a dinosaur lover and a bibliophile). Priyanka is a scientific enthusiast with a master’s in biotechnology. She has spent the last decade exploring science and technology with various research institutes and multinational corporations. She fervently setups the labs and scientific procedures, as well as participates in biotech agricultural research on a variety of crops with renowned scientists in the area. Right now, she is deep diving into the regulatory processes in the pharmaceutical industry. In her leisure time, she likes spending time with friends and family, playing Scrabble and hosting get togethers.