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Your answer was posted but to be honest I do not know where it went now.
As far as a dog breeder and the tax due to Iowa, yes, this type of business is required to collect sales tax even if you are selling at wholesale.
"Most horses, mules, dogs, cats, other pets, racing animals, and other creatures not generally associated with agricultural production are subject to sales tax, unless purchased to be immediately offered for resale."
Since you are breeding the dogs then you are required to collect the sales tax due.
Unless you are given an exception certificate by the buyer you are to collect the sales tax. You are still required to report the tax on your sales tax return even if you accept exemption certificates. Iowa sees them as tangible property and not livestock.
The state appears to be cracking down on puppy sales and individuals that breed puppies for retail and wholesale in all facets of the industry.
I have not read anything where Iowa offers a Grandfather Clause on Sales tax. I would think you best chance would be to show the stores where you sold the puppies to and see if the exemption certificates for those stores can be retroactive to the date you started the wholesale to them. Since the stores themselves would need to show the Sales Tax themselves they should have records of the dealings with you.