I never heard of Jonathan apples before this series LOL. Granny Smith is definitely the one I usually see being suggested as cooking apples for the same reasons stated. It's more tart, it's crispier/harder so it won't get soggy in pies, and stuff like that.
Did it go out of popularity or is it just more preferred in certain locations? I definitely have never seen that here, but I rarely actually pay attention to names of apple kinds. In the grocery, I mostly identify apples just by colour, like "the pink one", "the green one", "the dark red one".
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Momoyama, or Adzuchi-Momoyama is a very short period referring to the reigns of Oda Nobunaga and Toyotomi Hideyoshi (around 1570s-1600). Both men loved art, so under their patronage various kinds of unique and luxurious artwork were developed. Examples of what could be called the "bold new kind" of pottery from that time are the Oribe wares and some pieces of Seto wares.
The Seto kilns pre-existed the era, but they were able to create some noteworthy pieces during this time, and was counted as "Momoyama pottery".