New sequencing technique boosts gene editing potential

Gene editing has been touted as a revolutionary technology for plant breeding.

It allows scientists to delete genes from a plant’s genomes or add genes from the same family of plants to achieve a desired crop trait.

Maybe a canola with more resistance to a fungal disease.

But there’s one problem.

Much of the time, scientists don’t know which genes to remove or which ones to add.

“Where we still struggle, I think every breeder would say this, is there are a lot of genes,” said Richard Cuthbert, a wheat breeder with Agriculture Canada in Swift Current. “In bread wheat there’s 120,000 genes, roughly. Which ones do we target for gene editing?… (It) does promise to be a powerful tool, but there still has to be a lot of understanding of those genes and how they work.”

A new technology may provide an answer to this dilemma.

On Aug. 10, University of Saskatchewan and Agriculture Canada researchers said they had decoded the full genome of the black mustard plant. Black mustard is grown in India and other countries in South Asia. It’s closely related to the mustard and canola grown in Western Canada.

“This work provides a new model for building other genome assemblies for crops such as wheat, canola and lentils. Essentially, it’s a recipe for generating a genome sequence that works for any crop,” said Andrew Sharpe, director of the Plant Phenotyping and Imaging Research Centre at the U of Sask.

“This means we can make breeding more efficient because we can more easily select genes for specific desired traits.”

The scientists used Nanopore, a long read sequencing technology developed in England, to piece together the black mustard genome. In a paper published in Plant Nature, the researchers said the technology could unravel the mysteries within a plant’s DNA.

One of the technologies used in this University of Saskatchewan’s crop research is the MinIon, at less than about $1,300 the Oxford Nanopore’s miniature tool for gennome sequencing is lowering the cost the process and making it more available to researchers. The tool uses protein nonopores to sequence DNA in real time. | University of Oxford photo

“It is only recently, with the advent of long read sequencing technologies, that we are beginning to uncover previously uncharted regions of complex… plant genomes,” they wrote. “Such information also provides a foundational tool for crop improvement… (and) the rapid selection of agronomically important traits and to exploit modern breeding tools such as genome editing.”

During the last decade, scientists have sequenced the genomes of multiple crops. They used technology that could read the genetic code of small fragments of DNA. The fragments were then pieced together into a genomic sequence.

“LRS (long read sequencing) allows for the retrieval of much longer sequencing reads than widely used SRS (short read) systems (75-300 base pairs),” says the University of Cambridge. “Some long-read sequencing platforms have produced sequence reads of 882,000 (base pairs)…. However, read lengths of 10,000-100,000 (base pairs) are more common.”

The technology is not perfect, but it allows scientists to peek at “previously hidden features of plant genomes,” said Isobel Parkin, a canola genomics expert with Agriculture Canada in Saskatoon.

“This… enables the identification of novel structural variation — now known to play an important role in the control of many key agronomic traits,” Parkin said.

The research, conducted in Saskatoon, was a national and international partnership. U of S and Ag Canada scientists collaborated with researchers from the University of Ottawa, Thompson River University, the National Research Council and scientists from the United Kingdom and China.

Sharpe and his U of S team are now applying their knowledge from the black mustard research to sequence the genomes of more complex crops.

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