SNP, SNP, SNP
Wednesday, September 1, 2010
filed under: Research and Development
Sure you do. You know exactly what “SNP” stands for. It’s single-nucleotide polymorphism, right?
OK, so maybe that term is not part of most folks’ everyday vocabulary. But those three letters — SNP — carry huge implications for the future of the sunflower industry.
SNPs (pronounced “snips”) were on hardly anyone’s radar a decade ago. Back then, had you asked even a group of plant scientists what the term meant, most probably would have said it had something to do with getting a haircut.
Today, however, the crop science community and the seed industry know that SNP-related technology holds vital keys to the development of the hybrids that will be planted by farmers in years to come.
SNPs fall into the complex world of DNA, chromosomes, genetic mapping and sequencing — a world that’s basic to animal and plant life, but also one that’s largely unfamiliar to most of us. SNPs are DNA markers, pieces of DNA located in or near a gene. Knowing the nature and location of markers within a given organism’s chromosome structure allows scientists to determine that organism’s unique DNA sequence pattern. As molecular biologists and plant breeders become more adept at “fingerprinting” an organism’s genetic makeup, they likewise are much more efficient at pinpointing useful traits and plugging those traits into new breeding populations and, eventually, commercial varieties.
Brent Hulke, research geneticist with the USDA-ARS Sunflower Research Unit at Fargo, N.D., uses the analogy of digital camera development to illustrate this concept. Think back to the first generation of digital cameras, he suggests; then compare that with today’s advanced high-resolution digital cameras. “Ten years ago, you could barely get a small photo from a digital camera to appear decent,” Hulke points out. “Now, images from digital cameras can be blown up to the size of wall murals and still retain their integrity.”
That comparison can be extrapolated into the realms of traditional plant breeding methodology and the new genomic approaches incorporating SNPs. Traditional methods focus on phenotyping — i.e., working through large populations in the lab, the greenhouse and out in the field to visually determine which lines or crosses carry the trait(s) one is seeking. Crossing and backcrossing through multiple generations is required to get the desired trait(s) into finished lines without dragging along undesired traits.
“SNPs allow for detailed analysis of breeding populations using methods we’ve never used before,” Hulke emphasizes. “And because of computers, we’ll be able to make this [process] even easier and cheaper in the future.
“Up until now, markers have been pieces of DNA that, in most cases, are not associated directly with [specific] genes,” he continues. “They’re just ‘hooks.’ So it’s kind of like putting a stake next to a rock in a field. You can’t put that stake directly on the rock; but you can place it by the rock. And you just hope the next time you see that stake out in the field, you don’t end up hitting the rock with your tractor.
“But with SNPs, we’re going to a technology that can actually ‘put the stake right through the middle of the rock.’ We’re to the point now where we can easily get SNPs that are actually a part of the gene of interest.”
Hulke uses downy mildew resistance as an example of how SNP technology can really pay dividends. With so many different races of downy mildew and so many different sources of resistance in the sunflower plant world, “putting multiple genes for downy mildew resistance together in the same breeding line is very difficult,” he says. In 2009, for instance, Hulke and ARS plant pathologist Tom Gulya and their team spent about three months just testing and retesting for downy mildew resistance.
“But if we had markers for each downy mildew resistance gene — a marker within the gene itself — we would have a very trustworthy marker that could be used in virtually every breeding application.” The much faster — and more cost-effective — procedure could conceivably reduce the three months of work mentioned earlier down to a week or two, Hulke envisions.
Sclerotinia resistance is another prime area for SNP dividends. Hulke says the ARS group currently has data on 262 diverse lines of sunflower from around the world with varying degrees of Sclerotinia resistance. “If we can tie that very big data set with a very big set of markers — [e.g.,] 10,000 — we would be able to get down nearly to the gene level with markers and possibly find key resistance genes within a full set of 262 lines,” he observes. “This is unprecedented, because we have been doing it two lines at a time. So we’re going from two to 262.” The bottom line is that such technology would allow scientists to become much more efficient at finding resistance to Sclerotinia and incorporating it into commercial sunflower hybrids.
There’s much more scope and detail to the SNP/sunflower story, of course. The ultimate goal of those entities and individuals involved is to keep sunflower profitable for growers — which in turn keeps the overall industry viable and healthy.
That objective is taking on an added urgency due to other crops already utilizing such technology. That’s making such crops more competitive — which then threatens sunflower’s acreage base and potential growth as an industry.
“Over the past couple years, there has been a lot of discussion about how other crops are able to bring [desired] traits to the market a lot faster than we can in sunflower,” notes Steve Kent, president of Seeds 2000 and current chairman of the National Sunflower Association Research Committee. “As an industry, it became more urgent when seed corn companies recently announced they will be introducing drought-tolerant corn varieties into the marketplace in the very near future.”
Why is that development so important to the sunflower sector? “Sunflower has long been known as a drought-tolerant crop,” Kent points out. “One of the threats we see from crops like drought-tolerant corn would be those crops moving into our main production areas.”
Sunflower seed companies and other industry leaders “realized we cannot continue to ‘plod along’ at the rate we have been,” Kent notes. “Not that we haven’t made progress; we have. But we need to progress faster.”
In March, the National Sunflower Association Board of Directors heard recommendations from its research committee on projects for funding. The board also invited a presentation by representatives from BioDiagnostics, Inc., a River Falls, Wis.-based company that focuses on the development of DNA-based diagnostic services for the seed industry. The NSA board then voted to immediately allocate $100,000 to initiate research aimed at facilitating marker-assisted breeding in sunflower.
Within a week, the NSA Research Committee had assembled a group of public and private breeders to put the project in motion. The first priority, Kent reports, “was to identify six sunflower breeding lines that had a great diversity in their genetic background, to begin the initial sequencing of those lines as the first step in the marker-assisted development.” That process is underway.
The next step, Kent explains, “is to develop a higher-throughput technology that allows marker-assisted breeding to be cost-effective.” Doing so required a commitment of 960 breeding lines from the public and private sectors “in order to raise enough money and to match up with the number of lines that can be done in a batch.” This large number of lines will also allow sunflower scientists to find and use the most-informative markers in future studies.
Part of the $100,000 NSA allocation went toward the first phase (sequencing). The second phase of fingerprinting is much more expensive, requiring $250,000. That pot of money was put together quickly, with some funds coming from the NSA and USDA. The rest of this round of funding is coming from several sunflower seed companies — each of which has committed a minimum of 100 lines and $25,000 to the program.
“It’s amazing that in a few short months, our industry not only recognized the importance of developing this technology, but is also doing something about it,” Kent concludes.
“We are moving in the right direction.” — Don Lilleboe