Preheat oven to 375°.
Lightly spoon flours into dry measuring cups; level with a knife. Combine flours, granulated sugar, and next 5 ingredients (through salt) in a large bowl, stirring with a whisk.
Combine pumpkin and the next 4 ingredients (through applesauce) in a medium bowl, stirring with a whisk. Add pumpkin mixture to flour mixture, stirring just until moist. Spoon batter into 16 muffin cups coated with cooking spray. Bake at 375° for 20 minutes or until muffins spring back when touched lightly in center. Cool muffins in pans 5 minutes on a wire rack; remove from pans. Cool completely on a wire rack.