Winter 2009

Tribal members from the Bad River Band of Lake Superior Chippewa (Ojibwe) havest wild rice on the Kakagon Sloughs near Ashland, the only large, pristine coastal population of wild rice remaining in the entire Great Lakes region Photo: Tim Tynan
Sea Grant Research

"Fingerprinting" Wild Rice

Examining its genetic makeup may reveal critical evidence to aid restoration

By Kathleen Schmitt Kline

Wild rice was once so abundant in Wisconsin that it gave its name to many bodies of water throughout the state. One or more “Rice Lakes” are located in 21 of Wisconsin’s 72 counties, but today many of them are rice lakes in name only. Since the settlement of Europeans, people have altered the landscape and made it difficult for the plant to succeed.

Along the shores of Lake Superior and Lake Michigan, wild rice has suffered a similar fate. Today, just one large population remains—on the Lake Superior shore of Ashland County—along with a few other small, remnant populations scattered around the Wisconsin coastline. A Sea Grant-funded researcher is examining the genetic makeup of these remaining populations to find out how to preserve the identity of wild rice while expanding its distribution along the Lake Superior and Lake Michigan coastlines.

Anthony Kern is a plant geneticist at Northland College in Ashland, Wis. He said that in coastal habitats, wild rice (Zizania palustris) thrives in shallow water with a current and silty bottom—typically at the mouths of river estuaries. Over the years, channelization, ­sedimentation, and industrialization altered most coastal areas where the grain once thrived. Even in areas where the habitat has improved, boat traffic, shoreline development, beavers, and carp can make it difficult for the remaining stands to persist. But Kern said these outside factors aren’t the only problems facing wild rice—one problem may be found in the plant itself, buried deep in its genetic makeup.

The St. Louis River estuary near Superior is one of many areas in Wisconsin that was once filled with wild rice. Today, only a few isolated populations remain. “These populations have become separated from each another—they’ve become fragmented,” Kern said. If these populations have become so isolated that they no longer share pollen, and therefore genes, “there’s some concern from a genetic standpoint,” he said. “Small populations—especially of annual plants like wild rice—will inevitably be subject to inbreeding.”

Just like in humans, inbreeding can result in problems that impair individuals and entire populations. Previous research suggests that inbred wild rice plants are smaller, weaker, and produce less seed—characteristics that could cause a dramatic decline in an already small, struggling wild rice population.

Kern is using molecular tools to discern whether or not inbreeding is taking place in fragmented populations of wild rice. Together with Ronald Phillips at the University of Minnesota, he spent two years combing through the wild rice genome to identify 40 distinct regions of DNA called microsatellites. These are particular locations on a DNA strand that contain a repetitive sequence of genetic information. All wild rice plants will have each sequence of repetitions at each particular chromosome location, but the number of repetitions will vary from population to population, and from plant to plant. (Microsatellites are the same molecular markers used in human DNA fingerprinting, an important tool in forensic and parentage studies.)

Kern will use the molecular markers to determine whether fragmented populations of wild rice, once part of a single continuous population, have now become genetically distinct and are experiencing inbreeding. By noting various physical traits of the plants he samples over the next two seasons and correlating those physical measures with his molecular analyses, he will try to quantify the degree of inbreeding that is taking place and assess how it is affecting the health of the population. Kern will also compare the genetic variability in fragmented populations to that of the Bad River/Kakagon Sloughs near Ashland, the only large, pristine coastal population of wild rice remaining in the entire Great Lakes region.

While still in the first year of the study, Kern is hoping that his results will eventually aid wild rice conservation work that is underway throughout the Great Lakes region by a network of state, federal, and tribal agencies. The molecular markers he developed will be available to anyone seeking to determine the genetic variability of specific wild rice populations. And for the small, remnant populations that agencies may wish to expand, understanding genetic variability is critical to selecting seed sources. The key is to provide enough variability to prevent inbreeding without introducing deleterious traits that could weaken the population. One potential strategy that could result from Kern’s study would be to mix seed from nearby fragmented populations within the same river estuary, essentially mimicking historical patterns of gene flow and potentially reducing inbreeding at the same time.

“Some people say throw in seed from a bunch of sources and let the best genotypes win,” Kern said. “That may be fine in places where wild rice has been completely wiped out or where it never existed before. But where there is a remnant population, it’s a very special, unique situation, because those remnant populations serve as reservoirs for genetic adaptations that are unique to that particular habitat. We want to conserve as much genetic diversity in the plant across its range and maintain as much of the normal, historic patterns of genetic diversity and its distribution as possible. And in the places where there are remnant populations of wild rice, there are some very special considerations for restoration.”

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