New plant gene editing approach improves speed, scalability and heritability.
A study recently published in Nature Plants outlines a new approach that may significantly speed the development of new plant varieties by skipping tissue culture and boosting heritability. The technique, developed by Evan Ellison, a graduate student in the lab of Dan Voytas, a professor in the College of Biological Sciences' Department of Genetics, Cell Biology and Development, draws on the ability of RNA viruses to effectively deliver genetic information to plant cells. Ellison collaborated on the study with Voytas, a master's student in the Voytas lab, and colleagues at the University of California, Davis.
We anticipate the outcome of our research program will be a highly facile gene targeting system that can be employed in a variety of plant species to study gene function.
Homologous recombination in plants
Various plant genome projects have made great strides in identifying the many genes that dictate plant growth and development. Understanding how plant genes work in metabolic and developmental pathways is the current challenge faced by plant functional genomics. Although a number of tools are available to study plant gene function, one tool is sorely lacking: the ability to make precise insertions, deletions or substitutions in plant genes through homologous recombination or gene targeting. Gene targeting will make it possible to take plant genomics to the next level, by linking DNA sequences to biological functions unique to plants. Furthermore, gene targeting enables the biosynthetic capacity of plants to be harnessed to produce the many products required by a growing world population, including specialty chemicals, proteins, oils and carbohydrates for food, medicine and industry.
The Voytas lab has implemented a method for gene targeting that allows specific DNA sequence changes to be introduced into plant chromosomes with high efficiency (Plant Journal 44:693). Fundamentally, gene targeting is a DNA swapping reaction. A DNA fragment carrying a desired sequence is introduced into a plant cell, and it replaces the native or endogenous copy of the gene. To enhance the efficiency of gene targeting, a chromosome break is created at the site of modification (the target). An enzyme called a zinc finger nuclease (ZFN) is used to generate the chromosome break. ZFNs have two components: a DNA recognition domain (a zinc finger array) and a nuclease that cleaves the chromosome. Zinc finger arrays can be designed to recognize any site in the plant genome, thereby making it possible modify any chromosomal sequence.
Current research is directed at developing zinc finger nuclease-assisted gene targeting for widespread use, including establishing key parameters for high frequency gene replacement and robust methods for the design of zinc finger arrays. Achieving this goal is facilitated by the Zinc Finger Consortium—a group of scientists dedicated to promoting applications of zinc finger proteins for genome modification.
Helpful Research Links
The Center for Precision Plant Genomics
University of Minnesota Center within the College of Biological Sciences. Developing plant genomes-by-design, made possible by recent advances in gene editing and plant synthetic biology.
TAL Effector Science (scoop.it)
Information on novel DNA-binding proteins of bacteria and their biotech use
TAL Effector Nucleotide
Targeter 2.0
Cornell University targeting tools.
The Center for Genome Engineering
University of Minnesota within the Medical School. Developing methods for modifying DNA in living cells. Applications of CGE technology range from enabling gene discovery, to making better plants and animals for agriculture, to regenerative medicine, and to providing therapeutic strategies to correct mutations underlying genetic disease.
The Zinc Finger Consortium
Maintained by the Joung lab at Massachusetts General Hospital and Harvard Medical School. Committed to developing resources, software, and other tools for engineering zinc fingers and for performing genome engineering that are robust, user-friendly, and publicly available to the academic scientific community.
The Zinc Finger Database
ZiFDB is a web-accessible database that houses information on individual C2H2 zinc fingers (ZFs) and engineered zinc finger arrays (ZFAs). ZiFDB serves as a resource for biologists interested in engineering ZFAs for use as sequence-specific DNA-binding reagents.
Learn more about the ZiFDB in our 2013 Nucleic Acids Research publication.
Genome Engineering Toolkit
Online resource to aid in vector selection and construct design. Learn more about the toolkit in our 2017 Plant Cell manuscript A multi-purpose toolkit to enable advance genome engineering in plants.
AddGene
A nonprofit global plasmid repository. They archive and distribute plasmids for the Voytas lab.
TalEngineering.org
Maintained by the Massachusetts General Hospital. A comprehensive resource of information for practicing engineered TAL (Transcription Activator-Like) effector technology.
This newsgroup may be particularly useful to novice genome engineers