Your motherboard does indeed affect your GPU performance. In fact, it can be the limiting factor in your system's overall performance. The reason for this is that the motherboard is responsible for connecting all of your system's components together. If your motherboard is not able to provide a fast and stable connection to your GPU, then your GPU will not be able to perform at its best.
There are a few things that you can do to make sure that your motherboard is not the bottleneck in your system. First, make sure that you have the latest BIOS update for your motherboard. This can often provide significant performance improvements. Second, if you are using a discrete GPU, make sure that it is properly seated in the PCI-E slot on your motherboard. Third, make sure that your power supply is able to provide enough power to your system. A weak or unstable power supply can also cause performance issues.
If you are still having performance issues after taking these steps, then it is possible that your motherboard is simply not compatible with your GPU. In this case, you will need to replace your motherboard with a new one.