About Boot Mode
The Raspberry Pi 3 can now be booted from a compatible USB drive. It works pretty well, but there are no noticeable differences in speed between a good SD card and a good USB drive. Primarily, cost may be a factor, as good USB drives are generally cheaper than good SD cards. Not all USB drives are supported–my Sandisk Ultra Fit worked, but my Trancend JetFlash did not.
Read the official documentation to learn how to set it up.
Boot Mode and Updates
I used apt-get update/upgrade to update my Raspberry Pi, which wiped out the boot mode. Make sure not to upgrade the bootloader, or save an edited bootable sd card to reapply the boot mode edits.
sudo mkdir /mnt/target
sudo mount /dev/sda2 /mnt/target/
sudo mkdir /mnt/target/boot
sudo mount /dev/sda1 /mnt/target/boot/
sudo mount --bind /dev dev
sudo mount --bind /sys sys
sudo mount --bind /proc proc
sudo chroot /mnt/target
sudo BRANCH=next rpi-update
sudo umount dev
sudo umount sys
sudo umount proc
Official forums also have some more information.