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Impact of Sunflower Genome Sequencing

Tuesday, September 1, 2009
filed under: Research and Development

Steve Knapp’s professional life revolves around a world with which most of us are only vaguely familiar — but one that impacts all of us in the most basic of ways. It’s a world of genomes, chromosomes, genes and DNA, of genomic mapping and sequencing.

Knapp — whose University of Georgia title definitely fills up his business card (Georgia Research Alliance Eminent Scholar in the Institute of Plant Breeding, Genetics & Genomics) — delivered an update on his research during the National Sunflower Association’s 2009 Summer Seminar in June. (An introduction to the Georgia scientist’s genomic work appeared in the October/November 2008 issue of The Sunflower.)

Knapp, who established the Sunflower Genome Program in 1992 while at Oregon State University, is a leader in the mapping of the extremely diverse, complex sunflower genome. At a length of about 3.5 billion “bases,” the sunflower genome is actually longer than the human genome. Until Knapp’s initiative, however, very little work had been done in the field of sunflower genome research.

Today, this program encompasses a multi-scientist, multi-institution effort that has secured more than $17 million in government and industry grants during the past year. The initial beneficiaries of its fruits are public and private sunflower breeders. They’ll have access to a significantly expanded gene base — a base that will speed up the process of identifying useful genetic materials and incorporating desired traits into finished hybrids. From that, of course, the farmer benefits. He will be able to produce higher-yielding, better-quality hybrids with improved resistance to diseases and other stress factors. It’s a process from which larger-acreage crops — e.g., corn and soybeans — are already reaping substantial rewards.

One of the largest sunflower genome grants actually comes from Canada and was prompted by interest in biofuels applications. Genome Canada has invested about $7.7 million in the Sunflower Genome Program. Much of the motivation behind that investment, Knapp says, lies in the potential for developing a fuel source from woody-stemmed sunflower plants.

That research is currently focusing on two desert-dwelling, drought-tolerant wild species: the silverleaf sunflower (Helianthus argophyllus) and the Algodones Dune sunflower (Helianthus tephrodes). The silverleaf sunflower is, in essence, a miniature annual tree, with the chemical composition of its wood being quite similar to quaking aspen and poplar.

According to the University of British Columbia’s Loren Rieseberg, Genome Canada’s sunflower project director, this could lead to farmers eventually reaping two economic harvests from every sunflower crop: a seed (oil) use and a woody stalk (fuel) use.

Knapp says that what is learned from the genomic mapping of the woody-stemmed ecotypes will aid the entire sunflower genome mapping and sequencing effort. “There will be collateral benefits,” he emphasizes. “Though [this project] focuses on the biofuel aspect, the idea is to learn as much as we can about silverleaf sunflower and bring as much useful diversity [as possible] into breeding for better sunflower hybrids.”

Exceptional drought resistance is the primary trait of the Algodones Dune sunflower in which scientists are interested. They’re currently working to produce a set of introgression lines that can be used to test-cross Algodunes Dune with current breeding materials. The crossings will be conducted by Brent Hulke, USDA-ARS sunflower research geneticist.

Another example of an “exotic” sunflower population being accessed via genomic mapping and sequencing for a hitherto unavailable trait is the so-called Hopi landrace. These lines were “bred” centuries ago by the Hopi Indians in the American Southwest and are rich sources of novel traits not found in the parentage of current elite single-cross hybrids. Breeders now believe these materials will ultimately contribute to higher yields for farmers. At least one private seed company has already produced promising sunflower inbreds using the Hopi lines, and USDA’s Hulke is testing the advanced lines — developed through the genomic effort — in two Dakota locations this year.

In his remarks to the NSA Summer Seminar audience, Knapp noted that to date, scientists have mapped about half of sunflower’s huge gene base. The ongoing genomic sequencing work will provide those missing pieces. Complicating the effort, however, is the fact that many genes are weakly expressed and thus particularly difficult to map and sequence.

Disease resistance is, of course, a primary emphasis. “Downy mildew and rust genes that we’ve been studying are enormously complex clusters, called ‘encoding genes,’ ” Knapp says. Again, scientists believe they’ve probably captured about half of those genes.

All of this work greatly benefits marker-assisted breeding (MAB). Already routine used in many private and public programs, MAB allows breeders to locate and utilize useful genes much more quickly than is the case under traditional methods (i.e., physically crossing lines in the greenhouse or out in the field).

“The other big issue is genetically modified traits,” Knapp remarked. While crops like soybeans, corn and canola are deeply invested in GM traits (e.g., Roundup Ready® soybeans), sunflower is not yet participating in that movement — the main reason being the concern over GM sunflower out-crossing into the wild species. Knapp, for one, is a proponent of sunflower’s participation in GM development. — Don Lilleboe

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