Background: plant science

I do not need to convince anyone of the importance of studying cancer treatment, heart disease prevention or the mechanisms of HIV/AIDS. The importance of plant science, on the other hand, is not that clear to everyone. This is a shame, because plant science has the potential to save many lives ánd to decrease the negative impact of humans on our planet.

Food shortage and hunger
In 2015 about 795 million people in the world did not have access to enough food to meet the minimum daily dietary energy requirements [1]. This is a huge number compared to the amount of people being diagnosed with cancer, 14 million in 2012 [2], or living with HIV / AIDS, 36.7 million in 2015 [3]. Hunger is caused by many factors, among them economic and political ones.  Environmental factors also explain a large part of food shortage in certain areas. Plant diseases cause 10 to 40% crop loss – depending on who you ask – each year [4,5], drought and extreme temperatures result in additional losses. Increasing temperatures due to climate change and stricter rules for the application of pesticides and fertilizers will increase the severity of these problems in the years to come. And remember, without food, there will be no people to get diseases for which we need to find a cure…


Increasing food availability through plant science
Plant science encompasses many subfields that together cover a wide variety of topics, including but not limited to: plant disease, plant response to abiotic factors such as light, temperature or nutrient concentrations, plant development, plant interactions with microbes in the surroundings and plant ecology. All of these subfields look at plants from different angles and not all of them have clear follow-ups that will increase food production. However, any extra knowledge that we gather on plants will help us understand them better. Ultimately, this will increase our ability to grow them optimally in the field and thus to increase food production.

A science success story
The discovery of the so-called submergence-tolerant (Sub1) rice varieties is a clear success story showing how data gathered in a laboratory can lead to increased food production. Rice is an important food source for many people, especially in Asia and Africa. While rice is a relatively flood tolerant crop, modern rice varieties do not do well when they are completely under water (submerged) or in low floods over long periods. While several local rice land races are tolerant to flooding, they have other traits that prevent farmers from using them, such as low yields or poor grain quality.

Discovery of a gene that makes rice plants flood tolerant
Researchers were interested in those local varieties, though: they wanted to discover which genes lead to the increased tolerance. They studied this by crossing food tolerant and flood intolerant rice varieties, like in the paper I described earlier on the discovery of another gene, HCR1, that was found to possibly have changed in plants in response to different aboveground water environments to increase plant fitness. Like in the previously described paper, a part in the genome was found to correlate with the phenotype of interest, in this case the increased tolerance to flooding. This part of the genome was named submergence-tolerant (SUB) 1.

Making varieties used in the field flood resistant
After the discovery of the part of the genome that makes local land races flood resistant, people wanted to use this knowledge to increase flood tolerance of varieties used by farmers in the field. In 2003, the International Rice Research Institute (IRRI) started a breeding program in which they crossed land races with SUB1 in their genome on the one hand with varieties used in the field on the other hand. Offspring with the full genome of the agriculture variety with only the addition of the SUB1 part from the land races were selected and distributed among farmers in, among other countries, Bangladesh and India. Large field trials were conducted and showed no difference between Sub1 rice and the original varieties apart from increased tolerance to submergence. This makes sense, considering that SUB1 is only expressed in submergence conditions. As visible in the photo below, Sub1 rice has a much greater crop yield then the commonly used varieties in flooded fields.

The original modern variety on the left, the variety with the SUB1 part of the genome from a local land race on the right
The original modern variety on the left, the variety with the SUB1 part of the genome from a local land race on the right. Photo source

Sub1 rice is a great success. Many parties, such as the Bill & Melinda Gates Foundation, are contributing financially to further distribution and research. For more information, visit the research organization’s  website.

Changing my blog’s focus
I am a plant scientist and very enthusiastic and optimistic about the ways that plant science can contribute to our society. With sufficient funds and talented people I think it is possible to create more success stories like the Sub1 rice variety. In the past months I have realized that only few people are aware of this important possible contribution of plant science to society. Therefore, I have decided to shift the focus of my ‘journal club’ and ‘background’ stories to be mostly plant related. In this way, I hope to open more people’s eyes to the possibilities of plant science. Who knows, maybe one day this increased awareness will result in something like a ‘plant research to feed the world fund’ in addition to the ‘world cancer research fund’ and the many other disease-related funds out there.

1: The State of Food Insecurity in the World 2015, by the Food and Agricultural Associations of the United Nations.
2:Cancer, by the World Health Organisation.
3: Global health observatory data: HIV / AIDS, by the World Health Organisation.
4: Combating plant diseases is key for sustainable crops, by Science Daily (2011)
5: Almost 40 per cent of worldwide crops lost to disease, by The Crop Site, 2012

Information on the Sub1 research and application is from:
Ismail AM, Singh US, Singh S, Dar MH, Mackill DJ (2013) The contributin of submergence-tolerant (Sub1) rice varieties to food security in flood-prone rainfed lowland areas in Asia. Field Crops Research 152: 83-93.

Background: RNA sequencing (method 1)

The goal of the method
RNA sequencing is a method that is used a lot in molecular biology laboratories around the world. The method is used to measure the expression of genes. All cells in a certain organism have the same genes. Differences in the expression of those genes between the cells results in different cells being able to perform different functions: an immune cell can combat pathogens, a muscle cell can contract, a cell in a plant leaf can perform photosynthesis. Therefore, studying gene expression can learn us more about the developmental processes underlying the differentiation of the cells and the formation of multicelllular organisms like us humans. In addition, changes in gene expression allow a cell – and thus also multicellular organisms –  to respond to the environment. Knowing which genes are expressed in response to certain stresses, such as heart failure in humans, or drought in plants, can give us an idea of how cells and organisms deal with those stresses. Ultimately, this can aid in for example developing treatments to prevent heart failure in humans or breeding programs to increase tolerance to drought in crop species.

The method itself
RNA sequencing measures gene expression by measuring the amount of RNA present. As explained here, RNA is the intermediate in the process of using the DNA code as a ‘building plan’ to form a protein. The more RNA from a certain gene is detected, the more active the gene was. Once the order of letters in a string of RNA, in other words the sequence of a piece of RNA, is known, it is easy to determine from which gene it originated. This is easy because the sequence of a piece of RNA corresponds to certain letters of the DNA sequence it was made from: an A in the RNA is a T in the DNA, a G in the RNA is a C in the DNA, etc. Thus, once the sequence of a piece of RNA is known, one can deduce the sequence of the DNA it was made from. With databases on the internet, the gene corresponding to this DNA sequence can be determined.

To measure the amount of RNA present, the RNA is first converted to cDNA (complementary DNA) by the researcher. Thus, synthetic A, T, C and Gs are combined with the mRNA pieces, in addition to ‘reverse transcriptase’: a protein that can bind DNA nucleotides one by one to an mRNA molecule to create a complementary piece of DNA: the cDNA. This is necessary, because the sequencer, the machine that reads the sequences, cannot read RNA. The cDNA samples are then sent off to a sequencing facility, where the sequencer ‘reads’ all the pieces of cDNA. In other words, it reads the order of A, T, C and Gs of all the pieces of the cDNA present. This information is put into a huge file, containing all the sequences, the so-called reads, that the sequencer read. This file is returned back to the researcher, who can use a computer program to find out from which DNA the RNA-turned-into-cDNA pieces originated.


In the above-shown case, the red lines represent the RNA sequences of which the cDNA pieces were read by the sequencer. The black line represents the DNA of the studied organism. With a computer program the reads have been aligned to the genome based on their sequence . Finally, by looking up which parts of the DNA correspond to genes – this information is available online for most organisms -, the researcher knows which genes are expressed. In this case, gene 3 is expressed a lot, whereas gene 4 is not expressed at all.

Use of the method
Generally, the gene expression of not one, but several samples is determined in an RNA sequencing. A healthy heart of a newborn and a healthy heart of an adult, for example, or a diseased heart and a healthy heart. By comparing gene expression in the two (or more) conditions, one can learn about developmental processes and/or stress responses.

RNA sequencing is used in many different fields of biology, ranging from cancer biology to microbiology. On this website several papers are discussed using this method: this paper on light perception in plant roots and this paper on heart development.

Background: DNA and the central dogma

DNA and its messenger RNA
DNA is the genetic code that every organism inherits from its parent(s). If you compare a cell with a factory, the DNA is the entire set of building plans for all the different machines in the factory and any other instructions necessary for the factory to function. Genes are the parts of the DNA that correspond to the building plans. In the case of a cell, the building plans contain the instructions for the formation of proteins and other biomolecules essential to the cell’s survival. To build a machine in a factory, a copy of the correct building plan needs to be taken to a workshop. Similarly, to construct proteins in a cell, a copy of the correct gene needs to be taken to the protein-builders: the ribosomes. This copy is called messenger RNA (or mRNA).

DNA and RNA composition
When observed under a microcope, DNA looks like a twisted ladder. This structure is called a helix. It consists of two parallel strands of chemical compounds called nucleotides, each of which is loosely bound to its partner nucleotide on the parallel strand. DNA consists of four nucleotides: adenine (A), thymine (T), cytosine (C) and guanine (G). A can only loosely bind to T, and vice versa, and C can only bind to G. Thus, if one strand of the DNA helix reads ‘AGATCC’, the parallel strand, read in the same direction, will read ‘TCTAGG’. RNA also consists of nucleotides, but instead of T, it contains uracil (U). In contrast to DNA, RNA is most often single stranded.

The central dogma
When a certain protein is required in a cell, an mRNA copy has to be made from the corresponding gene. To make this copy, the DNA at the site of the gene detaches from the parallel strand. This unwinding of the helix lets RNA nucleotides bind. Once the entire gene is covered by the correct RNA nucleotides, the formed mRNA strand leaves and moves to the ribosomes, that is, the protein builders. There, the mRNA ‘building plan’ is used to make the required protein. DNA –> mRNA –> protein is known as the ‘central dogma’ of molecular biology.

Gene expression determines a cell’s function
Each cell of a multicellular organism, such as a plant, fish and yourself, contains the same DNA. However, cells within the organism can perform very diverse functions. This is possible because different genes are active in different cells. Ultimately, this results in different proteins being made and different cells being able to perform different functions: an immune cell can combat pathogens, a muscle cell can contract, a cell in a plant leaf can perform photosynthesis. Changes in the environment also influence gene activity, allowing a cell or organism to respond to the changes.

Genes are the parts of the DNA that code for proteins. To make proteins, a copy of the DNA, called mRNA, is moved towards the protein-builders, where the new protein is made. Changes in gene expression govern cell development and function and its responses to the environment. In multicellular organisms, gene expression in all the individual cells ultimately determines the appearance and fitness of the total organism.

For more information, see: