Brown whole grain mustard comes from Brassica juncea, a native Himalayan plant. According to Purdue University, healers in India use this mustard as an arthritis treatment. The seed color varies from light tan to dark brown. People in the United States sometimes refer to whole grain brown mustard as deli mustard. It tastes spicier than yellow mustard.
White mustard seeds come from the Sinapis alba plant, also native to the Mediterranean. The seeds from Sinapis alba are a light tan color. After preparation this whole grain mustard has a very mild flavor. Manufacturers use this particular seed for making "ballpark" style mustard.
Black mustard seeds come from the Brassica nigra that's native to Asia Minor and the Middle East. The seeds from this mustard vary in color from dark brown to black. They make a very spicy whole grain condiment, suitable for grilling rubs.
Yellow mustard seeds come from the Brassica hirta plant, of which about 90% of the world's crop grows in the United States. This mustard plant matures early, yielding yellow or brownish seeds. In whole form these seeds often appear in pickling recipes. Sometime production processes for whole grain yellow mustard include toasting the seeds.