Preheat oven to 350°F. Place 12 muffin liners in tin.
Whisk together flours, baking powder, baking soda, and salt in large bowl. Combine juice, zest, yogurt, sugar, oil, milk, and egg in small bowl. Pour wet mixture into dry mixture and stir until just combined. Fold in chia seeds.
Spoon about 1/3 of batter into muffin liners. Place a scant teaspoon of jam in the center of each muffin, then top with remaining batter. Bake for about 18 minutes, or until muffins are golden in color and toothpick inserted into center of muffin comes out clean.