This is a simple tutorial about how to create transparent area into your texture.
In my example is about Dandelion model.
The model is created with Blender 3D software and is upload with Sketchfab blender 3D addon.
Next use Manage button to edit all your materials and textures.
You need to select just the OPACITY with the texture for transparent area like flowers or for each leaf.
For example in this screenshot is not selected the texture, but you can select for each area of 3D model.
This is result of my work with Dandelion 3D model: