U.S. Federal horticultural certification is administered by the States, because they are permitted to add additional requirements -- and many do.
So you start by contacting your county agricultural department, or if your state doesn't have these then you contact them directly.
You will need multiple licenses that build you up to the qualification level. These include nursery stock license (you are breeding trees), an agricultural pesticide license, a permit for applying agricultural pesticide at your site, and a few USDA compliance agreements that lead to a designated quarantine area at your site. The pesticide licenses provide support for the latter in the view of the inspectors. Depending on your state requirements, you'll have 1-4 inspections per year for your operation.
I don't believe so. At the very least you'll need to have a county or state business license for a farm or agricultural research operation -- which the USDA can look up for verification purposes.