Over the years, continued planting of soybean varieties with PI 88788 resistance has caused soybean cyst nematode to develop resistance to SCN-resistant soybean varieties. There are hundreds of SCN resistant varieties available, but almost all of them have resistance genes from the PI 88788 breeding line. Fewer than 5% of SCN-resistant soybean varieties available for farmers to plant have the alternative source of resistance named Peking.

There are yield consequences to this situation, similar to using the same herbicide on weeds continually for a number of years. Over time, the weeds develop resistance and are more difficult to control. For decades, farmers have planted SCN-resistant soybean varieties to manage SCN using the PI 88788 trait each time.