New Leaf Hybrid Genetics

The main difficulty with getting the more rare hybrids seems to arise
from not keeping careful track of the specific parent combinations 
required when making the "special" versions of normal colors.

Calling the red roses needed for blue roses "hybrid red" or 
"special red" or "red+" or "red*" can lead to confusion when you 
don't understand that there are several possible ways to breed a 
red with different color parents, but only one of those combinations 
will produce the red necessary for breeding blue roses.

Hence I prefer to use this terminology: 
[**]Color where the ** are the first letters of the parent colors. 
[XX]Color means the parents can be of any color including store bought seeds.

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Blue roses:

[XX]White + [XX]White = [WW]Purple

[XX]Red + [XX]Yellow = [RY]Orange

[RY]Orange + [WW]Purple = [OP]Red

[OP]Red + [OP]Red = [RR]Blue

Notes: [OP]Red + [OP]Red can produce [RR]Red offspring, which can NOT make 
[RR]Blue [RY]Orange and [WW]Purple can be bred with others of the same color.
The resulting [OO]Orange and [PP]Purple offspring are slightly better at 
producing [OP]Red offspring. 
The reason for this is the reduced range of outcomes:
[OP]Orange, [OP]Yellow, [OP]White, [OP]Purple, [OP]Red 
vs
[OP]Orange, [OP]Purple, [OP]Red

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Purple pansies:

[XX]White + [XX]White = [WW]Blue

[XX]Red + [XX]Yellow = [RY]Orange

[XX]Red + [WW]Blue = [RB]Red

[RY]Orange + [WW]Blue = [OB]Orange

Unusually, pansies have several possible pairings which result in purple:

[RB]Red + [RB]Red = [RR]Purple
or
[OB]Orange + [OB]Orange = [OO]Purple
or
[RB]Red + [WW]Blue = [RB]Purple
or
[OB]Orange + [WW]Blue = [OB]Purple

Notes: The red offspring of [RB]Red pairs or orange offspring of [OB]Orange 
pairs will not be useful for breeding purple, however second generation blue, 
written as [BB]Blue, will work fine.

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Placement to maximize daily hybrid chances is the final key to covering your 
town in pretty hybrids.

Make sure there are no possible breeding pairs in the non-beach sections of 
town, as your animals will water flowers randomly while using beautiful 
ordinance, which should definitely be on if you're trying to breed hybrids. 
I presume that other ordinances limit you to 2 hybrids per day as a "default" 
outcome.

Either move all non-interesting flowers to a secluded part of your beach, 
or cover any adjacent squares with non-compatible flowers, patterns, trees, 
fruit, or anything else which will keep you from getting three brand new 
useless pink roses thanks to your villagers being "helpful" and watering 
a patch of reds.

Now find a section of the beach with no animal houses nearby and no ramp 
nearby, ideally one that you have never seen an animal roaming around on.

If you haven't been buying fertilizer daily after getting your final store 
upgrade, begin doing so, as the golden shovel (obtained after buying 
50 fertilizer bags) seems to add another possible hybrid per day when it is 
used to bury fertilizer, while fertilizer by itself also seems to add one 
possible hybrid slot per day, giving the best possible outcomes as below:

3 per day with beautiful ordinance
4 per day with fertilizer and beautiful ordinance
5 per day with fertilizer buried with golden shovel and beautiful ordinance

I have yet to see more than 5 hybrids in one day, and I don't think it is 
guaranteed to get 5, it simply adds a good chance to get another hybrid 
slot when you use the golden shovel to bury fertilizer.

Now, opinions will vary on the "best" layout, but if you are trying to 
maximize the odds of a specific group breeding specific offspring, I have 
yet to find a better arrangement than this:

# is an empty square
O is a parent flower
f is fertilizer


# O # O #
O # O # O
# O f O #
O # O # O
# O # O #

This layout has the fertilizer adjacent to four flowers, and each of those 
four are adjacent to four flowers. There are more than 5 possible breeding 
pairs, allowing for up to 5 new hybrids, while allowing enough open space 
for the offspring to spawn.