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A ‘Game Changer’

Monday, August 28, 2017
filed under: Research and Development

       USDA-ARS sunflower research geneticist Brent Hulke calls it a “game changer.”
       “It” is the successful sequencing of the complete domesticated sunflower genome, a watershed achievement that was announced in the June issue of Nature magazine.  Listed as authors of the article are dozens of European and North American scientists who worked on the undertaking during the past several years. Nicolas Langlade of the French National Institute for Agricultural Research in Toulouse, France, led the international collaboration.
       Though this development didn’t generate headlines among the mass media, it truly is, as Hulke indicates, a very big deal for the sunflower industry and for the scientific community in general.  It fleshes out the sunflower genome “roadmap,” allowing plant breeders and other scientists to more effectively discover and incorporate critical traits like better disease resistance, enhanced drought resistance and improved oil profiles into breeding lines that constitute the basis of future commercial hybrids.
       Genome sequencing is a hugely complex endeavor — one whose methodology and terminology are acutely foreign to most laymen.  A “genome” is, in essence, all of a living thing’s genetic material.  “It is the entire set of hereditary instructions for building, running and maintaining an organism, and passing life on to the next generation,” explains Genome News Network.  At its core, “genome sequencing” is the process of determining the complete DNA sequence of an organism’s genome — in essence, mapping its entire makeup.

       Sunflower ranks among the most challenging genomes published to date, says Loren Rieseberg, a senior author on the Nature paper and director of the Biodiversity Research Centre, Department of Botany, at the University of British Columbia.  “Not only have we sequenced sunflower’s genome, but we’ve built physical and genetic maps of its structure — which increases the genome’s value for research and breeding,” he notes.
       With more than 20,000 genes, sunflower’s genome is actually larger than the human genome.  In comparison to maize (corn), it is 40%-plus larger.  One of the world’s five leading oilseed crops (the other four being soybean, rapeseed, peanut and cottonseed), sunflower is the last of these five to have its genome fully sequenced.
       The Asterid classification of flowering plants, to which sunflower belongs, is the largest plant family on Earth, representing approximately 10% of all flowering plants.  The European/North American team involved in sequencing the genome of the common sunflower, Helianthus annuus L, also performed comparative and genome-wide analyses that provided insights into the evolutionary history of Asterids, a history that dates back — get this — about 29 million years.  Their findings suggest that ancient copies of genes can retain their functionality and still influence traits of interest (e.g., flowering time, oil metabolism) after tens of millions of years.
       “Like many plant genomes, the sunflower genome is highly repetitive,” notes John Burke, professor of plant biology and member of the University of Georgia Plant Center.  However, he adds, “the repetitive elements within the [sunflower] genome arose relatively recently, meaning that they haven’t had time to differentiate.  It’s therefore like putting together a massive puzzle wherein many pieces look exactly the same, or nearly so.”  Burke, whose lab studies the genomic basis of evolutionary divergence within the sunflower family, was involved in the genetic mapping upon which the genome assembly was based. 
 
       USDA’s Hulke has actually been using the sunflower genome for a few years (through a Materials Transfer Agreement) while the authors were preparing their manuscript for Nature.  “Our research program requires the genome as a centerpiece,” he explains.  “All of our non-variety-release work depends on it to structure our own sequencing work.  If we have a list of genes that could be responsible for a trait, and we compare that list to similar genes in crops with a lot more investment, and someone in those crops has found the actual function for that gene, it provides us a lot of evidence for the importance of the sunflower gene near that marker.” 
       For example, earlier this summer Hulke and his team finished mapping the “glandular trichome density” trait in sunflower that may contribute to increased resistance to sunflower moth.  Through this web of information, they ascertained that the most important QTL for this trait was at the same location as the sunflower version of a gene previously shown to be important in the development of trichomes in globe artichoke and several other crops.  “We leveraged the discoveries in these other crops to make discoveries in sunflower,” Hulke says.
       How does the USDA sunflower geneticist view the importance of the genome sequencing completion to the sunflower industry in general, including sunflower producers?
       “An understanding of the sunflower genome is critical to understanding what our crop is capable of, compared to the competitors (corn, soybeans, etc.),” he states.  “Everyone understands that different crops have different appearances and different uses.  This is tied to biology.”
       Drought tolerance is an excellent example.  “Companies and governments have spent untold amounts of money to improve the drought tolerance of corn; but have they surpassed sunflower in drought tolerance?  No, they haven’t,” Hulke states.  “Breeding can enhance it slowly, and biotechnology can help.  But sunflower benefits from having evolved to fill a place in our world in which drought tolerance is key to survival; for corn, this was not as true.
       “With the genome sequence, we now have the ability to compare the genes present in sunflower with those of other crops — understanding that as species developed, some genes changed dramatically, some did not change at all, and others developed independently with some new purpose.”
       Understanding the genetic basis of why sunflower is unique “is a huge stepping stone toward future breeding advances,” Hulke emphasizes.  Along with improved mapping via leveraging information from multiple plant genomes and being able to access the “gene list” of sunflower to know what scientists are (and are not) capable of achieving through breeding, “we plan to use this information to direct the breeding program for all traits,” he says. 
         “The dense marker data we can get through sequencing allow us to developing forecasting models that take results from the last decade of breeding trials, reduce them to the responsible locations on the genome — and then use the information to pick better breeding lines from future crosses without requiring as much effort in field testing,” Hulke relates.  “This will allow us to ‘throw out the worst’ breeding lines so we focus attention only on the ones that show promise in providing the next high-yield, low-disease, high-quality hybrid.” – Don Lilleboe       
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