A runt is the very smallest baby animal in a litter — and it's also a derogatory word for a small person. If your little brother is sensitive about his height, it would be mean to call him a runt.
The tiniest piglet in a pile of baby pigs at a local farm is the runt. In animal litters, the runt often suffers from being small and weak, and is sometimes unable to get enough of its mother's milk to live. It's clear where the disparaging version of runt came from; when you call someone a runt, you're calling them a weakling.