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Fast Track Designer Genes
People who eat pasta made from Canadian durum don’t expect to be exposed to a heavy metal that if eaten in high enough concentrations could have toxic consequences for their health.
So when rising concentrations of cadmium, a naturally occurring heavy metal in Prairie soils, were threatening Canada’s role as a leading supplier to pasta mills around the globe, it was important for researchers to act quickly.
Thanks to modern computing power that speeds up data processing and the precision of genetic markers for selecting traits, scientists quickly identified varieties that were two- to three -times lower in cadmium.
Curtis Pozniak , who heads the Crop Development Centre at the University of Saskatchewan in Saskatoon, and his team used DNA markers to identify plants that absorbed less cadmium from the soil.
“We could do it very quickly compared to traditional tests where we would have to grow it in the field, harvest the samples, do very complex biochemical analysis to quantify the cadmium levels,” Pozniak said. “This way we could do it with a simple DNA test and really move quickly. The whole program, in a matter of just a couple of years, was all low cadmium types.”
The precision with which Pozniak and other plant breeders today can select for the traits they want would amaze those of an earlier time.
Even in the 20 years that Pozniak, has been working as a durum breeder, technology has changed considerably.
That will continue, he says, but the need to plant seeds will always exist.
“These technologies will make things more efficient, I think, but the reality is we’ll still be putting material into the field for phenotyping and for selection,” Pozniak said.
Humans have been breeding plants for thousands of years, taming wild varieties of crops we know now as wheat, corn, potatoes and others for better yields and cultivation. Parent plants were selected for different attributes and crossed to produce progeny that were in turn selected for their attributes.
Gregor Mendel’s work in plant heredity, published in 1866 but not truly recognized until 1900, ushered in the science of genetics.
Cross breeding, hybrids, mutation breeding and tissue cultures followed. Genetic modification and gene transfer, DNA markers and genomic selection have characterized the last quarter century.
Pozniak said computers were probably one of the biggest technological changes for breeders because they could store all the information they gathered. The technology has also created efficiencies that make it possible to get new varieties to the field sooner.
When he was hired at the CDC in 2002, doubled haploidy technology was just taking off. That reduced breeding time by a couple of years, he said.
“What I’ve seen change the most over the last 20 years is the precision at which we’re able to select from some traits using DNA-based technologies,” Pozniak said. “We’re seeing technologies like DNA testing that allow us to get very precise DNA tests for specific traits, for example for disease resistance or end-use quality, where the breeder is able to make selections without even doing field testing.”
Rapid DNA sequencing tests allow breeders to look at DNA fingerprints and select even more efficiently. And, as more genomes are sequenced, more precise breeding will follow.
The durum experience is an example of the time saved from doing in a lab what previously had to be done in a field .
In the last few years CRISPR technology, clustered regularly interspaced short palindromic repeats, has been gaining attention for its potential in crop improvement.
But Pozniak said it will be a while before it could replace existing technology.
CRISPR has the ability to precisely edit a specific piece of DNA to get something desirable. He said the possibility of being able to alter a specific gene precisely to get a predictable phenotype sounds exciting.
“The thing that we have to be aware of though is that many of the traits that we’re working with aren’t controlled just by one single gene,” he said. “If you think of grain yield, for example, it’s a very complex trait so being able to edit one gene to improve yield is probably not realistic.”
Pozniak said another concern is which genes are edited. He said plant genomics can identify the genes but doesn’t tell scientists what they do.
“In wheat, there’s about 130,000 genes. Which of those 130,000 should we edit and how should we edit? What should we change them to?” he said.
Listen to the Genes
To hear the sound of sequencing genes click the play button in the bottom left hand corner of the video.
What you’re hearing is a synthesizer synched up to an algorithm built from more than 1,000 plant genes.
The work is based on the oneKP Initiative led by the University of Alberta.
The scientific community is pushing toward functional genomics, which would determine what each gene does. Pozniak said this work has to be done before gene editing could be implemented widely in plant breeding programs.
“As these functional genomic experiments are conducted and published and verified that’s when gene editing really presents itself as an opportunity,” he said.
Pozniak cautions that gene editing will not replace plant breeding. It is one tool that breeders may be able to use if it is the most appropriate one for their programs.
Planting material in fields will still be necessary to evaluate potential varieties in different environments. Plant breeders strive to select varieties that are the most stable performers across a number of environments and that has to be measured, he said.
That becomes more important as the climate changes. Pozniak said it takes repeated selections over six to 10 years generally to result in a new variety and exposing the selections to good, bad and ugly conditions helps ensure they can withstand those different conditions.
Another evolving technology that breeders are watching is digital phenotyping using drones fitted with special cameras to capture information the human eye perhaps can’t see.
All these lead back to his assertion that computers were the biggest technological change for breeders. Vast amounts of data are generated by technology. For example, wheat has a genome size of 16 billion base pairs; that’s 16 billion bytes of data for one variety. Plus there is all the data gathered from the field.
Being able to store and access that data is key. But even as plant breeders turn to new technologies the past isn’t always far away.
While a lot of breeding material is tossed, some is retained because it contains a desirable quality, such as disease resistance, and might be useful in the future.
Pozniak is currently leading projects looking at the value of heritage varieties and even wild relatives of crops that are now cultivated. Collections for a number of crops have been curated and put into gene banks so that breeders have access to them.
For example, durum is extremely sensitive to fusarium head blight and it’s hard to find genetic resistance.
“There is resistance there but it’s very complex and so what we have been doing is going back to the wild relatives and screening them specifically for fusarium head blight resistance and identifying those that have really good resistance, a lot better that we have in our commercial varieties, and then crossing them with the new commercial varieties to develop varieties that yield well and have good quality,” Pozniak explained.
The process is difficult because wild relatives aren’t adapted to field conditions, don’t yield well and don’t have good end use quality. All of that has to be eliminated, likely through the use of DNA tools, to create something that works.
In the case of wheat, more than 500,000 accessions have been curated around the world and tremendous efforts are underway with most crops to maintain wild species, heritage varieties and land races in order to access genes in the future, he said.
Contributor: Karen Briere