Apricot Seeds (x4)
honey lemon - Pineapple (middle) - honey lemon
Pineapple (middle) V Pineapple (middle)
honey lemon - Pineapple (middle) - honey lemon
rolanberry - Pineapple (middle) - rolanberry
Pineapple (middle) V Pineapple (middle)
rolanberry - Pineapple (middle) - rolanberry
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Royal Kukuru (x4+)
Apricot - Honey Lemon (middle) - Apricot
Honey Lemon (middle) V Honey Lemon (middle)
Apricot - Honey Lemon (middle) - Apricot
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Apricot seeds (x2) AND La Noscea Leek seeds (x2)
dez tomato - pineapple (middle) - honey lemon
pineapple (middle) V pineapple (middle)
honey lemon - pineapple (middle) - dez tomato
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Glazenuts (x4+)
Apricot - Royal Kukuru (Middle) - Apricot
Royal Kukuru (middle) V Royal Kukuru (middle)
Apricot - Royal Kukuru (Middle) - Apricot
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Broombush
Almonds - Halone Gerbera (middle) - Almonds
Halone Gerbera (middle) V Halone Gerbera (middle)
Almonds - Halone Gerbera (middle) - Almonds
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Azeyma Rose
Mandrake - Flax (middle) - Mandrake
Flax (middle) V Flax (middle)
Mandrake - Flax (middle) - Mandrake
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Royal Kukuru (x2) AND Apricot (x2)
Apricot - Honey Lemon (middle) - Dz Tomato
Honey Lemon (middle) V Honey Lemon (middle)
Dz Tomato - Honey Lemon (middle) - Apricot
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Star Anise
Mandrake - Azeyma Rose (middle) - Mandrake
Azeyma Rose (middle) V Azeyma Rose (middle)
Mandrake - Azeyma Rose (middle) - Mandrake
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Jute
Star Anise - Almond (middle) - Star Anise
Almond (middle) V Almond (middle)
Star Anise - Almond (middle) - Star Anise
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Halone Gerbera
Chamomile - Azemya Rose (middle) - Chamomile
Azemya Rose (middle) V Azemya Rose (middle)
Chamomile - Azemya Rose (middle) - Chamomile
Apparently crossbreeding takes place when it's planted, not during growing. For things like Apricots or Royal Kukuru you can use Grade 2 Thanalan Topsoil but when you make Glazenuts you use Grade 3 Thanalan Topsoil. The rarer seeds take longer to grow and need to be watered more often, maybe once every 10 or so hours while things like apricots are fine even with once every 20ish it seems.
If you wanna grow some glazenuts you should have at least 2 patches, if you have 3 it's even better. With 3 you can grow 1 for the Royal Kukuru, 1 to crossbreed with the RK to make Glazenuts and then 1 spare for planting together with the Glazenut seeds so you can keep replanting them for a lot of Glazenuts. Good to have some spares around if you're unlucky with harvesting.
For chocobo food you can use Shroud Topsoil for yield, unless you want to crossbreed rare seed + chocobo food for Thav onion (or rare seeds into rare chocobo food). You'll need Thanalan topsoil then. Use Fishmeal on the plants once an hour to cut the grow time by 1 hour.
You can crossbreed a lot more stuff but that list should get you started. Plant clockwise.