image: The presence or absence of remaining foreign DNA from the crossbred progeny of the genome-edited crop and the original crop cultivar can be determined by GenEditScan, based on the k-mer method.
Credit: National Agriculture and Food Research Organization (NARO)
Genetic changes have the ability to alter crop characteristics, and some crop breeding techniques take advantage of this. Conventionally, genetic engineering has relied on natural or artificial mutations. In recent years, genome editing technology has been grabbing attention. Genome editing technology can target and cut specific DNA sequences, causing mutations in target genes. This makes it possible to develop new cultivars efficiently.
A common method for creating genome-edited crops involves introducing foreign DNA temporarily that produces an enzyme to cut the target DNA. However, when the crops are grown outdoors, it is necessary to ensure that the foreign DNA has been removed in Japan.
NARO has developed the world's first k-mer analysis method and has been publishing analysis tools since 2020. The k-mer analysis can efficiently and accurately detect foreign DNA sequences by analyzing huge amounts of DNA sequence data decoded by next-generation sequencers and conducting statistical tests. However, the procedure for using the tool was complicated, as it required a researcher specialized in genome analysis and also it doesn’t have any correction function to reduce false positives. Therefore, this time NARO has improved the existing analysis tools to be user friendly with more accurate determinations and developed an analysis tool called "GenEditScan". This analysis tool is available in this website. (https://github.com/hirsakai/GenEditScan)
GenEditScan has been designed to analyze the presence or absence of the genome editing enzyme gene in a single step. The user has to input genomic information of the genome-edited crop and the original crop cultivar decoded by a next-generation sequencer, and the nucleotide sequence information of the genome editing enzyme gene. Also, by correcting the statistical test results generated in the analysis process, false positives when performing simulations under specific conditions can be reduced to less than one-third. This enables us to achieve more accurate determinations.
Researcher Dr. Hiroaki Sakai said, "A major feature of GenEditScan is that anyone can easily obtain the same results, regardless of their knowledge or experience. It can be used for various agricultural, forestry, and fishery products, and its accuracy has been demonstrated in tests using actual genome-edited crops. We hope that GenEditScan will become a new option for testing genome-edited crops in the future."
The analysis tool that preceded GenEditScan has a track record of being used in Japan as a testing method for growing genome-edited crops outdoors (three cases: rice, potato, and wheat). In the future, GenEditScan is expected to be used as the standard testing method for growing genome-edited crops outdoors, both domestically and internationally. We also hope that it will contribute to the efficient development of useful crops using genome editing technology.
This research was carried out at the Research Center for Advanced Analysis, NARO (NAAC) under the support by MAFF Commissioned project study on “Accumulation of scientific knowledge for promoting public understanding of genome editing technologies” Grant Number JPJ008723.
In addition to developing the above-mentioned programs, NAAC is also actively promoting program construction, research and analysis support, provision of equipment and facility use, and collaborative research and development based on these activities.
About National Agriculture and Food Research Organization (NARO)
NARO is the core institute in Japan for conducting research and development in a wide range of fields, from basic to applied, for the development of agriculture and food industries.
For more information, visit https://www.naro.go.jp/english/index.html .
Method of Research
Data/statistical analysis
Subject of Research
Not applicable
COI Statement
The authors declare no conflicts of interest associated with this release.