In order to synthesize the Great Tree Seedling, you will need Plant Seeds and a Nectar.

Make sure to clear the following requirements before proceeding:

1. Unlock the recipes for Plant Seeds and Nectar: The Great Tree Seedling recipe requires a Plant Seed and a Nectar. 
2. Raise your Staff’s Gathering Rank: You will need it to obtain a Sapling Branch for the Plant Seed recipe.
3. Create a Grass Sickle with Gathering Rank 2: The Nectar recipe needs an Ancient Branch. You will obtain it by using a Grass Sickle with the Capable Cutting effect.
4. Synthesize two Great Tree Seedlings: You will need a second one further into the main story.

Obtaining the Recipes

After completing Beyond the Cliff, part 1, return to the Atelier. You will automatically obtain the recipe for the Great Tree Seedling.

Next, unlock the Nectar and Plant Seeds recipes in the Skill Tree.

The Plant Seeds recipe is on the top of the Skill Tree. Unlocking this node will cost you 400 SP.

The Nectar recipe is located on the left side of the Skill Tree. You will find it a few nodes below the Plant Seeds.

Unlocking the Nectar node costs 350 SP.

Make sure to also pick up the first “Staff Rank +1” node, which is on the right side of the Skill Tree. This node costs 250 SP to unlock.

Creating a Grass Sickle With Capable Cutting

In order to obtain a Grass Sickle with Gathering Rank 2, you will need the Capable Cutting effect.

You can unlock this effect by leveling up the Grass Sickle’s Effect 1 loop. At Fire Element level 7, this loop will add the Capable Cutting effect.

The Effect 1 loop requires Large Bones as the ingredient.

Insert a Lumber-type ingredient in the Traits loop.

Add an Ore-type ingredient to the Quality loop.

You can then synthesize the recipe after that to obtain a Grass Sickle with Gathering Rank 2.

Collecting the Ingredients: Sapling Branch, Ancient Branch, Red Puniball

You will need a Sapling Branch for the Plant Seeds. The Nectar recipe, meanwhile, requires an Ancient Branch and a Red Puniball.

You can obtain the Sapling Branch and the Ancient Branch from the same gathering node.

Fast travel to Valley of Winds – Windmuhle Valley. Cross the bridge to the north and you will reach a small pond.

Use the staff on the saplings to obtain the Sapling Branch.

Switch to the Grass Sickle and use it on the saplings to obtain the Ancient Branch.

You can obtain the Red Puniball as a common drop from the Red Punis in the Maiden’s Catacombs.

Synthesizing Plant Seeds and Nectar

Once you have all ingredients, return to the Atelier. You will need to synthesize the Plant Seeds and the Nectar.

In the Plant Seeds recipe, insert a Sapling Branch in the Quality loop.

Use a Fruit-type ingredient in the Effect 2 loop to the right.

Insert an Uni-type ingredient in the Effect 3 loop to the left.

Complete the recipe by inserting another Uni-type ingredient in the Effect 1 loop on the top.

Once you’ve added all four ingredients, you can synthesize the Plant Seeds.

Next, it’s time to synthesize a Nectar.

Start by adding a Red Puniball to the Traits loop in the center.

Insert the Ancient Branch in the bottom Effect 2 loop.

Add a Magical-type ingredient to the Effect 1 loop on the top.

Synthesize the recipe to obtain a Nectar.

Creating the Great Tree Seedling

Select the Great Tree Seedling recipe from the cauldron’s menu.

Insert a Plant Seed in the Effect 1 loop.

Insert a Nectar in the Traits loop to the left.

Finish the recipe by adding a Sapling Branch to the Traits loop on the right.

After that, you can synthesize the recipe to obtain a Great Tree Seedling.

Repeat the process and create a second Great Tree Seedling. You will need to use another one further into the main story.