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Using RNA-seq to understand plants and improve crop yield

Plants are the basis of all life on earth, sustaining most of the Earth’s ecosystem by providing humans and animals with food and other resources. Green plants provide most of the world’s oxygen and harness the sun’s energy to produce their own food which provides the energy to sustain the ecosystems in which they are found. As a result, humans, and animals are directly and indirectly dependant on plants for food. There are over 370,000 species of plants currently identified on Earth. Aside from food, plants are also important for use as raw materials in industry and energy production. Plants are also used in medicines, spices, paper products, clothing, and building materials. Farmers and agriculture are important for producing the plants that humans depend on in large quantities to ensure food security for the increasing population. To help farmers to do this, scientists carry out research that looks at how plants work and how they respond to different conditions to help improve plant breeding.

Plant science or botany is multidisciplinary and has become increasingly more important to improve agriculture and increase crop production as the world’s population continues to grow. This branch of science has grown from understanding how and why plants grow the way they do to tackling some of the most important challenges of our time such as how plants may adapt to climate change, how we can ensure food security for a growing population and how to protect biodiversity. Recent research has looked to investigate these problems by looking at how plants can cope with stress and what can be done to improve the resilience of crop plants to increase production. For example, wild relatives of plants used in agriculture have the potential to contain numerous genes that can provide genetic sources for germplasm improvement by incorporation or introgression of new genes into the breeding population. What this means simply is that scientists can transfer genes from wild populations to closely related crop plants which has been shown to increase stress resistance and improve crop yield.

To first understand what roles genes play in plant survival under certain conditions, researchers need an annotated genome. A genome is a complete set of genetic information of an organism and it can be deciphered using RNA-sequencing technologies (RNA-seq). RNA-seq is a next-generation sequencing (NGS) technique that can be used to examine the RNA sequences that are present in a sample. The full range of RNA expressed by an organism is known as the transcriptome. Understanding this transcriptome is essential for linking the information contained within the genome with the functional proteins that are expressed. RNA-seq can be used to tell us which genes are turned on or off within a cell, under what conditions they are activated, and what their level of expression is. This information allows scientists to understand the biology of a cell and assess the changes that occur under different conditions. For example, researchers can use RNA-seq data to look at the role genes play in stress resistance and improving crop survival. If we take plant research as an example, this could include looking at stressed and non-stressed cells that have been exposed to different levels of salinity and comparing the transcriptome between cells from different tissues or across samples from different plants. This would enable the researchers to gain an insight into how plants may respond to a certain condition.

RNA-seq is a more powerful tool than traditional techniques as it not only allows researchers to look at the transcript numbers of different genes to see what genes are being transcribed at any given time but it could also highlight novel transcripts, alternative splicing, and transcript variations. In addition, this technique can also be used to identify biomarkers that are present under certain conditions. RNA-seq technologies offer high throughput and high accuracy and unlike more traditional methods such as quantitative polymerase chain reaction (qPCR) require low initial RNA amounts. Research in this area has further benefited from the expertise of Novogene, a leading company in RNA-seq technologies. Novogene has extensive experience in RNA-seq and offers several solutions for assessing changes in the transcriptome. When coupled with Novogene’s expert skills in bioinformatics, this provides researchers with the whole picture of what is going on with a cell’s transcriptome instead of analyzing individual genes as is done is more traditional techniques which could cause them to miss key changes in gene transcript numbers that could provide important information for advancing our understanding of plant science.

The use of RNA-seq technologies has already been used to identify differences in gene expression between wheat and barley and their closely related wild plants. This has enabled researchers to identify genes that could be used to benefit wheat breeding and improvement. Wheat is a staple food source for a large percentage of the world and its production is expected to double by 2050. The use of RNA-seq technologies, therefore, has great potential in advancing plant science and taking steps towards providing food security for an ever-increasing global population.


  1. Liu, Y., Dai, X.B., Zhao, L.K., Huo, K.S., Jin, P.F., Zhao, D.L., Zhou, Z.L., Tang, J., Xiao, S.Z. and Cao, Q.H., 2020. RNA-seq reveals the salt tolerance of Ipomoea pes-caprae, a wild relative of sweet potato. Journal of Plant Physiology, 255, p.153276.
  2. Zhou, Y., Bai, S., Li, H., Sun, G., Zhang, D., Ma, F., Zhao, X., Nie, F., Li, J., Chen, L. and Lv, L., 2021. Introgressing the Aegilops tauschii genome into wheat as a basis for cereal improvement. Nature Plants, 7(6), pp.774-786.
  3. Zhu, W., Xu, J., Chen, S., Chen, J., Liang, Y., Zhang, C., Li, Q., Lai, J. and Li, L., 2021. Large-scale translatome profiling annotates the functional genome and reveals the key role of genic 3′ untranslated regions in translatomic variation in plants. Plant Communications, p.100181.