Toughness defense is based on Stamina and is resistance to direct damage or harm, and overall durability.
Toughness, can only be increased above your base Stamina rank using advantages and powers, not by direct spending of character points. This reflects that greater-than-normal Toughness is virtually always some sort of special ability. See Advantages and Powers for various options for improving Toughness, notably the defensive Roll advantage and the Protection effect.
Mutants & Masterminds Hero’s Handbook, Copyright 2011, Green Ronin Publishing; Author Steve Kenson. Chapter-3 Abilities, Pg 54-59
D20Hero SRD Character Creation Article-http://www.d20herosrd.com/character-creation