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Building a Genomic Map of Sunflower

Saturday, November 1, 2008
filed under: Research and Development

Though Steve Knapp is not a cartographer, the University of Georgia professor is, nonetheless, a central figure in the construction of a very important road map. He is mapping the genome of sunflower — a process whose fruits already are becoming invaluable to plant breeders and other scientists working to provide farmers with progressively better sunflower hybrids for their fields.

Knapp’s laboratory in Athens, where he is Georgia Research Alliance Eminent Scholar in the Institute of Plant Breeding, Genetics & Genomics, is a long way from the sunflower fields of the Dakotas and High Plains. But the type of work he does is not geographically dependent. It revolves instead around DNA and chromosomes, genetic mapping and sequencing. While those are worlds largely unfamiliar to most of us, we are affected by them in the most basic of ways.

Every living organism — humans, other animals, plants, fungi, bacteria — contains DNA. DNA is a molecule that encodes an organism’s genetic information. Nucleic acids — of which there are just four (referred to by the letters A, G, C and T)) — are the building blocks for DNA. The pattern in which those four nucleic acids exist within a given organism comprises its genetic code. The term “genome” refers to an organism’s complete set of DNA.

A “marker” is a snippet of DNA located in or near a gene. Knowing the nature and location of markers within an organism’s chromosome makeup allows scientists to determine that organism’s unique DNA sequence pattern. That knowledge is essential for genotyping — i.e., classifying an organism according to its genetic makeup as opposed to its physical appearance (known as “phenotyping”).

Still with us? Good.

The field of genomics did not emerge until the 1980s; indeed, the term was not coined until 1987, says Steve Knapp. Trained as a traditional plant breeder with an emphasis in applied statistics and quantitative genetics, Knapp joined the faculty at Oregon State University in 1985 after two years in the seed industry. He remained at OSU until moving to Georgia in 2004.

Assigned to focus on oilseeds when he came to Oregon State, Knapp chose sunflower. “Virtually nothing was being done in sunflower genomics when I started the program,” he recounts, “and most of the genomics research up to then was being done by groups that were not sharing information or resources.” He officially established the Sunflower Genome Program in 1992 by securing funding from federal competitive grant programs and from private industry. (These remain the sources for 100% of his sunflower genome research funding.)

How does genomic research benefit the sunflower industry and its growers? There are several ways, according to Knapp:

• Improved disease resistance is among the most important dividends. Genomic approaches have already led to “the discovery of several novel disease resistance genes, [and] a much greater understanding of the genetics of disease resistance in sunflower,” according to Knapp. DNA markers used by seed industry breeders to manipulate disease resistance genes in hybrid breeding programs have been developed as well.

• Knapp and his collaborators also are using genomic approaches to study wild sunflower species native to deserts and other arid habitats. The objective is to enhance drought tolerance in future commercial hybrids by identifying wild species genes that can by used by breeders to maximize seed yield under drought conditions. Currently, this effort is focusing on two species: the silverleaf sunflower (native to southern Texas) and the Algodones dune sunflower (a native of southern California).

• “We recently initiated biofuel research in sunflower and have proposed developing completely new types of hybrids for producing cellulosic biofuel feedstocks,” Knapp says. “This research was sparked by the discovery of wild species that produce woody stems. We are currently using genomic approaches to study wood formation, cellulosic biomass traits and biomass yield in sunflower.”

• Additionally, there’s a significant effort to identify genes in land races and wild species for enhancing the performance of modern oil-type sunflower hybrids. “This work focuses on broadening genetic diversity and supplying breeders with libraries of [what are] called ‘wild introgression’ lines,” Knapp explains. Such lines can be used as the starting material for developing new inbred lines and hybrids with higher yield capacity, enhanced disease resistance and/or important quality traits.

• “Finally, we study how the genomes of wild species differ from the genome of common sunflower,” Knapp advises. “We do this by ‘comparative genetic mapping’ (building genomic blueprints). This knowledge can be used to assist breeders in moving genes from wild species into common sunflower.” Knapp and his associates already have constructed genomic blueprints for five wild species and are developing others.

• One of Knapp’s top priorities is to fully sequence the sunflower genome. (“Sequence” refers to how the four nucleic acids are arranged, side by side or in sequence, along a strand of DNA — for instance: CCATTG. That order supplies the genetic instructions that in turn provide an organism with its set of unique traits.) “While we currently do not have funding to fully sequence the sunflower genome, we have generated a lot of DNA sequence information for sunflower and believe we will eventually be able [to accomplish the full sequencing],” Knapp observes.

One current roadblock in the process of getting from Point A (successfully mapping and sequencing the sunflower genome) to Point B (incorporating useful

“fresh” genes into commercial hybrids) is the lack of an efficient transformation system (i.e., the conduit that will transport the genes from Point A to Point B). However, Knapp says recent work by Ohio State University’s John Finer “could fundamentally advance and enable routine sunflower transformation.” That’s essential to understanding gene function and being able to introduce foreign genes, he stresses.

Knapp knows that the genomic work conducted by him and his cooperators at other institutions probably seems very foreign to sunflower growers and most others within the sunflower industry. “However, we work on traits of critical importance to sunflower producers,” he emphasizes. “Our research mainly impacts the seed industry by providing commercial seed breeders and biotechnologists with resources and knowledge for developing genetically superior hybrids.”

The bottom line for sunflower plant breeders — and, ultimately, sunflower producers — is that a thorough knowledge of the sunflower genome will both (1) expand the gene base to which breeders have access and (2) speed up the process by which they can identify useful genetic materials and eventually incorporate them into finished hybrids.

“Genomics-assisted breeding is done on a large and serious scale in crops like soybeans and corn,” Knapp continues. “Our research is designed to enable the application of such approaches in sunflower on the same scale. This will be critical for the long-term competitiveness of sunflower.”

Knapp is either the principal investigator or a co-investigator on several active projects that together are funded to the tune of about $11.3 million. “These efforts will supply the research community with DNA sequences for more than 90% of the genes and will enable unparalleled genomics research in sunflower,” he reports. Prominent among Knapp’s fellow investigators in the sequencing of the sunflower genome is Loren Rieseberg, distinguished professor of biology at Indiana University. The primary research interest of Rieseberg’s laboratory concerns how new plant species arise — one of the most fundamental questions in biology. Much of his work focuses on members of the Helianthus (sunflower) genus. — Don Lilleboe
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