How to write programs for a custom SAMD21 board using Arduino IDE

@meghdadi I presume that the bootloader upload was successful.

One fuse to check is the BOOTPROT or bootloader protection fuse. This should be (depending on your version of Microchip/Atmel Studio 7) either 0x7 or 0 bytes.

Arduino's bootloader doesn't set this fuse, other bootloaders such as Adafruit's UF2 does.