Here is a big family tree lol

starting from the top from Left to right:

Gen 1: Unknown pony, Grand Pear, Granny Smith, Random pony

Gen 2: Bow Hothoof, Windy Whistles, Bright Mac, Pear Butter, Nimbus (Mr. Shy), Petunia Shy (Mrs. Shy)
I gave fluttershy's parents names cuz they never got any in the show soo

Gen 3: Rainbow Dash, Apple Jack, Apple Bloom, Big Mac, Fluttershy, Zephyr Breeze, Lightning Dust, Sugar Belle, Angel Wings, Rara

Gen 4: Leona, Farren, Melody, Big Sugar (Little Mac), Flora

Backstory:
Apple Jack and Rara:
Apple Jack and Rara had a happy relationship but it failed after AJ found out about Rara's backstage affair at one of her shows heartbroken AJ found comfort with Rainbow but didn't get into a relationship with Rainbow until a year after. a couple months after the break up AJ found out about Rara being pregnant with her child after a magic incident they had before the breakup.

Big Mac and Sugar Belle:

Big mac and Sugar Belle were hanging out one night at a bar when they both got drunk and ended up having a one night stand getting Sugar Belle Pregnant while in a relationship with Fluttershy and to this day Fluttershy still doesn't know about the baby or the one night stand.

Time taken: 5 hours
Program used: Paint Tool Sia ver 2
Base by: Hazardous-Andy
Edits by me