Adjust oven rack to lower middle position and heat oven to 375 degrees. Mix flour, baking powder, baking soda, poppy seeds, and salt in medium bowl; set aside.
Beat butter and sugar with electric mixer on medium-high speed until light and fluffy, about 2 minutes. Add lemon zest to butter-sugar mixture. Add eggs, one at a time, beating well after each addition. Beat in one-half of dry ingredients. Beat in one-third of yogurt. Beat in remaining dry ingredients in two batches, alternating with yogurt, until incorporated.
Spray twelve-cup muffin tin with vegetable cooking spray or coat lightly with butter. Use large ice cream scoop to divide batter evenly among cups. Bake until muffins are golden brown, 25 to 30 minutes. Set on wire rack to cool slightly, about 5 minutes. Remove muffins from tin and glaze.
For Glaze: While muffins are baking, heat 1/4 cup granulated sugar and lemon juice in small saucepan until sugar dissolves and mixture forms light syrup, 3 to 4 minutes. Brush warm syrup over warm muffins and serve.