Preheat the oven to 375 degrees F (190 degrees C).
Grease a 12-cup muffin pan with butter. In the bowl of a mixer, beat together the Unsalted Butter (1/2 cup), Granulated Sugar (1/2 cup) and Dark Brown Sugar (1/4 cup), until fluffy. Scrape down the sides of the bowl with a rubber spatula.
Add the Large Egg (1) and mix well, stopping to scrape the bowl if necessary.
Beat in the Low-Fat Plain Yogurt (1 cup). The batter will look grainy.
Add the Whole Wheat Flour (1 cup), All-Purpose Flour (1 cup), Baking Powder (1 teaspoon), Baking Soda (1 teaspoon), Ground Nutmeg (1/2 teaspoon), Salt (1/4 teaspoon), Ground Cinnamon (1 tablespoon), Ground Cloves (1/4 teaspoon). Beat on low speed until just combined. The batter will be very thick.
Add the Granny Smith Apple (2 cup) and mix until just combined. Do not over-mix.
Use an ice-cream scooper or large spoon to divide the batter evenly among the prepared muffin cups. The cups should be full. Sprinkle the Dark Brown Sugar (6 teaspoon) evenly over top.
Bake the muffins for 25 to 30 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
Remove the muffins from the oven, cool them for 5 minutes in the pan, then turn them out onto a rack to finish cooling completely. Serve and enjoy!