Novel tool to inducibly knockout genes at cellular resolution in plants

Genome editing techniques have revolutionized research in life sciences. The Mähönen group at the University of Helsinki took advantage of these techniques and developed a novel genetic tool for plant research that enables efficient generation of target gene knockouts in desired cell types and at desired times.

Most of the discoveries in the modern plant biology have originated from studies utilizing molecular biology or molecular genetic techniques. In this approach, mutation in a gene i.e. gene knockout reveals its role in a biological process. However, some genes are central players in plant physiology or development – a mutation in these genes cause lethality or severe developmental defects. Typically, such mutants have several defects in their development and physiology, thus making it challenging to separate the primary defect from the secondary defects caused by the mutation.

To identify the primary defects of such, essential genes, researchers have developed various conditional gene manipulation systems. However, the challenge is, there are currently no genetic systems available to knockout a gene conditionally, completely or cell-type-specific manner. Such a system would enable identification of primary functions of the essential genes.

Research group led by Dr. Ari Pekka Mähönen is studying development of vascular cambium, a lateral meristem that produces wood in trees and in other plant species. Vascular cambium appears late in development, therefore knockouts in several essential genes cause strong phenotypes in plants long before the cambium has even been established. This makes the identification of the role of the essential genes in cambium development even more difficult than in younger part of plants.

“To tackle the problem, Xin Wang, a PhD student in my lab decided to combine a tissue-specific inducible system developed earlier in my lab with the popular CRISPR-Cas9 genome editing system. With such a system, one could knockout genes in desired cells at desired times. Initially, I thought that the genome editing system might not be efficient enough to knockout target genes in the somatic cells. Luckily, he nevertheless decided to generate the system and test it in Arabidopsis thaliana. To my big surprise, the system worked efficiently and precisely in the targeted cells.”

The inducible genome editing (IGE) system performed well with three different genes tested. These studies enabled the identification and confirmation of the precise function of the three genes in root development. The IGE system and these findings were published in Nature Plants. Additionally, beyond the published paper, the Mähönen lab has successfully tested the IGE system with several other target genes. Plasmids containing the IGE system has already been distributed to several other labs around the world, thus it is possible that the IGE system will be widely used within plant biology community. Perhaps, with help of IGE system, we will have better understanding how the essential genes function in plants.

Original publication:

Nature Plants: “An inducible genome editing system for plants“, doi: 10.1038/s41477-020-0695-2

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