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The Guardian Saplings are sacred trees (「御神木」?; oshinboku) spread around Nippon to protect the land.
The Guardian Saplings are smaller, yet still powerful, divine offshoots of the roots of Konohana, Sakuya's sacred tree. They're are only seven Guardian Saplings throughout Nippon. Unfortunately, like Konohana, they are affected by evil and darkness, which causes them to wither. When this happens, their power drains away and this makes it very easy for a cursed zone to appear. Throughout their journey, Amaterasu and Chibiterasu must find and restore the saplings to drive away the curse that plagues the land of Nippon. Doing so grants them Praise and allows them to explore the area.
The well-being of the Guardian Saplings affects Sakuya, who gradually becomes weaker when the Saplings are withered. With the saplings restored, Sakuya also regains her powers. Interestingly, there are a few saplings that are still seedlings, and need certain conditions to grow. It's because of that the evil energy in these areas was enough to cause the Saplings to reduce in size.
A long time ago, about one hundred years prior to the events of the game, Nippon was once said to be a land full of sadness, and implied to be full of war alongside the countless demons that plagued the lands that came from the north. Two sisters from a distant land far from Nippon, and seeing the land's grief and dreary state, began a pilgrimage and planted Guardian Saplings in the hopes of bringing happiness to these lands as it did in their homelands. Around the time of Kamiki Village's dreaded custom of sacrificing a virgin woman every year on the time of a full moon, and the night of the heroic Nagi's efforts, a Guardian Sapling was planted, and so was the wood sprite Sakuya was born.
Spoilers end here.
Shinshu Field: In plain sight a short distance away from the entrance from Kamiki Village, at the center of the field.
Hana Valley: In a shrine at the end of the trail leading up through the valley.
Taka Pass: Across a bridge at the top of a cliff which must be reached by going through a cave.
Ryoshima Coast: At the top of a hill with several dried-up ponds. It needs water before it can be restored.
North Ryoshima Coast: On an island near the mainland. Waka has already restored it by the time Amaterasu arrives.
Kamui: Hidden inside a cliff which must be destroyed to expose the sapling.
At the end of Ōkami, a baby Guardian Sapling can be seen in Waka's hand, presumably to be planted on the Celestial Plain.
Whenever Amaterasu restores a Guardian Sapling, Konohana will bear a fruit. If she Power Slashes these fruits, they will fall and yield treasures.
Per Issun's words in Ōkamiden, each Guardian Sapling's main branch curls like Sakuya's hair knot.
The Guardian Saplings may have been planted across Nippon by Camille's and Camellia's ancestors, Peoni and Peony. Peony held in her hands a tiny bag containing a newly sprouted Guardian Sapling. They also said that they wish to rid the land from evil and impurity by spreading the saplings in every corners of Nippon[Citation needed].
The real and first Guardian Sapling was never mentioned, only most of them were planted across Nippon by Peoni and Peony. Though, it is possible that the first sapling planted is Konohana, because all other saplings are its extended roots, and there were no saplings at Shinshu Field during Peony and Peoni's time.