Thanks for your answer,
This is link to the Atmel application note and associate source code :
Application Note
Source code
I followed this Note and loaded two exemples given by Atmel and it worked (leds connected on port 17, 20 and 21 blinked).
But when I try to load Arduino compiled binary and execute it with the custom bootloader it doesn't work.
This compiled binary is a simple blink given by Arduino exemples. So when it upload and launch, LED connected on port 13 should blink but it doesn't.