Two mysterious alfalfa diseases have cropped up in fields in recent years. Deborah Samac, a research plant pathologist with USDA’s Agricultural Research Service, says both attack crown buds and roots, producing thin stands.

Samac is working to identify the fungi causing the diseases and, long-term, find varieties that can stand up to them.

“One of the diseases was found by researchers in Wyoming years ago,” she says. (See photo at right.)

“I have recently found it on plants from Michigan, Minnesota and Wisconsin. The fungus isolated from the infected plants has some similarity to the fungus causing stagonospora leaf spot and root rot, which has been found in limited areas in the U.S. But it is not the same species and, so far, we haven’t seen any leaf-spot symptoms from this fungus. We’re primarily seeing a rot of crown buds and of fine, fibrous roots.

“Then there’s this disease that I’m calling ‘rough root rot.’ (At left.) The bark on the roots is very rough, and there is decay of the lateral and tap roots. I’ve only found it in a couple locations in Wisconsin and Minnesota.”

The diseases make a field look “unthrifty. The foliage is somewhat stunted, and it’s probably because plants have lost their fine roots and are having problems taking on nutrients and fixing nitrogen.”

At this point, Samac is completing work to inoculate plants in the greenhouse and reproduce field symptoms. The next steps would likely be to design DNA-based assays to rapidly identify the fungi and find varieties resistant to them.

It’s also likely that a new race of the pathogen causing aphanomyces root rot is emerging in alfalfa-growing regions, she says. Current varieties are available with aphanomyces race 1 and 2 resistance. But Wisconsin and New York field surveys are showing resistance breakthroughs.

As part of a five-year research project, Samac hopes to identify DNA markers associated with race 1 and 2 resistance that would provide a simpler way of selecting for resistance. “The long-term goal then is to identify plants that have broad race non-specific resistance so we don’t have continuing development of new races of the pathogen.”

Samac has also been searching for alfalfa plants resistant to brown root rot (BRR), which, like the mystery diseases, sports stand-thinning symptoms.

Resistant germplasm could be developed within the next few years. “We have material that survived in a very highly infested field, so we are assuming that it has resistance. We’re selecting plants out of that population to intercross again. So far we’ve done two cycles of selection.”

Some current cultivars persist well under BRR pressure, she adds. See Winter Survival, Fall Dormancy and Pest Resistance Ratings for Alfalfa, pages VL-1 through VL-8 of this issue, for varieties offering such persistence. Also see Brown Root Rot of Alfalfa, which Samac co-authored, at

“Plant breeders have done a great job in introducing resistance into alfalfa cultivars, but we know very little about the genes underlying resistance and even less about how those genes function to prevent disease from occurring. So there is still a lot to learn to improve resistance and combine disease resistance with traits to enhance yield and stand longevity and density,” she says.